paperpile.bib

@PHDTHESIS{Asp2018-rr,
  title    = "Spatially Resolved Gene Expression Analysis",
  author   = "Asp, Michaela",
  year     =  2018,
  school   = "KTH Royal Institute of Technology",
  keywords = "Mendeley Import (Feb 23)"
}

@MISC{Somers2018-pu,
  title        = "The friendship that made Google huge",
  booktitle    = "The New Yorker",
  author       = "Somers, J",
  year         =  2018,
  howpublished = "\url{https://www.newyorker.com/magazine/2018/12/10/the-friendship-that-made-google-huge}",
  keywords     = "Mendeley Import (Feb 23)"
}

@MISC{Birgitta2020-kb,
  title        = "On Pair Progamming",
  author       = "Birgitta, Bockeler and Siessegger, Nina",
  year         =  2020,
  howpublished = "\url{https://martinfowler.com/articles/on-pair-programming.html}",
  keywords     = "Mendeley Import (Feb 23)"
}

@INPROCEEDINGS{Bjorklund2020-hk,
  title    = "Exploring the Impact of Mob Programming on the {Well-Being} of
              Developers: Insights from a Software Company",
  author   = "Bj{\"o}rklund, Philip and Fridebo, Jacob and Dalipi, Fisnik",
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Hui2011-oh,
  title    = "Pair Programming and {LSs} in Computing Education: Its Impact on
              Students' Performances",
  author   = "Hui, Tie Hui and Umar, Irfan Naufal",
  abstract = "Learning to programme requires complex cognitive skills that
              computing students find it arduous in comprehension. PP (pair
              programming) is an intensive style of programme cooperation where
              two people working together in resolving programming scenarios.
              It begins to draw the interests of educators as a teaching
              approach to facilitate learning and improve programming
              performance. The approach of PP, its model, benefits and
              limitations as well as the LS (learning style) preference are
              presented in the first part of this paper. The research findings
              and discussion on the application of PP involving 96 first year
              computing students are incorporated in the second part of this
              paper. The participants in these two intact classes were randomly
              assigned either to the experimental group that received PP or to
              the control group that received DI (direct instruction) method
              only. In PP group, students worked in pairs based on the
              visual-verbal LS dimension and those of DI group work
              individually. During a seven-week treatment, both groups applied
              program flowcharts and pseudocode in solving programming tasks.
              This study used two assessment methods--the formative and
              summative to examine the students' programming achievements. Two
              programming assignments were used as a formative assessment tool,
              also the CPPT (computer programming performance test) as the
              second tool which comprises of a pre-test, an immediate post-test
              and a delayed post-test, was administrated to assess the
              students' programming recall and retention. The result findings
              indicated that students in PP group significantly outperformed
              those in DI group for both the formative and summative
              assessments. However, only the visual and verbal students
              performed significantly better in recall than the retention. The
              analysis on the interaction effects revealed that learning is
              within inner self with regard to the instructional strategies
              applied and LS preference in classroom environment. In this case,
              the effectiveness of instructional strategies adopted to foster
              learning somehow depends on the type of learners. Therefore,
              educators should reflect on individual learning abilities while
              applying PP to stimulate students' engagement and critical
              thinking skills that subsequently will have positive influence on
              academic performance. (Contains 4 figures and 3 tables.)",
  journal  = "Online Submission",
  year     =  2011,
  keywords = "Cognitive Style; College Students; Comparative Analysis; Computer
              Science Education; Control Groups; Cooperative Learning; Direct
              Instruction; Educational Strategies; Experimental Groups;
              Formative Evaluation; Instructional Effectiveness; Interaction;
              Learning Modalities; Learning Processes; Preferences; Pretests
              Posttests; Programming; Quasiexperimental Design; Recall
              (Psychology); Retention (Psychology); Summative
              Evaluation;Mendeley Import (Feb 23)"
}

@INPROCEEDINGS{Srikanth2004-ql,
  title     = "On pair rotation in the computer science course",
  booktitle = "Software Engineering Education Conference, Proceedings",
  author    = "Srikanth, Hema and Williams, Laune and Wiebe, Eric and Miller,
               Carol and Balik, Suzanne",
  abstract  = "In a course environment, pairing a student with one partner for
               the entire semester is beneficial, but may not be optimal. The
               authors conducted a study in two undergraduate level courses to
               observe the advantages and disadvantages of pair rotation
               whereby a student pairs with several different students
               throughout the semester. This paper summarizes teaching staff
               and student perceptions on the viability of pair rotation.
               Teachers find pair rotation valuable because the teaching staff
               can obtain multiple peer evaluations on each student and because
               dysfunctional pairs are regularly disbanded. However, pair
               rotation adds to the burden of assigning pairs multiple times
               per semester. The majority of students in the study perceived
               pair rotation to be a desirable approach. Additionally, most
               students considered peer evaluation to be an effective means of
               providing feedback to teaching staff. However, they did not
               significantly believe that peer evaluation was an effective
               means for motivating students.",
  year      =  2004,
  keywords  = "Mendeley Import (Feb 23)"
}

@ARTICLE{Nosek1998-hy,
  title    = "The Case for Collaborative Programming",
  author   = "Nosek, John T",
  journal  = "Commun. ACM",
  year     =  1998,
  keywords = "Mendeley Import (Feb 23)"
}

@INPROCEEDINGS{Bird2013-je,
  title     = "Expectations, Outcomes, and Challenges of Modern Code Review",
  booktitle = "Proceedings of the International Conference on Software
               Engineering",
  author    = "Bird, Christian and Bacchelli, Alberto",
  abstract  = "Code review is a common software engineering practice employed
               both in open source and industrial contexts. Review today is
               less formal and more ``lightweight'' than the code inspections
               performed and studied in the 70s and 80s. We empirically explore
               the motivations, challenges, and outcomes of tool-based code
               reviews. We observed, interviewed, and surveyed developers and
               managers and manually classified hundreds of review comments
               across diverse teams at Microsoft. Our study reveals that while
               finding defects remains the main motivation for review, reviews
               are less about defects than expected and instead provide
               additional benefits such as knowledge transfer, increased team
               awareness, and creation of alternative solutions to problems.
               Moreover, we find that code and change understanding is the key
               aspect of code reviewing and that developers employ a wide range
               of mechanisms to meet their understanding needs, most of which
               are not met by current tools. We provide recommendations for
               practitioners and researchers.",
  publisher = "IEEE",
  month     =  may,
  year      =  2013,
  keywords  = "Mendeley Import (Feb 23)"
}

@INPROCEEDINGS{Doutreligne2014-ly,
  title     = "{UnityMol}: Interactive scientific visualization for integrative
               biology",
  booktitle = "{IEEE} Symposium on Large Data Analysis and Visualization 2014,
               {LDAV} 2014 - Proceedings",
  author    = "Doutreligne, S{\'e}bastien and Cragnolini, Tristan and Pasquali,
               Samuela and Derreumaux, Philippe and Baaden, Marc",
  abstract  = "A broad challenge facing scientists today is the availability of
               huge amounts of data from various sources. Computers are
               required to store, analyze, explore and represent these data in
               order to extract useful information. With UnityMol, we pursue
               the ambitious goal to create an interactive virtual laboratory
               enabling researchers in biology to visualize biomolecular
               systems, run simulations and interact with physical models and
               data. Visual effects can enrich the dynamic and immersive
               aspects. Ultimately, we want to combine an appealing visual
               feedback already in place with a set of analysis features to
               extract information about properties of the fascinating
               biomolecular systems under study.",
  year      =  2014,
  keywords  = "Biology and Genetics; I.6.6 [Simulation and Modeling];
               Simulation Output Analysis; J.3 [Computer Applicat;Mendeley
               Import (Feb 23)"
}

@ARTICLE{Xu2020-xz,
  title    = "{VRmol}: an Integrative {Web-Based} Virtual Reality System to
              Explore Macromolecular Structure",
  author   = "Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao,
              Lingyun and Wang, Hong-Wei and Zhang, Qiangfeng Cliff",
  abstract = "Structural visualization and analysis are fundamental to explore
              macromolecular functions. Here we present a novel integrative
              web-based virtual reality (VR) system - VRmol, to visualize and
              study molecular structures in an immersive virtual environment.
              Importantly, it is integrated with multiple online databases and
              able to couple structure studies with associated genomic
              variations and drug information in a visual interface by
              cloud-based drug docking. VRmol thus can serve as an integrative
              platform to aid structure-based translational research and drug
              design. VRmol is freely available (https://VRmol.net), with
              detailed manual and tutorial (https://VRmol.net/docs). The code
              of VRmol is available as open source under the MIT license at
              http://github.com/kuixu/VRmol. Supplementary data are available
              at Bioinformatics online.",
  journal  = "Bioinformatics",
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Stefani2018-om,
  title    = "{ConfocalVR}: Immersive Visualization for Confocal Microscopy",
  author   = "Stefani, Caroline and Lacy-Hulbert, Adam and Skillman, Thomas",
  abstract = "ConfocalVR is a virtual reality (VR) application created to
              improve the ability of researchers to study the complexity of
              cell architecture. Confocal microscopes take pictures of
              fluorescently labeled proteins or molecules at different focal
              planes to create a stack of two-dimensional images throughout the
              specimen. Current software applications reconstruct the
              three-dimensional (3D) image and render it as a two-dimensional
              projection onto a computer screen where users need to rotate the
              image to expose the full 3D structure. This process is mentally
              taxing, breaks down if you stop the rotation, and does not take
              advantage of the eye's full field of view. ConfocalVR exploits
              consumer-grade VR systems to fully immerse the user in the 3D
              cellular image. In this virtual environment, the user can (1)
              adjust image viewing parameters without leaving the virtual
              space, (2) reach out and grab the image to quickly rotate and
              scale the image to focus on key features, and (3) interact with
              other users in a shared virtual space enabling real-time
              collaborative exploration and discussion. We found that immersive
              VR technology allows the user to rapidly understand cellular
              architecture and protein or molecule distribution. We note that
              it is impossible to understand the value of immersive
              visualization without experiencing it first hand, so we encourage
              readers to get access to a VR system, download this software, and
              evaluate it for yourself. The ConfocalVR software is available
              for download at http://www.confocalvr.com, and is free for
              nonprofits.",
  journal  = "J. Mol. Biol.",
  year     =  2018,
  keywords = "ImageJ; cellular visualization; confocal microscopy; virtual
              collaboration; virtual reality;Mendeley Import (Feb 23)"
}

@ARTICLE{Theart2017-dk,
  title    = "Virtual reality assisted microscopy data visualization and
              colocalization analysis",
  author   = "Theart, Rensu P and Loos, Ben and Niesler, Thomas R",
  abstract = "Background: Confocal microscopes deliver detailed
              three-dimensional data and are instrumental in biological
              analysis and research. Usually, this three-dimensional data is
              rendered as a projection onto a two-dimensional display. We
              describe a system for rendering such data using a modern virtual
              reality (VR) headset. Sample manipulation is possible by
              fully-immersive hand-tracking and also by means of a conventional
              gamepad. We apply this system to the specific task of
              colocalization analysis, an important analysis tool in biological
              microscopy. We evaluate our system by means of a set of user
              trials. Results: The user trials show that, despite inaccuracies
              which still plague the hand tracking, this is the most productive
              and intuitive interface. The inaccuracies nevertheless lead to a
              perception among users that productivity is low, resulting in a
              subjective preference for the gamepad. Fully-immersive
              manipulation was shown to be particularly effective when defining
              a region of interest (ROI) for colocalization analysis.
              Conclusions: Virtual reality offers an attractive and powerful
              means of visualization for microscopy data. Fully immersive
              interfaces using hand tracking show the highest levels of
              intuitiveness and consequent productivity. However, current
              inaccuracies in hand tracking performance still lead to a
              disproportionately critical user perception.",
  journal  = "BMC Bioinformatics",
  year     =  2017,
  keywords = "3D Microscopic reconstruction; Colocalization analysis; Confocal
              microscopy visualization; Hand tracking; Region of interest
              selection; Virtual reality; Volume rendering;Mendeley Import (Feb
              23)"
}

@ARTICLE{Blanc2020-hs,
  title    = "Genuage: visualize and analyze multidimensional single-molecule
              point cloud data in virtual reality",
  author   = "Blanc, Thomas and El Beheiry, Mohamed and Caporal, Cl{\'e}ment
              and Masson, Jean Baptiste and Hajj, Bassam",
  abstract = "Experimentally recorded point cloud data, such as those generated
              by single-molecule localization microscopy, are continuously
              increasing in size and dimension. Gaining an intuitive
              understanding and facilitating the analysis of such
              multidimensional data remains challenging. Here we report a new
              open-source software platform, Genuage, that enables the easy
              perception of, interaction with and analysis of multidimensional
              point clouds in virtual reality. Genuage is compatible with
              arbitrary multidimensional data extending beyond single-molecule
              localization microscopy.",
  journal  = "Nat. Methods",
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Yang2018-cv,
  title    = "starmap: Immersive visualisation of single cell data using
              smartphone-enabled virtual reality",
  author   = "Yang, Andrian and Yao, Yu and Li, Jianfu and Ho, Joshua",
  abstract = "We report a new smartphone-enabled virtual reality (VR) program,
              starmap (https://vccri.github.io/starmap/), that enables
              immersive visualisation of single-cell data for hundreds of
              thousands of cells using a mobile-enabled web browser and
              low-cost VR head mount device.",
  journal  = "bioRxiv",
  year     =  2018,
  keywords = "Bioinformatics; Biology; Computer graphics (images); Immersion
              (virtual reality); Mount; Virtual reality; Visualization;Mendeley
              Import (Feb 23)"
}

@ARTICLE{Stein2020-np,
  title    = "{singlecellVR}: interactive visualization of single-cell data in
              virtual reality",
  author   = "Stein, David F and Chen, Huidong and Vinyard, Michael E and
              Pinello, Luca",
  abstract = "Single-cell assays have transformed our ability to model
              heterogeneity within cell populations and tissues. Virtual
              reality has recently emerged as a powerful technology to
              dynamically explore complex data. However, expensive hardware or
              advanced data preprocessing skills are required to adapt such
              technology to single-cell data. To address current shortcomings,
              we built singlecellVR, a user-friendly website for visualizing
              single-cell data, designed for cheap and easily available virtual
              reality hardware (e.g., Google Cardboard, ~\$8). We provide a
              companion package, scvr to streamline data conversion from the
              most widely-adopted single-cell analysis tools and a database of
              pre-analyzed datasets to which users can contribute.Competing
              Interest StatementThe authors have declared no competing
              interest.",
  journal  = "bioRxiv",
  pages    = "2020.07.30.229534",
  month    =  jan,
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Poco2011-bx,
  title    = "A framework for exploring multidimensional data with {3D}
              projections",
  author   = "Poco, J and Etemadpour, R and Paulovich, F V and Long, T V and
              Rosenthal, P and Oliveira, M C F and Linsen, L and Minghim, R",
  abstract = "Visualization of high-dimensional data requires a mapping to a
              visual space. Whenever the goal is to preserve similarity
              relations a frequent strategy is to use 2D projections, which
              afford intuitive interactive exploration, e.g., by users locating
              and selecting groups and gradually drilling down to individual
              objects. In this paper, we propose a framework for projecting
              high-dimensional data to 3D visual spaces, based on a
              generalization of the Least- Square Projection (LSP). We compare
              projections to 2D and 3D visual spaces both quantitatively and
              through a user study considering certain exploration tasks. The
              quantitative analysis confirms that 3D projections outperform 2D
              projections in terms of precision. The user study indicates that
              certain tasks can be more reliably and confidently answered with
              3D projections. Nonetheless, as 3D projections are displayed on
              2D screens, interaction is more difficult. Therefore, we
              incorporate suitable interaction functionalities into a framework
              that supports 3D transformations, predefined optimal 2D views,
              coordinated 2D and 3D views, and hierarchical 3D cluster
              definition and exploration. For visually encoding data clusters
              in a 3D setup, we employ color coding of projected data points as
              well as four types of surface renderings. A second user study
              evaluates the suitability of these visual encodings. Several
              examples illustrate the framework's applicability for both visual
              exploration of multidimensional abstract (non-spatial) data as
              well as the feature space of multi-variate spatial data.
              \copyright{} 2011 The Author(s).",
  journal  = "Comput. Graph. Forum",
  year     =  2011,
  keywords = "Mendeley Import (Feb 23)"
}

@INPROCEEDINGS{Colange2019-sl,
  title     = "Interpreting Distortions in Dimensionality Reduction by
               Superimposing Neighbourhood Graphs",
  booktitle = "2019 {IEEE} Visualization Conference, {VIS} 2019",
  author    = "Colange, Benoit and Vuillon, Laurent and Lespinats, Sylvain and
               Dutykh, Denys",
  abstract  = "To perform visual data exploration, many dimensionality
               reduction methods have been developed. These tools allow data
               analysts to represent multidimensional data in a 2D or 3D space,
               while preserving as much relevant information as possible. Yet,
               they cannot preserve all structures simultaneously and they
               induce some unavoidable distortions. Hence, many criteria have
               been introduced to evaluate a map's overall quality, mostly
               based on the preservation of neighbourhoods. Such global
               indicators are currently used to compare several maps, which
               helps to choose the most appropriate mapping method and its
               hyperparameters. However, those aggregated indicators tend to
               hide the local repartition of distortions. Thereby, they need to
               be supplemented by local evaluation to ensure correct
               interpretation of maps.In this paper, we describe a new method,
               called MING, for ``Map Interpretation using Neighbourhood
               Graphs''. It offers a graphical interpretation of pairs of map
               quality indicators, as well as local evaluation of the
               distortions. This is done by displaying on the map the nearest
               neighbours graphs computed in the data space and in the
               embedding. Shared and unshared edges exhibit reliable and
               unreliable neighbourhood information conveyed by the mapping. By
               this mean, analysts may determine whether proximity (or
               remoteness) of points on the map faithfully represents
               similarity (or dissimilarity) of original data, within the
               meaning of a chosen map quality criteria. We apply this approach
               to two pairs of widespread indicators: precision/recall and
               trustworthiness/continuity, chosen for their wide use in the
               community, which will allow an easy handling by users.",
  year      =  2019,
  keywords  = "Evaluation - Qualitative Evaluation; Non-Spatial Data and
               Techniques - Dimensionality R; Visual Analysis and Knowledge
               Discovery - Visual K;Mendeley Import (Feb 23)"
}

@ARTICLE{Sanftmann2012-zp,
  title    = "{3D} scatterplot navigation",
  author   = "Sanftmann, Harald and Weiskopf, Daniel",
  abstract = "For 3D scatterplots, we present an interpolation and projection
              technique that supports the smooth exchange of one or two data
              dimensions at a time. Even though this exchange can be considered
              as a rotation in 4D or 5D data domains, we guarantee that the
              projection to image space is perceived as a 3D rigid body
              rotation---with a consistent motion of the data points. We
              conducted a controlled user study showing that 3D rigid body
              rotations outperform direct transition between scatterplots. We
              further extend our technique to support navigation between 3D
              scatterplots by introducing 3D scatterplot matrices. The
              usefulness of our approach is demonstrated by application
              examples, including a case study with a natural language
              processing expert. \copyright{} 1995-2012 IEEE.",
  journal  = "IEEE Trans. Vis. Comput. Graph.",
  year     =  2012,
  keywords = "Visualization; coordinated and multiple views; multidimensional
              data; scatterplot;Mendeley Import (Feb 23)"
}

@ARTICLE{Coimbra2016-ba,
  title    = "Explaining three-dimensional dimensionality reduction plots",
  author   = "Coimbra, Danilo B and Martins, Rafael M and Neves, T{\'a}cito T A
              T and Telea, Alexandru C and Paulovich, Fernando V",
  abstract = "Understanding three-dimensional projections created by
              dimensionality reduction from high-variate datasets is very
              challenging. In particular, classical three-dimensional
              scatterplots used to display such projections do not explicitly
              show the relations between the projected points, the viewpoint
              used to visualize the projection, and the original data
              variables. To explore and explain such relations, we propose a
              set of interactive visualization techniques. First, we adapt and
              enhance biplots to show the data variables in the projected
              threedimensional space. Next, we use a set of interactive bar
              chart legends to show variables that are visible from a given
              viewpoint and also assist users to select an optimal viewpoint to
              examine a desired set of variables. Finally, we propose an
              interactive viewpoint legend that provides an overview of the
              information visible in a given three-dimensional projection from
              all possible viewpoints. Our techniques are simple to implement
              and can be applied to any dimensionality reduction technique. We
              demonstrate our techniques on the exploration of several
              real-world high-dimensional datasets.",
  journal  = "Inf. Vis.",
  year     =  2016,
  keywords = "Dimensionality reduction; Explanatory visualization; Multivariate
              visualization; Scatterplots;Mendeley Import (Feb 23)"
}

@ARTICLE{Packer2019-we,
  title    = "A lineage-resolved molecular atlas of C. Elegans embryogenesis at
              single-cell resolution",
  author   = "Packer, Jonathan S and Zhu, Qin and Huynh, Chau and
              Sivaramakrishnan, Priya and Preston, Elicia and Dueck, Hannah and
              Stefanik, Derek and Tan, Kai and Trapnell, Cole and Kim, Junhyong
              and Waterston, Robert H and Murray, John I",
  abstract = "Caenorhabditis elegans is an animal with few cells but a wide
              diversity of cell types. In this study, we characterize the
              molecular basis for their specification by profiling the
              transcriptomes of 86,024 single embryonic cells. We identify 502
              terminal and preterminal cell types, mapping most single-cell
              transcriptomes to their exact position in C. elegans' invariant
              lineage. Using these annotations, we find that (i) the
              correlation between a cell's lineage and its transcriptome
              increases from middle to late gastrulation, then falls
              substantially as cells in the nervous system and pharynx adopt
              their terminal fates; (ii) multilineage priming contributes to
              the differentiation of sister cells at dozens of lineage
              branches; and (iii) most distinct lineages that produce the same
              anatomical cell type converge to a homogenous transcriptomic
              state.",
  journal  = "Science",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Qadir2020-ds,
  title    = "Single-cell resolution analysis of the human pancreatic ductal
              progenitor cell niche",
  author   = "Qadir, Mirza Muhammad Fahd and {\'A}lvarez-Cubela, Silvia and
              Klein, Dagmar and van Dijk, Jasmijn and Mu{\~n}iz-Anquela,
              Roc{\'\i}o and Moreno-Hern{\'a}ndez, Yaisa B and Lanzoni, Giacomo
              and Sadiq, Saad and Navarro-Rubio, Bel{\'e}n and Garc{\'\i}a,
              Michael T and D{\'\i}az, {\'A}ngela and Johnson, Kevin and Sant,
              David and Ricordi, Camillo and Griswold, Anthony and Pastori,
              Ricardo Luis and Dom{\'\i}nguez-Bendala, Juan",
  abstract = "We have described multipotent progenitor-like cells within the
              major pancreatic ducts (MPDs) of the human pancreas. They express
              PDX1, its surrogate surface marker P2RY1, and the bone
              morphogenetic protein (BMP) receptor 1A (BMPR1A)/activin-like
              kinase 3 (ALK3), but not carbonic anhydrase II (CAII). Here we
              report the single-cell RNA sequencing (scRNA-seq) of
              ALK3bright+-sorted ductal cells, a fraction that harbors
              BMP-responsive progenitor-like cells. Our analysis unveiled the
              existence of multiple subpopulations along two major axes, one
              that encompasses a gradient of ductal cell differentiation
              stages, and another featuring cells with transitional phenotypes
              toward acinar tissue. A third potential ducto-endocrine axis is
              revealed upon integration of the ALK3bright+ dataset with a
              single-cell whole-pancreas transcriptome. When transplanted into
              immunodeficient mice, P2RY1+/ALK3bright+ populations (enriched in
              PDX1+/ALK3+/CAII− cells) differentiate into all pancreatic
              lineages, including functional $\beta$-cells. This process is
              accelerated when hosts are treated systemically with an ALK3
              agonist. We found PDX1+/ALK3+/ CAII− progenitor-like cells in the
              MPDs of types 1 and 2 diabetes donors, regardless of the duration
              of the disease. Our findings open the door to the pharmacological
              activation of progenitor cells in situ.",
  journal  = "Proc. Natl. Acad. Sci. U. S. A.",
  year     =  2020,
  keywords = "Human pancreatic progenitors; Islet regeneration; Single-cell RNA
              sequencing; Transplantation; Type 1 diabetes;Mendeley Import (Feb
              23)"
}

@ARTICLE{Cakir2020-no,
  title    = "Comparison of visualisation tools for single-cell {RNAseq} data",
  author   = "Cakir, Batuhan and Prete, Martin and Huang, Ni and van Dongen,
              Stijn and Pir, Pnar and Kiselev, Vladimir Yu",
  abstract = "In the last decade, single cell RNAseq (scRNAseq) datasets have
              grown from a single cell to millions of cells. Due to its high
              dimensionality, the scRNAseq data contains a lot of valuable
              information, however, it is not always feasible to visualise and
              share it in a scientific report or an article publication format.
              Recently, a lot of interactive analysis and visualisation tools
              have been developed to address this issue and facilitate
              knowledge transfer in the scientific community. In this study, we
              review and compare several of the currently available analysis
              and visualisation tools and benchmark those that allow to
              visualize the scRNAseq data on the web and share it with others.
              To address the problem of format compatibility for most
              visualisation tools, we have also developed a user-friendly R
              package, sceasy, which allows users to convert their own scRNAseq
              datasets into a specific data format for visualisation.",
  journal  = "bioRxiv",
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{ORourke1982-bb,
  title    = "A new linear algorithm for intersecting convex polygons",
  author   = "O'Rourke, Joseph and Chien, Chi Bin and Olson, Thomas and Naddor,
              David",
  abstract = "An algorithm is presented that computes the intersection of two
              convex polygons in linear time. The algorithm is fundamentally
              different from the only known linear algorithms for this problem,
              due to Shamos and Hoey. These algorithms depend on a division of
              the plane into either angular sectors (Shamos) or parallel slabs
              (Hoey), and are mildly complex. Our algorithm searches for the
              intersection points of the polygons by adbancing a single pointer
              around each polygon, and is very easy to program. \copyright{}
              1982.",
  journal  = "Computer Graphics and Image Processing",
  year     =  1982,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Barber1996-mj,
  title    = "The Quickhull Algorithm for Convex Hulls",
  author   = "Barber, C Bradford and Dobkin, David P and Huhdanpaa, Hannu",
  abstract = "The convex hull of a set of points is the smallest convex set
              that contains the points. This article presents a practical
              convex hull algorithm that combines the two-dimensional Quickhull
              Algorithm with the general-dimension Beneath-Beyond Algorithm. It
              is similar to the randomized, incremental algorithms for convex
              hull and Delaunay triangulation. We provide empirical evidence
              that the algorithm runs faster when the input contains nonextreme
              points and that it uses less memory. Computational geometry
              algorithms have traditionally assumed that input sets are well
              behaved. When an algorithm is implemented with floating-point
              arithmetic, this assumption can lead to serious errors. We
              briefly describe a solution to this problem when computing the
              convex hull in two, three, or four dimensions. The output is a
              set of ``thick'' facets that contain all possible exact convex
              hulls of the input. A variation is effective in five or more
              dimensions.",
  journal  = "ACM Trans. Math. Softw.",
  year     =  1996,
  keywords = "Algorithms; Convex hull; Delaunay triangulation; Halfspace
              intersection; I.3.5 [Computer Graphics]: Computational Geometry;
              Reliability; Voronoi diagram;Mendeley Import (Feb 23)"
}

@ARTICLE{Han2018-om,
  title    = "Mapping the Mouse Cell Atlas by {Microwell-Seq}",
  author   = "Han, Xiaoping and Wang, Renying and Zhou, Yincong and Fei,
              Lijiang and Sun, Huiyu and Lai, Shujing and Saadatpour, Assieh
              and Zhou, Zimin and Chen, Haide and Ye, Fang and Huang, Daosheng
              and Xu, Yang and Huang, Wentao and Jiang, Mengmeng and Jiang,
              Xinyi and Mao, Jie and Chen, Yao and Lu, Chenyu and Xie, Jin and
              Fang, Qun and Wang, Yibin and Yue, Rui and Li, Tiefeng and Huang,
              He and Orkin, Stuart H and Yuan, Guo Cheng and Chen, Ming and
              Guo, Guoji",
  abstract = "Single-cell RNA sequencing (scRNA-seq) technologies are poised to
              reshape the current cell-type classification system. However, a
              transcriptome-based single-cell atlas has not been achieved for
              complex mammalian systems. Here, we developed Microwell-seq, a
              high-throughput and low-cost scRNA-seq platform using simple,
              inexpensive devices. Using Microwell-seq, we analyzed more than
              400,000 single cells covering all of the major mouse organs and
              constructed a basic scheme for a mouse cell atlas (MCA). We
              reveal a single-cell hierarchy for many tissues that have not
              been well characterized previously. We built a web-based
              ``single-cell MCA analysis'' pipeline that accurately defines
              cell types based on single-cell digital expression. Our study
              demonstrates the wide applicability of the Microwell-seq
              technology and MCA resource. Development of Microwell-seq allows
              construction of a mouse cell atlas at the single-cell level with
              a high-throughput and low-cost platform.",
  journal  = "Cell",
  year     =  2018,
  keywords = "Microwell-seq; cell type classification; cellular heterogeneity;
              cross-tissue cellular network; mammalian cell map; mouse cell
              atlas; scMCA analysis; single cell RNA-seq; single-cell analysis;
              transcriptome analysis;Mendeley Import (Feb 23)"
}

@ARTICLE{Cao2019-po,
  title    = "The single-cell transcriptional landscape of mammalian
              organogenesis",
  author   = "Cao, Junyue and Spielmann, Malte and Qiu, Xiaojie and Huang,
              Xingfan and Ibrahim, Daniel M and Hill, Andrew J and Zhang, Fan
              and Mundlos, Stefan and Christiansen, Lena and Steemers, Frank J
              and Trapnell, Cole and Shendure, Jay",
  abstract = "Mammalian organogenesis is a remarkable process. Within a short
              timeframe, the cells of the three germ layers transform into an
              embryo that includes most of the major internal and external
              organs. Here we investigate the transcriptional dynamics of mouse
              organogenesis at single-cell resolution. Using single-cell
              combinatorial indexing, we profiled the transcriptomes of around
              2 million cells derived from 61 embryos staged between 9.5 and
              13.5 days of gestation, in a single experiment. The resulting
              `mouse organogenesis cell atlas' (MOCA) provides a global view of
              developmental processes during this critical window. We use
              Monocle 3 to identify hundreds of cell types and 56 trajectories,
              many of which are detected only because of the depth of cellular
              coverage, and collectively define thousands of corresponding
              marker genes. We explore the dynamics of gene expression within
              cell types and trajectories over time, including focused analyses
              of the apical ectodermal ridge, limb mesenchyme and skeletal
              muscle.",
  journal  = "Nature",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@MISC{Gray_Camp2019-lj,
  title    = "Mapping human cell phenotypes to genotypes with single-cell
              genomics",
  author   = "Gray Camp, J and Platt, Randall and Treutlein, Barbara",
  abstract = "The cumulative activity of all of the body's cells, with their
              myriad interactions, life histories, and environmental
              experiences, gives rise to a condition that is distinctly human
              and specific to each individual. It is an enduring goal to
              catalog our human cell types, to understand how they develop, how
              they vary between individuals, and how they fail in disease.
              Single-cell genomics has revolutionized this endeavor because
              sequencing-based methods provide a means to quantitatively
              annotate cell states on the basis of high-information content and
              high-throughput measurements. Together with advances in stem cell
              biology and gene editing, we are in the midst of a fascinating
              journey to understand the cellular phenotypes that compose human
              bodies and how the human genome is used to build and maintain
              each cell. Here, we will review recent advances into how
              single-cell genomics is being used to develop personalized
              phenotyping strategies that cross subcellular, cellular, and
              tissue scales to link our genome to our cumulative cellular
              phenotypes.",
  journal  = "Science",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Ahrlund-Richter2019-fm,
  title    = "A whole-brain atlas of monosynaptic input targeting four
              different cell types in the medial prefrontal cortex of the mouse",
  author   = "{\"A}hrlund-Richter, Sofie and Xuan, Yang and van Lunteren,
              Josina Anna and Kim, Hoseok and Ortiz, Cantin and Pollak Dorocic,
              Iskra and Meletis, Konstantinos and Carl{\'e}n, Marie",
  abstract = "The local and long-range connectivity of cortical neurons are
              considered instrumental to the functional repertoire of the
              cortical region in which they reside. In cortical networks,
              distinct cell types build local circuit structures enabling
              computational operations. Computations in the medial prefrontal
              cortex (mPFC) are thought to be central to cognitive operation,
              including decision-making and memory. We used a retrograde
              trans-synaptic rabies virus system to generate brain-wide maps of
              the input to excitatory neurons as well as three inhibitory
              interneuron subtypes in the mPFC. On the global scale the input
              patterns were found to be mainly cell type independent, with
              quantitative differences in key brain regions, including the
              basal forebrain. Mapping of the local mPFC network revealed high
              connectivity between the different subtypes of interneurons. The
              connectivity mapping gives insight into the information that the
              mPFC processes and the structural architecture underlying the
              mPFC's unique functions.",
  journal  = "Nat. Neurosci.",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Spark2020-hl,
  title    = "{vLUME}: {3D} Virtual Reality for Single-molecule Localization
              Microscopy",
  author   = "Spark, Alexander and Kitching, Alexandre and Esteban-ferrer,
              Daniel and Handa, Anoushka and Carr, Alexander R and Needham,
              Lisa-Maria and Ponjavic, Aleks and Da Cunha Santos, Mafalda and
              Mccoll, James and Leterrier, Christophe and Davis, Simon J and
              Henriques, Ricardo and Lee, Steven F and Alexander, R and
              Needham, Lisa-Maria and Ponjavic, Aleks and Da, Mafalda and
              Santos, Cunha and Mccoll, James and Davis, Simon J and Henriques,
              Ricardo and Lee, Steven F",
  abstract = "Super-Resolution (SR) Microscopy based on 3D Single-Molecule
              Localization Microscopy (SMLM) is now well established and its
              wide-spread adoption has led to the development of more than 36
              software packages, dedicated to quantitative evaluation of the
              spatial and temporal detection of fluorophore photoswitching.
              While the initial emphasis in the 3D SMLM field has clearly been
              on improving resolution and data quality, there is now a marked
              absence of 3D visualization approaches that enable the
              straightforward, high-fidelity exploration of this type of data.
              Inspired by the horological phosphorescence points that
              illuminate watch-faces in the dark, we present vLUME
              (Visualization of the Universe in a Micro Environment, pronounced
              'volume') a free-for-academic-use immersive virtual reality-based
              (VR) visualization software package purposefully designed to
              render large 3D-SMLM data sets. vLUME enables robust
              visualization, segmentation and quantification of millions of
              fluorescence puncta from any 3D SMLM technique. vLUME has an
              intuitive user-interface and is compatible with all commercial VR
              hardware (Oculus Rift/Quest and HTC Vive). vLUME accelerates the
              analysis of highly complex 3D point-cloud data and the rapid
              identification of defects that are otherwise neglected in global
              quality metrics.",
  journal  = "bioRxiv",
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Hu2020-ew,
  title    = "{ZipSeq} : Barcoding for Real-time Mapping of Single Cell
              Transcriptomes",
  author   = "Hu, Kenneth H and Eichorst, John P and McGinnis, Christopher S
              and Patterson, David M and Chow, Eric D and Kersten, Kelly and
              Jameson, Stephen C and Gartner, Zev Jordan and Rao, Arjun A and
              Krummel, Matthew F",
  abstract = "Spatial transcriptomics seeks to integrate single-cell
              transcriptomic data within the 3-dimensional space of
              multicellular biology. Current methods use glass substrates
              pre-seeded with matrices of barcodes or fluorescence
              hybridization of a limited number of probes. We developed an
              alternative approach, called ZipSeq, that uses patterned
              illumination and photocaged oligonucleotides to serially print
              barcodes (Zipcodes) onto live cells within intact tissues, in
              real-time and with on-the-fly selection of patterns. Using
              ZipSeq, we mapped gene expression in three settings: in-vitro
              wound healing, live lymph node sections and in a live tumor
              microenvironment (TME). In all cases, we discovered new gene
              expression patterns associated with histological structures. In
              the TME, this demonstrated a trajectory of myeloid and T cell
              differentiation, from periphery inward. A variation of ZipSeq
              efficiently scales to the level of single cells, providing a
              pathway for complete mapping of live tissues, subsequent to
              real-time imaging or perturbation.",
  journal  = "bioRxiv",
  pages    = "2020.02.04.932988",
  month    =  jan,
  year     =  2020,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Winnubst2019-mg,
  title    = "Reconstruction of 1,000 Projection Neurons Reveals New Cell Types
              and Organization of {Long-Range} Connectivity in the Mouse Brain",
  author   = "Winnubst, Johan and Bas, Erhan and Ferreira, Tiago A and Wu,
              Zhuhao and Economo, Michael N and Edson, Patrick and Arthur, Ben
              J and Bruns, Christopher and Rokicki, Konrad and Schauder, David
              and Olbris, Donald J and Murphy, Sean D and Ackerman, David G and
              Arshadi, Cameron and Baldwin, Perry and Blake, Regina and
              Elsayed, Ahmad and Hasan, Mashtura and Ramirez, Daniel and Dos
              Santos, Bruno and Weldon, Monet and Zafar, Amina and Dudman,
              Joshua T and Gerfen, Charles R and Hantman, Adam W and Korff,
              Wyatt and Sternson, Scott M and Spruston, Nelson and Svoboda,
              Karel and Chandrashekar, Jayaram",
  abstract = "An efficient pipeline for brain-wide imaging and morphological
              reconstruction of individual neurons, including long-range
              projection neurons, is presented along with a searchable database
              containing more than 1,000 fully reconstructed neurons in the
              mouse neocortex, hippocampus, thalamus, and hypothalamus.",
  journal  = "Cell",
  year     =  2019,
  keywords = "automated reconstruction; axonal morphology; long-range
              projections; morphology database; neuronal cell types; neuronal
              connectivity; projection neurons; single-cell reconstruction;
              whole brain;Mendeley Import (Feb 23)"
}

@ARTICLE{Ortiz2019-oy,
  title    = "Molecular Atlas of the Adult Mouse Brain",
  author   = "Ortiz, Cantin and Navarro, Jose Fernandez and Jurek, Aleksandra
              and M{\"a}rtin, Antje and Lundeberg, Joakim and Meletis,
              Konstantinos",
  abstract = "Brain maps are essential for integrating information and
              interpreting the structure-function relationship of circuits and
              behavior. We aimed to generate a systematic classification of the
              adult mouse brain organization based on unbiased extraction of
              spatially-defining features. Applying whole-brain spatial
              transcriptomics, we captured the gene expression signatures to
              define the spatial organization of molecularly discrete
              subregions. We found that the molecular code contained
              sufficiently detailed information to directly deduce the complex
              spatial organization of the brain. This unsupervised molecular
              classification revealed new area- and layer-specific subregions,
              for example in isocortex and hippocampus, and a new division of
              striatum. The whole-brain molecular atlas further supports the
              identification of the spatial origin of single neurons using
              their gene expression profile, and forms the foundation to define
              a minimal gene set - a brain palette -- that is sufficient to
              spatially annotate the adult brain. In summary, we have
              established a new molecular atlas to formally define the identity
              of brain regions, and a molecular code for mapping and targeting
              of discrete neuroanatomical domains.",
  journal  = "bioRxiv",
  pages    = "784181",
  month    =  jan,
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Asp2019-zh,
  title     = "A Spatiotemporal {Organ-Wide} Gene Expression and Cell Atlas of
               the Developing Human Heart",
  author    = "Asp, Michaela and Giacomello, Stefania and Larsson, Ludvig and
               Wu, Chenglin and F{\"u}rth, Daniel and Qian, Xiaoyan and
               W{\"a}rdell, Eva and Custodio, Joaquin and Reimeg{\aa}rd, Johan
               and Salm{\'e}n, Fredrik and {\"O}sterholm, Cecilia and
               St{\aa}hl, Patrik L and Sundstr{\"o}m, Erik and {\AA}kesson,
               Elisabet and Bergmann, Olaf and Bienko, Magda and
               M{\aa}nsson-Broberg, Agneta and Nilsson, Mats and Sylv{\'e}n,
               Christer and Lundeberg, Joakim",
  abstract  = "The process of cardiac morphogenesis in humans is incompletely
               understood. Its full characterization requires a deep
               exploration of the organ-wide orchestration of gene expression
               with a single-cell spatial resolution. Here, we present a
               molecular approach that reveals the comprehensive
               transcriptional landscape of cell types populating the embryonic
               heart at three developmental stages and that maps
               cell-type-specific gene expression to specific anatomical
               domains. Spatial transcriptomics identified unique gene profiles
               that correspond to distinct anatomical regions in each
               developmental stage. Human embryonic cardiac cell types
               identified by single-cell RNA sequencing confirmed and enriched
               the spatial annotation of embryonic cardiac gene expression. In
               situ sequencing was then used to refine these results and create
               a spatial subcellular map for the three developmental phases.
               Finally, we generated a publicly available web resource of the
               human developing heart to facilitate future studies on human
               cardiogenesis.",
  journal   = "Cell",
  publisher = "Cell Press",
  volume    =  179,
  number    =  7,
  pages     = "1647--1660.e19",
  month     =  dec,
  year      =  2019,
  keywords  = "Mendeley Import (Feb 23)"
}

@ARTICLE{Moon2017-pz,
  title    = "{PHATE}: A Dimensionality Reduction Method for Visualizing
              Trajectory Structures in {High-Dimensional} Biological Data",
  author   = "Moon, Kevin R and van Dijk, David and Wang, Zheng and Chen,
              William and Hirn, Matthew J and Coifman, Ronald R and Ivanova,
              Natalia B and Wolf, Guy and Krishnaswamy, Smita",
  abstract = "In recent years, dimensionality reduction methods have become
              critical for visualization, exploration, and interpretation of
              high-throughput, high-dimensional biological data, as they enable
              the extraction of major trends in the data while discarding
              noise. However, biological data contains a type of predominant
              structure that is not preserved in commonly used methods such as
              PCA and tSNE, namely, branching progression structure. This
              structure, which is often non-linear, arises from underlying
              biological processes such as differentiation, graded responses to
              stimuli, and population drift, which generate cellular (or
              population) diversity. We propose a novel, affinity-preserving
              embedding called PHATE (Potential of Heat-diffusion for
              Affinity-based Trajectory Embedding), designed explicitly to
              preserve progression structure in data. PHATE provides a
              denoised, two or three-dimensional visualization of the complete
              branching trajectory structure in high-dimensional data. It uses
              heat-diffusion processes, which naturally denoise the data, to
              compute cell-cell affinities. Then, PHATE creates a
              diffusion-potential geometry by free-energy potentials of these
              processes. This geometry captures high-dimensional trajectory
              structures, while enabling a natural embedding of the intrinsic
              data geometry. This embedding accurately visualizes trajectories
              and data distances, without requiring strict assumptions
              typically used by path-finding and tree-fitting algorithms, which
              have recently been used for pseudotime orderings or
              tree-renderings of cellular data. Furthermore, PHATE supports a
              wide range of data exploration tasks by providing interpretable
              overlays on top of the visualization. We show that such overlays
              can emphasize and reveal trajectory end-points, branch points and
              associated split-decisions, progression-forming variables (e.g.,
              specific genes), and paths between developmental events in
              cellular state-space. We demonstrate PHATE on single-cell RNA
              sequencing and mass cytometry data pertaining to embryoid body
              differentiation, IPSC reprogramming, and hematopoiesis in the
              bone marrow. We also demonstrate PHATE on non-single cell data
              including single-nucleotide polymorphism (SNP) measurements of
              European populations, and 16s sequencing of gut microbiota.",
  journal  = "bioRxiv",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Bergen2019-vm,
  title    = "Generalizing {RNA} velocity to transient cell states through
              dynamical modeling",
  author   = "Bergen, Volker and Lange, Marius and Peidli, Stefan and Wolf, F
              Alexander and Theis, Fabian J",
  abstract = "The introduction of RNA velocity in single cells has opened up
              new ways of studying cellular differentiation. The originally
              proposed framework obtains velocities as the deviation of the
              observed ratio of spliced and unspliced mRNA from an inferred
              steady state. Errors in velocity estimates arise if the central
              assumptions of a common splicing rate and the observation of the
              full splicing dynamics with steady-state mRNA levels are
              violated. With scVelo (), we address these restrictions by
              solving the full transcriptional dynamics of splicing kinetics
              using a likelihood-based dynamical model. This generalizes RNA
              velocity to a wide variety of systems comprising transient cell
              states, which are common in development and in response to
              perturbations. We infer gene-specific rates of transcription,
              splicing and degradation, and recover the latent time of the
              underlying cellular processes. This latent time represents the
              cell's internal clock and is based only on its transcriptional
              dynamics. Moreover, scVelo allows us to identify regimes of
              regulatory changes such as stages of cell fate commitment and,
              therein, systematically detects putative driver genes. We
              demonstrate that scVelo enables disentangling heterogeneous
              subpopulation kinetics with unprecedented resolution in
              hippocampal dentate gyrus neurogenesis and pancreatic
              endocrinogenesis. We anticipate that scVelo will greatly
              facilitate the study of lineage decisions, gene regulation, and
              pathway activity identification.",
  journal  = "bioRxiv",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Melsted2019-nf,
  title    = "Modular and efficient pre-processing of single-cell {RNA-seq}",
  author   = "Melsted, P{\'a}ll and Booeshaghi, A Sina and Gao, Fan and
              Beltrame, Eduardo and Lu, Lambda and Hjorleifsson, Kristj{\'a}n
              Eldj{\'a}rn and Gehring, Jase and Pachter, Lior",
  abstract = "Analysis of single-cell RNA-seq data begins with pre-processing
              of sequencing reads to generate count matrices. We investigate
              algorithm choices for the challenges of pre-processing, and
              describe a workflow that balances efficiency and accuracy. Our
              workflow is based on the kallisto () and bustools () programs,
              and is near-optimal in speed and memory. The workflow is modular,
              and we demonstrate its flexibility by showing how it can be used
              for RNA velocity analyses. Documentation and tutorials for using
              the kallisto | bus workflow are available at .",
  journal  = "bioRxiv",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Popescu2019-zg,
  title    = "Decoding human fetal liver haematopoiesis",
  author   = "Popescu, Dorin-Mirel and Botting, Rachel A and Stephenson, Emily
              and Green, Kile and Webb, Simone and Jardine, Laura and
              Calderbank, Emily F and Polanski, Krzysztof and Goh, Issac and
              Efremova, Mirjana and Acres, Meghan and Maunder, Daniel and Vegh,
              Peter and Gitton, Yorick and Park, Jong-Eun and Vento-Tormo,
              Roser and Miao, Zhichao and Dixon, David and Rowell, Rachel and
              McDonald, David and Fletcher, James and Poyner, Elizabeth and
              Reynolds, Gary and Mather, Michael and Moldovan, Corina and
              Mamanova, Lira and Greig, Frankie and Young, Matthew D and Meyer,
              Kerstin B and Lisgo, Steven and Bacardit, Jaume and Fuller,
              Andrew and Millar, Ben and Innes, Barbara and Lindsay, Susan and
              Stubbington, Michael J T and Kowalczyk, Monika S and Li, Bo and
              Ashenberg, Orr and Tabaka, Marcin and Dionne, Danielle and
              Tickle, Timothy L and Slyper, Michal and Rozenblatt-Rosen, Orit
              and Filby, Andrew and Carey, Peter and Villani,
              Alexandra-Chlo{\'e} and Roy, Anindita and Regev, Aviv and
              Ch{\'e}dotal, Alain and Roberts, Irene and G{\"o}ttgens, Berthold
              and Behjati, Sam and Laurenti, Elisa and Teichmann, Sarah A and
              Haniffa, Muzlifah",
  abstract = "Definitive haematopoiesis in the fetal liver supports
              self-renewal and differentiation of haematopoietic stem cells and
              multipotent progenitors (HSC/MPPs) but remains poorly defined in
              humans. Here, using single-cell transcriptome profiling of
              approximately 140,000 liver and 74,000 skin, kidney and yolk sac
              cells, we identify the repertoire of human blood and immune cells
              during development. We infer differentiation trajectories from
              HSC/MPPs and evaluate the influence of the tissue
              microenvironment on blood and immune cell development. We reveal
              physiological erythropoiesis in fetal skin and the presence of
              mast cells, natural killer and innate lymphoid cell precursors in
              the yolk sac. We demonstrate a shift in the haemopoietic
              composition of fetal liver during gestation away from being
              predominantly erythroid, accompanied by a parallel change in
              differentiation potential of HSC/MPPs, which we functionally
              validate. Our integrated map of fetal liver haematopoiesis
              provides a blueprint for the study of paediatric blood and immune
              disorders, and a reference for harnessing the therapeutic
              potential of HSC/MPPs. Single-cell transcriptomic profiling of
              fetal liver, skin, kidney and yolk sac reveals the
              differentiation trajectories of human haematopoietic stem cells
              and multipotent progenitors, which are validated to produce an
              integrated map of fetal liver haematopoiesis.",
  journal  = "Nature",
  year     =  2019,
  keywords = "Leukopoiesis; RNA sequencing; Statistical methods;Mendeley Import
              (Feb 23)"
}

@ARTICLE{Ximerakis2019-he,
  title    = "Single-cell transcriptomic profiling of the aging mouse brain",
  author   = "Ximerakis, Methodios and Lipnick, Scott L and Innes, Brendan T
              and Simmons, Sean K and Adiconis, Xian and Dionne, Danielle and
              Mayweather, Brittany A and Nguyen, Lan and Niziolek, Zachary and
              Ozek, Ceren and Butty, Vincent L and Isserlin, Ruth and Buchanan,
              Sean M and Levine, Stuart S and Regev, Aviv and Bader, Gary D and
              Levin, Joshua Z and Rubin, Lee L",
  abstract = "The mammalian brain is complex, with multiple cell types
              performing a variety of diverse functions, but exactly how each
              cell type is affected in aging remains largely unknown. Here we
              performed a single-cell transcriptomic analysis of young and old
              mouse brains. We provide comprehensive datasets of aging-related
              genes, pathways and ligand-receptor interactions in nearly all
              brain cell types. Our analysis identified gene signatures that
              vary in a coordinated manner across cell types and gene sets that
              are regulated in a cell-type specific manner, even at times in
              opposite directions. These data reveal that aging, rather than
              inducing a universal program, drives a distinct transcriptional
              course in each cell population, and they highlight key molecular
              processes, including ribosome biogenesis, underlying brain aging.
              Overall, these large-scale datasets (accessible online at
              https://portals.broadinstitute.org/single\_cell/study/aging-mouse-brain
              ) provide a resource for the neuroscience community that will
              facilitate additional discoveries directed towards understanding
              and modifying the aging process.",
  journal  = "Nat. Neurosci.",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@MISC{La_Manno2018-vl,
  title    = "{RNA} velocity of single cells",
  author   = "La Manno, Gioele and Soldatov, Ruslan and Zeisel, Amit and Braun,
              Emelie and Hochgerner, Hannah and Petukhov, Viktor and
              Lidschreiber, Katja and Kastriti, Maria E and L{\"o}nnerberg,
              Peter and Furlan, Alessandro and Fan, Jean and Borm, Lars E and
              Liu, Zehua and van Bruggen, David and Guo, Jimin and He, Xiaoling
              and Barker, Roger and Sundstr{\"o}m, Erik and Castelo-Branco,
              Gon{\c c}alo and Cramer, Patrick and Adameyko, Igor and
              Linnarsson, Sten and Kharchenko, Peter V",
  abstract = "RNA abundance is a powerful indicator of the state of individual
              cells. Single-cell RNA sequencing can reveal RNA abundance with
              high quantitative accuracy, sensitivity and throughput1. However,
              this approach captures only a static snapshot at a point in time,
              posing a challenge for the analysis of time-resolved phenomena
              such as embryogenesis or tissue regeneration. Here we show that
              RNA velocity-the time derivative of the gene expression state-can
              be directly estimated by distinguishing between unspliced and
              spliced mRNAs in common single-cell RNA sequencing protocols. RNA
              velocity is a high-dimensional vector that predicts the future
              state of individual cells on a timescale of hours. We validate
              its accuracy in the neural crest lineage, demonstrate its use on
              multiple published datasets and technical platforms, reveal the
              branching lineage tree of the developing mouse hippocampus, and
              examine the kinetics of transcription in human embryonic brain.
              We expect RNA velocity to greatly aid the analysis of
              developmental lineages and cellular dynamics, particularly in
              humans.",
  journal  = "Nature",
  year     =  2018,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Wang2019-pj,
  title    = "{TeraVR} empowers precise reconstruction of complete {3-D}
              neuronal morphology in the whole brain",
  author   = "Wang, Yimin and Li, Qi and Liu, Lijuan and Zhou, Zhi and Ruan,
              Zongcai and Kong, Lingsheng and Li, Yaoyao and Wang, Yun and
              Zhong, Ning and Chai, Renjie and Luo, Xiangfeng and Guo, Yike and
              Hawrylycz, Michael and Luo, Qingming and Gu, Zhongze and Xie, Wei
              and Zeng, Hongkui and Peng, Hanchuan",
  abstract = "Neuron morphology is recognized as a key determinant of cell
              type, yet the quantitative profiling of a mammalian neuron's
              complete three-dimensional (3-D) morphology remains arduous when
              the neuron has complex arborization and long projection.
              Whole-brain reconstruction of neuron morphology is even more
              challenging as it involves processing tens of teravoxels of
              imaging data. Validating such reconstructions is extremely
              laborious. We developed TeraVR , an open-source virtual reality
              annotation system, to address these challenges. TeraVR integrates
              immersive and collaborative 3-D visualization, interaction, and
              hierarchical streaming of teravoxel-scale images. Using TeraVR ,
              we produced precise 3-D full morphology of long-projecting
              neurons in whole mouse brains and developed a collaborative
              workflow for highly accurate neuronal reconstruction.",
  journal  = "Nat. Commun.",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Meagher1982-tu,
  title    = "Geometric modeling using octree encoding",
  author   = "Meagher, Donald",
  abstract = "A geometric modeling technique called Octree Encoding is
              presented. Arbitrary 3-D objects can be represented to any
              specified resolution in a hierarchical 8-ary tree structure or
              ``octree'' Objects may be concave or convex, have holes
              (including interior holes), consist of disjoint parts, and
              possess sculptured (i.e., ``free-form'') surfaces. The memory
              required for representation and manipulation is on the order of
              the surface area of the object. A complexity metric is proposed
              based on the number of nodes in an object's tree representation.
              Efficient (linear time) algorithms have been developed for the
              Boolean operations (union, intersection and difference),
              geometric operations (translation, scaling and rotation),
              N-dimensional interference detection, and display from any point
              in space with hidden surfaces removed. The algorithms require
              neither floating-point operations, integer multiplications, nor
              integer divisions. In addition, many independent sets of very
              simple calculations are typically generated, allowing
              implementation over many inexpensive high-bandwidth processors
              operating in parallel. Real time analysis and manipulation of
              highly complex situations thus becomes possible. \copyright{}
              1982.",
  journal  = "Computer Graphics and Image Processing",
  year     =  1982,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Pijuan-Sala2019-hx,
  title    = "A single-cell molecular map of mouse gastrulation and early
              organogenesis",
  author   = "Pijuan-Sala, Blanca and Griffiths, Jonathan A and Guibentif,
              Carolina and Hiscock, Tom W and Jawaid, Wajid and Calero-Nieto,
              Fernando J and Mulas, Carla and Ibarra-Soria, Ximena and Tyser,
              Richard C V and Ho, Debbie Lee Lian and Reik, Wolf and Srinivas,
              Shankar and Simons, Benjamin D and Nichols, Jennifer and Marioni,
              John C and G{\"o}ttgens, Berthold",
  abstract = "Across the animal kingdom, gastrulation represents a key
              developmental event during which embryonic pluripotent cells
              diversify into lineage-specific precursors that will generate the
              adult organism. Here we report the transcriptional profiles of
              116,312 single cells from mouse embryos collected at nine
              sequential time points ranging from 6.5 to 8.5 days
              post-fertilization. We construct a molecular map of cellular
              differentiation from pluripotency towards all major embryonic
              lineages, and explore the complex events involved in the
              convergence of visceral and primitive streak-derived endoderm.
              Furthermore, we use single-cell profiling to show that Tal1-/-
              chimeric embryos display defects in early mesoderm
              diversification, and we thus demonstrate how combining temporal
              and transcriptional information can illuminate gene function.
              Together, this comprehensive delineation of mammalian cell
              differentiation trajectories in vivo represents a baseline for
              understanding the effects of gene mutations during development,
              as well as a roadmap for the optimization of in vitro
              differentiation protocols for regenerative medicine.",
  journal  = "Nature",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Becht2019-fp,
  title    = "Dimensionality reduction for visualizing single-cell data using
              {UMAP}",
  author   = "Becht, Etienne and McInnes, Leland and Healy, John and Dutertre,
              Charles Antoine and Kwok, Immanuel W H and Ng, Lai Guan and
              Ginhoux, Florent and Newell, Evan W",
  abstract = "A benchmarking analysis on single-cell RNA-seq and mass cytometry
              data reveals the best-performing technique for dimensionality
              reduction.",
  journal  = "Nat. Biotechnol.",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Legetth2018-xm,
  title    = "{CellexalVR}: A virtual reality platform for the exploration and
              analysis of single-cell gene expression data",
  author   = "Legetth, Oscar and Rodhe, Johan and P{\aa}lsson, Joel and
              Wallerg{\aa}rd, Mattias and Lang, Stefan and Soneji, Shamit",
  abstract = "Single-cell RNAseq is a powerful tool for the dissection of cell
              populations at the transcriptome level, and a myriad of
              techniques are available to project cells on to 3-dimensional
              space to construct cellular maps that aid the visualisation of
              heterogeneity and any sub-populations formed. Current
              visualisation methods for 3-dimensional data on conventional
              computer displays are poor, and coupled with a lack of intuitive
              point/cell selection methods often hinders a rapid exploration of
              finer details contained in the data. Here we present CellexalVR
              (www.cellexalvr.med.lu.se), a feature-rich, fully interactive,
              and immersive virtual reality environment for the analysis of
              single-cell RNAseq experiments that allows researchers to quickly
              and intuitively gain an understanding of their data.",
  journal  = "bioRxiv",
  year     =  2018,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Rodriques2019-ym,
  title    = "Slide-seq: A Scalable Technology for Measuring {Genome-Wide}
              Expression at High Spatial Resolution",
  author   = "Rodriques, Samuel G and Stickels, Robert R and Goeva,
              Aleksandrina and Martin, Carly A and Murray, Evan and Vanderburg,
              Charles R and Welch, Joshua and Chen, Linlin M and Chen, Fei and
              Macosko, Evan Z",
  abstract = "The spatial organization of cells in tissue has a profound
              influence on their function, yet a high-throughput, genome-wide
              readout of gene expression with cellular resolution is lacking.
              Here, we introduce Slide-seq, a highly scalable method that
              enables facile generation of large volumes of unbiased spatial
              transcriptomes with 10 micron spatial resolution, comparable to
              the size of individual cells. In Slide-seq, RNA is transferred
              from freshly frozen tissue sections onto a surface covered in
              DNA-barcoded beads with known positions, allowing the spatial
              locations of the RNA to be inferred by sequencing. To demonstrate
              Slide-seq's utility, we localized cell types identified by
              large-scale scRNA-seq datasets within the cerebellum and
              hippocampus. We next systematically characterized spatial gene
              expression patterns in the Purkinje layer of mouse cerebellum,
              identifying new axes of variation across Purkinje cell
              compartments. Finally, we used Slide-seq to define the temporal
              evolution of cell-type-specific responses in a mouse model of
              traumatic brain injury. Slide-seq will accelerate biological
              discovery by enabling routine, high-resolution spatial mapping of
              gene expression.",
  journal  = "bioRxiv",
  year     =  2019,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Kiselev2018-lp,
  title    = "Scmap: Projection of single-cell {RNA-seq} data across data sets",
  author   = "Kiselev, Vladimir Yu and Yiu, Andrew and Hemberg, Martin",
  abstract = "scmap enables the comparison of disparate single-cell RNA-seq
              data sets by projecting individual cells or clusters from a query
              sample onto a reference sample or cell atlas.",
  journal  = "Nat. Methods",
  year     =  2018,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{McInnes2018-bi,
  title    = "{UMAP}: Uniform Manifold Approximation and Projection",
  author   = "McInnes, Leland and Healy, John and Saul, Nathaniel and
              Gro{\ss}berger, Lukas",
  abstract = "UMAP (Uniform Manifold Approximation and Projection) is a novel
              manifold learning technique for dimension reduction. UMAP is
              constructed from a theoretical framework based in Riemannian
              geometry and algebraic topology. The result is a practical
              scalable algorithm that applies to real world data. The UMAP
              algorithm is competitive with t-SNE for visualization quality,
              and arguably preserves more of the global structure with superior
              run time performance. Furthermore, UMAP as described has no
              computational restrictions on embedding dimension, making it
              viable as a general purpose dimension reduction technique for
              machine learning.",
  journal  = "Journal of Open Source Software",
  year     =  2018,
  keywords = "computational geometry; machine learning;Mendeley Import (Feb 23)"
}

@ARTICLE{Wolf2018-gt,
  title    = "{SCANPY}: Large-scale single-cell gene expression data analysis",
  author   = "Wolf, F Alexander and Angerer, Philipp and Theis, Fabian J",
  abstract = "Scanpy is a scalable toolkit for analyzing single-cell gene
              expression data. It includes methods for preprocessing,
              visualization, clustering, pseudotime and trajectory inference,
              differential expression testing, and simulation of gene
              regulatory networks. Its Python-based implementation efficiently
              deals with data sets of more than one million cells (
              https://github.com/theislab/Scanpy ). Along with Scanpy, we
              present AnnData, a generic class for handling annotated data
              matrices ( https://github.com/theislab/anndata ).",
  journal  = "Genome Biol.",
  year     =  2018,
  keywords = "Bioinformatics; Clustering; Differential expression testing;
              Graph analysis; Machine learning; Pseudotemporal ordering;
              Scalability; Single-cell transcriptomics; Trajectory inference;
              Visualization;Mendeley Import (Feb 23)"
}

@ARTICLE{Stoeckius2017-zc,
  title    = "Simultaneous epitope and transcriptome measurement in single
              cells",
  author   = "Stoeckius, Marlon and Hafemeister, Christoph and Stephenson,
              William and Houck-Loomis, Brian and Chattopadhyay, Pratip K and
              Swerdlow, Harold and Satija, Rahul and Smibert, Peter",
  abstract = "High-throughput single-cell RNA sequencing has transformed our
              understanding of complex cell populations, but it does not
              provide phenotypic information such as cell-surface protein
              levels. Here, we describe cellular indexing of transcriptomes and
              epitopes by sequencing (CITE-seq), a method in which
              oligonucleotide-labeled antibodies are used to integrate cellular
              protein and transcriptome measurements into an efficient,
              single-cell readout. CITE-seq is compatible with existing
              single-cell sequencing approaches and scales readily with
              throughput increases.",
  journal  = "Nat. Methods",
  volume   =  14,
  number   =  9,
  pages    = "865--868",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Haghverdi2015-xn,
  title    = "Diffusion maps for high-dimensional single-cell analysis of
              differentiation data",
  author   = "Haghverdi, Laleh and Buettner, Florian and Theis, Fabian J",
  abstract = "MOTIVATION: Single-cell technologies have recently gained
              popularity in cellular differentiation studies regarding their
              ability to resolve potential heterogeneities in cell populations.
              Analysing such high-dimensional single-cell data has its own
              statistical and computational challenges. Popular multivariate
              approaches are based on data normalisation, followed by dimension
              reduction and clustering to identify subgroups. However, in the
              case of cellular differentiation, we would not expect clear
              clusters to be present but instead expect the cells to follow
              continuous branching lineages. RESULTS: Here we propose the use
              of diffusion maps to deal with the problem of defining
              differentiation trajectories. We adapt this method to single-cell
              data by adequate choice of kernel width and inclusion of
              uncertainties or missing measurement values, which enables the
              establishment of a pseudo-temporal ordering of single cells in a
              high-dimensional gene expression space. We expect this output to
              reflect cell differentiation trajectories, where the data
              originates from intrinsic diffusion-like dynamics. Starting from
              a pluripotent stage, cells move smoothly within the
              transcriptional landscape towards more differentiated states with
              some stochasticity along their path. We demonstrate the
              robustness of our method with respect to extrinsic noise (e.g.
              measurement noise) and sampling density heterogeneities on
              simulated toy data as well as two single-cell quantitative
              polymerase chain reaction (qPCR) data sets (i.e. mouse
              haematopoietic stem cells and mouse embryonic stem cells) and an
              RNA-Seq data of human pre-implantation embryos. We show that
              diffusion maps perform considerably better than Principal
              Component Analysis (PCA) and are advantageous over other
              techniques for non-linear dimension reduction such as
              t-distributed Stochastic Neighbour Embedding (t-SNE) for
              preserving the global structures and pseudotemporal ordering of
              cells. AVAILABILITY: The Matlab implementation of diffusion maps
              for single-cell data is available at
              https://www.helmholtz-muenchen.de/icb/single-cell-diffusion-map.
              CONTACT: fbuettner.phys@gmail.com,
              fabian.theis@helmholtz-muenchen.de.",
  journal  = "Bioinformatics",
  volume   =  31,
  number   =  18,
  pages    = "2989--2998",
  year     =  2015,
  keywords = "Mendeley Import (Feb 23)"
}

@INPROCEEDINGS{Mao2015-so,
  title     = "Dimensionality Reduction Via Graph Structure Learning",
  booktitle = "{KDD} '15: Proceedings of the 21th {ACM} {SIGKDD} International
               Conference on Knowledge Discovery and Data Mining",
  author    = "Mao, Qi and Wang, Li and Goodison, Steve and Sun, Yijun",
  abstract  = "We present a new dimensionality reduction setting for a large
               family of real-world problems. Unlike traditional methods, the
               new setting aims to explicitly represent and learn an intrinsic
               structure from data in a high-dimensional space, which can
               greatly",
  year      =  2015,
  keywords  = "Mendeley Import (Feb 23)"
}

@ARTICLE{Weinreb2017-vr,
  title    = "{SPRING}: a kinetic interface for visualizing high dimensional
              single-cell expression data",
  author   = "Weinreb, Caleb and Wolock, Samuel and Klein, Allon M",
  abstract = "Motivation: Single-cell gene expression profiling technologies
              can map the cell states in a tissue or organism. As these
              technologies become more common, there is a need for
              computational tools to explore the data they produce. In
              particular, existing data visualization approaches are imperfect
              for studying continuous gene expression topologies. Results:
              Force-directed layouts of k-nearest-neighbor graphs can visualize
              continuous gene expression topologies in a manner that preserves
              high-dimensional relationships and allows manually exploration of
              different stable two- dimensional representations of the same
              data. We implemented an interactive web-tool to visualize
              single-cell data using force-directed graph layouts, called
              SPRING. SPRING reveals more detailed biological relationships
              than existing approaches when applied to branching gene
              expression trajectories from hematopoietic progenitor cells.
              Visualizations from SPRING are also more reproducible than those
              of stochastic visualization methods such as tSNE, a
              state-of-the-art tool. Availability:
              https://kleintools.hms.harvard.edu/tools/spring.html,
              https://github.com/AllonKleinLab/SPRING/\textbackslashr\textbackslashn\textbackslashr\textbackslashn",
  journal  = "Bioinformatics",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Pierson2015-wi,
  title    = "{ZIFA}: Dimensionality reduction for zero-inflated single-cell
              gene expression analysis",
  author   = "Pierson, Emma and Yau, Christopher",
  abstract = "Single-cell RNA-seq data allows insight into normal cellular
              function and various disease states through molecular
              characterization of gene expression on the single cell level.
              Dimensionality reduction of such high-dimensional data sets is
              essential for visualization and analysis, but single-cell RNA-seq
              data are challenging for classical dimensionality-reduction
              methods because of the prevalence of dropout events, which lead
              to zero-inflated data. Here, we develop a
              dimensionality-reduction method, (Z)ero (I)nflated (F)actor
              (A)nalysis (ZIFA), which explicitly models the dropout
              characteristics, and show that it improves modeling accuracy on
              simulated and biological data sets.",
  journal  = "Genome Biol.",
  volume   =  16,
  number   =  1,
  year     =  2015,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Van_Der_Maaten2008-uz,
  title    = "Visualizing Data using {t-SNE}",
  author   = "Van Der Maaten, Laurens and Hinton, Geoffrey",
  abstract = "We present a new technique called `` t-SNE '' that visualizes
              high-dimensional data by giving each datapoint a location in a
              two or three-dimensional map. The technique is a variation of
              Stochastic Neighbor Embedding (Hinton and Roweis, 2002) that is
              much easier to optimize, and produces significantly better
              visualizations by reducing the tendency to crowd points together
              in the center of the map. t-SNE is better than existing
              techniques at creating a single map that reveals structure at
              many different scales. This is particularly important for
              high-dimensional data that lie on several different, but related,
              low-dimensional manifolds, such as images of objects from
              multiple classes seen from multiple viewpoints. For visualizing
              the structure of very large data sets, we show how t-SNE can use
              random walks on neighborhood graphs to allow the implicit
              structure of all of the data to influence the way in which a
              subset of the data is displayed. We illustrate the performance of
              t-SNE on a wide variety of data sets and compare it with many
              other non-parametric visualization techniques, including Sammon
              mapping, Isomap, and Locally Linear Embedding. The
              visualiza-tions produced by t-SNE are significantly better than
              those produced by the other techniques on almost all of the data
              sets.",
  journal  = "J. Mach. Learn. Res.",
  volume   =  9,
  pages    = "2579--2605",
  year     =  2008,
  keywords = "dimensionality reduction; embedding algorithms; manifold
              learning; multidimensional scaling; visualization;Mendeley Import
              (Feb 23)"
}

@ARTICLE{Butler2017-fu,
  title    = "Integrated analysis of single cell transcriptomic data across
              conditions, technologies, and species",
  author   = "Butler, Andrew and Satija, Rahul",
  abstract = "Single cell RNA-seq (scRNA-seq) has emerged as a transformative
              tool to discover and define cellular phenotypes. While
              computational scRNA-seq methods are currently well suited for
              experiments representing a single condition, technology, or
              species, analyzing multiple datasets simultaneously raises new
              challenges. In particular, traditional analytical workflows
              struggle to align subpopulations that are present across
              datasets, limiting the possibility for integrated or comparative
              analysis. Here, we introduce a new computational strategy for
              scRNA-seq alignment, utilizing common sources of variation to
              identify shared subpopulations between datasets as part of our R
              toolkit Seurat. We demonstrate our approach by aligning scRNA-seq
              datasets of PBMCs under resting and stimulated conditions,
              hematopoietic progenitors sequenced across two profiling
              technologies, and pancreatic cell 'atlases' generated from human
              and mouse islets. In each case, we learn distinct or transitional
              cell states jointly across datasets, and can identify
              subpopulations that could not be detected by analyzing datasets
              independently. We anticipate that these methods will serve not
              only to correct for batch or technology-dependent effects, but
              also to facilitate general comparisons of scRNA-seq datasets,
              potentially deepening our understanding of how distinct cell
              states respond to perturbation, disease, and evolution.
              Availability: Installation instructions, documentation, and
              tutorials are available at http://www.satijalab.org/seurat",
  journal  = "bioRxiv",
  pages    = "164889",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Giustacchini2017-ej,
  title    = "Single-cell transcriptomics uncovers distinct molecular
              signatures of stem cells in chronic myeloid leukemia",
  author   = "Giustacchini, Alice and Thongjuea, Supat and Barkas, Nikolaos and
              Woll, Petter S and Povinelli, Benjamin J and Booth, Christopher A
              G and Sopp, Paul and Norfo, Ruggiero and Rodriguez-Meira, Alba
              and Ashley, Neil and Jamieson, Lauren and Vyas, Paresh and
              Anderson, Kristina and Segerstolpe, {\AA}sa and Qian, Hong and
              Olsson-Str{\"o}mberg, Ulla and Mustjoki, Satu and Sandberg,
              Rickard and Jacobsen, Sten Eirik W and Mead, Adam J",
  abstract = "Applying a new, more sensitive single-cell transcriptomics method
              to diagnosis, remission and progression samples from patients
              with chronic myeloid leukemia reveals insight into the
              heterogeneity of cells that resist treatment with targeted
              therapy, as well as into the dynamics of disease progression and
              its effects on nontransformed hematopoietic stem cells.",
  journal  = "Nat. Med.",
  volume   =  23,
  number   =  6,
  pages    = "692--702",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Lavin2017-yf,
  title    = "Innate Immune Landscape in Early Lung Adenocarcinoma by Paired
              {Single-Cell} Analyses",
  author   = "Lavin, Yonit and Kobayashi, Soma and Leader, Andrew and Amir, El
              ad David and Elefant, Naama and Bigenwald, Camille and Remark,
              Romain and Sweeney, Robert and Becker, Christian D and Levine,
              Jacob H and Meinhof, Klaus and Chow, Andrew and Kim-Shulze,
              Seunghee and Wolf, Andrea and Medaglia, Chiara and Li, Hanjie and
              Rytlewski, Julie A and Emerson, Ryan O and Solovyov, Alexander
              and Greenbaum, Benjamin D and Sanders, Catherine and Vignali,
              Marissa and Beasley, Mary Beth and Flores, Raja and Gnjatic,
              Sacha and Pe'er, Dana and Rahman, Adeeb and Amit, Ido and Merad,
              Miriam",
  abstract = "To guide the design of immunotherapy strategies for patients with
              early stage lung tumors, we developed a multiscale immune
              profiling strategy to map the immune landscape of early lung
              adenocarcinoma lesions to search for tumor-driven immune changes.
              Utilizing a barcoding method that allows a simultaneous
              single-cell analysis of the tumor, non-involved lung, and blood
              cells, we provide a detailed immune cell atlas of early lung
              tumors. We show that stage I lung adenocarcinoma lesions already
              harbor significantly altered T cell and NK cell compartments.
              Moreover, we identified changes in tumor-infiltrating myeloid
              cell (TIM) subsets that likely compromise anti-tumor T cell
              immunity. Paired single-cell analyses thus offer valuable
              knowledge of tumor-driven immune changes, providing a powerful
              tool for the rational design of immune therapies. Video Abstract",
  journal  = "Cell",
  volume   =  169,
  number   =  4,
  pages    = "750--765.e17",
  year     =  2017,
  keywords = "CD141+ DC; CD1c+ DC; NK Cell; T Cell; TIM; TLS; human non-small
              cell lung cancer (NSCLC); immune cell atlas; lung adenocarcinoma;
              tumor macrophage;Mendeley Import (Feb 23)"
}

@ARTICLE{Horning2018-kc,
  title    = "{Single-Cell} {RNA-seq} reveals a subpopulation of prostate
              cancer cells with enhanced {cell-Cycle--Related} transcription
              and attenuated androgen response",
  author   = "Horning, Aaron M and Wang, Yao and Lin, Che Kuang and Louie, Anna
              D and Jadhav, Rohit R and Hung, Chia Nung and Wang, Chiou Miin
              and Lin, Chun Lin and Kirma, Nameer B and Liss, Michael A and
              Kumar, Addanki P and Sun, Lu Zhe and Liu, Zhijie and Chao, Wei
              Ting and Wang, Qianben and Jin, Victor X and Chen, Chun Liang and
              Huang, Tim H M",
  abstract = "Increasing evidence suggests the presence of minor cell
              subpopulations in prostate cancer that are androgen independent
              and poised for selection as dominant clones after
              androgen-deprivation therapy. In this study, we investigated this
              phenomenon by stratifying cell subpopulations based on
              transcriptome profiling of 144 single LNCaP prostate cancer cells
              treated or untreated with androgen after cell cycle
              synchronization. Model-based clustering of 397 differentially
              expressed genes identified eight potential subpopulations of
              LNCaP cells, revealing a previously unappreciable level of
              cellular heterogeneity to androgen stimulation. One subpopulation
              displayed stem-like features with a slower cell doubling rate,
              increased sphere formation capability, and resistance to G2/M
              arrest induced by a mitosis inhibitor. Advanced growth of this
              subpopulation was associated with enhanced expression of 10 cell
              cycle-related genes (CCNB2, DLGAP5, CENPF, CENPE, MKI67, PTTG1,
              CDC20, PLK1, HMMR, and CCNB1) and decreased dependence upon
              androgen receptor signaling. In silico analysis of RNA-seq data
              from The Cancer Genome Atlas (TCGA) further demonstrated that
              concordant upregulation of these genes was linked to recurrent
              prostate cancers. Analysis of receiver-operating characteristic
              curves implicates aberrant expression of these genes and could be
              useful for early identification of tumors that subsequently
              develop biochemical recurrence. Moreover, this single-cell
              approach provides a better understanding of how prostate cancer
              cells respond heterogeneously to androgen-deprivation therapies
              and reveals characteristics of subpopulations resistant to this
              treatment.",
  journal  = "Cancer Res.",
  volume   =  78,
  number   =  4,
  pages    = "853--864",
  year     =  2018,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Chung2017-gv,
  title    = "Single-cell {RNA-seq} enables comprehensive tumour and immune
              cell profiling in primary breast cancer",
  author   = "Chung, Woosung and Eum, Hye Hyeon and Lee, Hae Ock and Lee, Kyung
              Min and Lee, Han Byoel and Kim, Kyu Tae and Ryu, Han Suk and Kim,
              Sangmin and Lee, Jeong Eon and Park, Yeon Hee and Kan, Zhengyan
              and Han, Wonshik and Park, Woong Yang",
  abstract = "Genetic heterogeneity in breast cancer has been demonstrated at a
              single-cell resolution with high levels of genome coverage. Here,
              the authors perform transcriptome analysis of 515 single cells
              from 11 patients and define core gene expression signatures for
              subtype-specific single breast cancer cells and
              tumour-infiltrating immune cells.",
  journal  = "Nat. Commun.",
  volume   =  8,
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Svensson2018-qq,
  title    = "Exponential scaling of single-cell {RNA-seq} in the past decade",
  author   = "Svensson, Valentine and Vento-Tormo, Roser and Teichmann, Sarah A",
  abstract = "Here Sarah Teichmann and colleagues provide a Perspective on the
              exponential scaling of single-cell RNA-sequencing experiments
              over the last decade, commenting on the methodological
              developments that have underpinned the advances in this
              technology.",
  journal  = "Nat. Protoc.",
  volume   =  13,
  number   =  4,
  pages    = "599--604",
  year     =  2018,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Stahl2016-cr,
  title    = "Visualization and analysis of gene expression in tissue sections
              by spatial transcriptomics",
  author   = "Stahl, P L and Salmen, F and Vickovic, S and Lundmark, A and
              Navarro, J F and Magnusson, J and Giacomello, S and Asp, M and
              Westholm, J O and Huss, M and Mollbrink, A and Linnarsson, S and
              Codeluppi, S and Borg, A and Ponten, F and Costea, P I and
              Sahlen, P and Mulder, J and Bergmann, O and Lundeberg, J and
              Frisen, J",
  abstract = "Analysis of the pattern of proteins or messengerRNAs (mRNAs) in
              histological tissue sections is a cornerstone in biomedical
              research and diagnostics. This typically involves the
              visualization of a few proteins or expressed genes at a time. We
              have devised a strategy, which we call ``spatial
              transcriptomics,'' that allows visualization and quantitative
              analysis of the transcriptome with spatial resolution in
              individual tissue sections. By positioning histological sections
              on arrayed reverse transcription primers with unique positional
              barcodes, we demonstrate high-quality RNA-sequencing data with
              maintained two-dimensional positional information from the mouse
              brain and human breast cancer. Spatial transcriptomics provides
              quantitative gene expression data and visualization of the
              distribution of mRNAs within tissue sections and enables novel
              types of bioinformatics analyses, valuable in research and
              diagnostics.",
  journal  = "Science",
  volume   =  353,
  number   =  6294,
  pages    = "78--82",
  year     =  2016,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Paul2015-zj,
  title    = "Transcriptional Heterogeneity and Lineage Commitment in Myeloid
              Progenitors",
  author   = "Paul, Franziska and Arkin, Ya'ara and Giladi, Amir and Jaitin,
              Diego Adhemar and Kenigsberg, Ephraim and Keren-Shaul, Hadas and
              Winter, Deborah and Lara-Astiaso, David and Gury, Meital and
              Weiner, Assaf and David, Eyal and Cohen, Nadav and Lauridsen,
              Felicia Kathrine Bratt and Haas, Simon and Schlitzer, Andreas and
              Mildner, Alexander and Ginhoux, Florent and Jung, Steffen and
              Trumpp, Andreas and Porse, Bo Torben and Tanay, Amos and Amit,
              Ido",
  abstract = "Within the bone marrow, stem cells differentiate and give rise to
              diverse blood cell types and functions. Currently, hematopoietic
              progenitors are defined using surface markers combined with
              functional assays that are not directly linked with in vivo
              differentiation potential or gene regulatory mechanisms. Here, we
              comprehensively map myeloid progenitor subpopulations by
              transcriptional sorting of single cells from the bone marrow. We
              describe multiple progenitor subgroups, showing unexpected
              transcriptional priming toward seven differentiation fates but no
              progenitors with a mixed state. Transcriptional differentiation
              is correlated with combinations of known and previously undefined
              transcription factors, suggesting that the process is tightly
              regulated. Histone maps and knockout assays are consistent with
              early transcriptional priming, while traditional transplantation
              experiments suggest that in vivo priming may still allow for
              plasticity given strong perturbations. These data establish a
              reference model and general framework for studying hematopoiesis
              at single-cell resolution.",
  journal  = "Cell",
  volume   =  163,
  number   =  7,
  pages    = "1663--1677",
  year     =  2015,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Regev2017-le,
  title    = "The human cell atlas",
  author   = "Regev, Aviv and Teichmann, Sarah A and Lander, Eric S and Amit,
              Ido and Benoist, Christophe and Birney, Ewan and Bodenmiller,
              Bernd and Campbell, Peter and Carninci, Piero and Clatworthy,
              Menna and Clevers, Hans and Deplancke, Bart and Dunham, Ian and
              Eberwine, James and Eils, Roland and Enard, Wolfgang and Farmer,
              Andrew and Fugger, Lars and G{\"o}ttgens, Berthold and Hacohen,
              Nir and Haniffa, Muzlifah and Hemberg, Martin and Kim, Seung and
              Klenerman, Paul and Kriegstein, Arnold and Lein, Ed and
              Linnarsson, Sten and Lundberg, Emma and Lundeberg, Joakim and
              Majumder, Partha and Marioni, John C and Merad, Miriam and
              Mhlanga, Musa and Nawijn, Martijn and Netea, Mihai and Nolan,
              Garry and Pe'er, Dana and Phillipakis, Anthony and Ponting, Chris
              P and Quake, Stephen and Reik, Wolf and Rozenblatt-Rosen, Orit
              and Sanes, Joshua and Satija, Rahul and Schumacher, Ton N and
              Shalek, Alex and Shapiro, Ehud and Sharma, Padmanee and Shin, Jay
              W and Stegle, Oliver and Stratton, Michael and Stubbington,
              Michael J T and Theis, Fabian J and Uhlen, Matthias and Van
              Oudenaarden, Alexander and Wagner, Allon and Watt, Fiona and
              Weissman, Jonathan and Wold, Barbara and Xavier, Ramnik and
              Yosef, Nir",
  abstract = "The recent advent of methods for high-throughput single-cell
              molecular profiling has catalyzed a growing sense in the
              scientific community that the time is ripe to complete the
              150-year-old effort to identify all cell types in the human body.
              The Human Cell Atlas Project is an international collaborative
              effort that aims to define all human cell types in terms of
              distinctive molecular profiles (such as gene expression profiles)
              and to connect this information with classical cellular
              descriptions (such as location and morphology). An open
              comprehensive reference map of the molecular state of cells in
              healthy human tissues would propel the systematic study of
              physiological states, developmental trajectories, regulatory
              circuitry and interactions of cells, and also provide a framework
              for understanding cellular dysregulation in human disease. Here
              we describe the idea, its potential utility, early
              proofs-of-concept, and some design considerations for the Human
              Cell Atlas, including a commitment to open data, code, and
              community.",
  journal  = "Elife",
  volume   =  6,
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Halpern2017-cp,
  title    = "Single-cell spatial reconstruction reveals global division of
              labour in the mammalian liver",
  author   = "Halpern, Keren Bahar and Shenhav, Rom and Matcovitch-Natan, Orit
              and T{\'o}th, Be{\'a}ta and Lemze, Doron and Golan, Matan and
              Massasa, Efi E and Baydatch, Shaked and Landen, Shanie and Moor,
              Andreas E and Brandis, Alexander and Giladi, Amir and
              Stokar-Avihail, Avigail and David, Eyal and Amit, Ido and
              Itzkovitz, Shalev",
  abstract = "The mammalian liver consists of hexagon-shaped lobules that are
              radially polarized by blood flow and morphogens. Key liver genes
              have been shown to be differentially expressed along the lobule
              axis, a phenomenon termed zonation, but a detailed genome-wide
              reconstruction of this spatial division of labour has not been
              achieved. Here we measure the entire transcriptome of thousands
              of mouse liver cells and infer their lobule coordinates on the
              basis of a panel of zonated landmark genes, characterized with
              single-molecule fluorescence in situ hybridization. Using this
              approach, we obtain the zonation profiles of all liver genes with
              high spatial resolution. We find that around 50\% of liver genes
              are significantly zonated and uncover abundant non-monotonic
              profiles that peak at the mid-lobule layers. These include a
              spatial order of bile acid biosynthesis enzymes that matches
              their position in the enzymatic cascade. Our approach can
              facilitate the reconstruction of similar spatial genomic
              blueprints for other mammalian organs.",
  journal  = "Nature",
  volume   =  542,
  number   =  7641,
  pages    = "1--5",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Zeisel2015-lx,
  title    = "Cell types in the mouse cortex and hippocampus revealed by
              single-cell {RNA-seq}",
  author   = "Zeisel, A and Manchado, a B M and Codeluppi, S and Lonnerberg, P
              and La Manno, G and Jureus, A and Marques, S and Munguba, H and
              He, L and Betsholtz, C and Rolny, C and Castelo-Branco, G and
              Hjerling-Leffler, J and Linnarsson, S",
  abstract = "The mammalian cerebral cortex supports cognitive functions such
              as sensorimotor integration, memory, and social behaviors. Normal
              brain function relies on a diverse set of differentiated cell
              types, including neurons, glia, and vasculature. Here, we have
              used large-scale single-cell RNA sequencing (RNA-seq) to classify
              cells in the mouse somatosensory cortex and hippocampal CA1
              region. We found 47 molecularly distinct subclasses, comprising
              all known major cell types in the cortex. We identified numerous
              marker genes, which allowed alignment with known cell types,
              morphology, and location. We found a layer I interneuron
              expressing Pax6 and a distinct postmitotic oligodendrocyte
              subclass marked by Itpr2. Across the diversity of cortical cell
              types, transcription factors formed a complex, layered regulatory
              code, suggesting a mechanism for the maintenance of adult cell
              type identity.",
  journal  = "Science",
  volume   =  347,
  number   =  6226,
  pages    = "1138--1142",
  year     =  2015,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Efroni2016-pw,
  title    = "The potential of single-cell profiling in plants",
  author   = "Efroni, Idan and Birnbaum, Kenneth D",
  abstract = "Single-cell transcriptomics has been employed in a growing number
              of animal studies, but the technique has yet to be widely used in
              plants. Nonetheless, early studies indicate that single-cell
              RNA-seq protocols developed for animal cells produce informative
              datasets in plants. We argue that single-cell transcriptomics has
              the potential to provide a new perspective on plant problems,
              such as the nature of the stem cells or initials, the plasticity
              of plant cells, and the extent of localized cellular responses to
              environmental inputs. Single-cell experimental outputs require
              different analytical approaches compared with pooled cell
              profiles and new tools tailored to single-cell assays are being
              developed. Here, we highlight promising new single-cell profiling
              approaches, their limitations as applied to plants, and their
              potential to address fundamental questions in plant biology.",
  journal  = "Genome Biol.",
  volume   =  17,
  number   =  1,
  year     =  2016,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Rosenberg2017-ps,
  title    = "Scaling single cell transcriptomics through split pool barcoding",
  author   = "Rosenberg, Alexander B and Roco, Charles and Muscat, Richard A
              and Kuchina, Anna and Mukherjee, Sumit and Chen, Wei and Peeler,
              David J and Yao, Zizhen and Tasic, Bosiljka and Sellers, Drew L
              and Pun, Suzie H and Seelig, Georg",
  abstract = "Constructing an atlas of cell types in complex organisms will
              require a collective effort to characterize billions of
              individual cells. Single cell RNA sequencing (scRNA-seq) has
              emerged as the main tool for characterizing cellular diversity,
              but current methods use custom microfluidics or microwells to
              compartmentalize single cells, limiting scalability and
              widespread adoption. Here we present Split Pool Ligation-based
              Transcriptome sequencing (SPLiT-seq), a scRNA-seq method that
              labels the cellular origin of RNA through combinatorial indexing.
              SPLiT-seq is compatible with fixed cells, scales exponentially,
              uses only basic laboratory equipment, and costs one cent per
              cell. We used this approach to analyze 109,069 single cell
              transcriptomes from an entire postnatal day 5 mouse brain,
              providing the first global snapshot at this stage of development.
              We identified 13 main populations comprising different types of
              neurons, glia, immune cells, endothelia, as well as types in the
              blood-brain-barrier. Moreover, we resolve substructure within
              these clusters corresponding to cells at different stages of
              development. As sequencing capacity increases, SPLiT-seq will
              enable profiling of billions of cells in a single experiment.",
  journal  = "bioRxiv",
  pages    = "105163",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Warfvinge2017-ul,
  title    = "Single-cell molecular analysis defines therapy response and
              immunophenotype of stem cell subpopulations in {CML}",
  author   = "Warfvinge, Rebecca and Geironson, Linda and Sommarin, Mikael N E
              and Lang, Stefan and Karlsson, Christine and Roschupkina, Teona
              and Stenke, Leif and Stentoft, Jesper and Olsson-Stromberg, Ulla
              and Hjorth-Hansen, Henrik and Mustjoki, Satu and Soneji, Shamit
              and Richter, Johan and Karlsson, Goran",
  abstract = "Understanding leukemia heterogeneity is critical for the
              development of curative treatments as the failure to eliminate
              therapy-persistent leukemic stem cells (LSCs) may result in
              disease relapse. Here we have combined high-throughput
              immunophenotypic screens with large-scale single-cell gene
              expression analysis to define the heterogeneity within the LSC
              population in chronic phase chronic myeloid leukemia (CML)
              patients at diagnosis and following conventional tyrosine kinase
              inhibitor (TKI) treatment. Our results reveal substantial
              heterogeneity within the putative LSC population in CML at
              diagnosis and demonstrate differences in response to subsequent
              TKI treatment between distinct subpopulations. Importantly, LSC
              subpopulations with myeloid and proliferative molecular
              signatures are proportionally reduced at a higher extent in
              response to TKI therapy compared with subfractions displaying
              primitive and quiescent signatures. Additionally, cell surface
              expression of the CML stem cell markers CD25, CD26, and IL1RAP is
              high in all subpopulations at diagnosis but downregulated and
              unevenly distributed across subpopulations in response to TKI
              treatment. The most TKI-insensitive cells of the LSC compartment
              can be captured within the CD45RA(-) fraction and further defined
              as positive for CD26 in combination with an aberrant lack of cKIT
              expression. Together, our results expose a considerable
              heterogeneity of the CML stem cell population and propose a
              Lin(-)CD34(+)CD38(-/low)CD45RA(-)cKIT(-)CD26(+) population as a
              potential therapeutic target for improved therapy response.",
  journal  = "Blood",
  volume   =  129,
  number   =  17,
  pages    = "2384--2394",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Cao2017-ay,
  title    = "Comprehensive single-cell transcriptional profiling of a
              multicellular organism",
  author   = "Cao, Junyue and Packer, Jonathan S and Ramani, Vijay and
              Cusanovich, Darren A and Huynh, Chau and Daza, Riza and Qiu,
              Xiaojie and Lee, Choli and Furlan, Scott N and Steemers, Frank J
              and Adey, Andrew and Waterston, Robert H and Trapnell, Cole and
              Shendure, Jay",
  abstract = "To resolve cellular heterogeneity, we developed a combinatorial
              indexing strategy to profile the transcriptomes of single cells
              or nuclei, termed sci-RNA-seq (single-cell combinatorial indexing
              RNA sequencing). We applied sci-RNA-seq to profile nearly 50,000
              cells from the nematode Caenorhabditis elegans at the L2 larval
              stage, which provided >50-fold `` shotgun '' cellular coverage of
              its somatic cell composition. From these data, we defined
              consensus expression profiles for 27 cell types and recovered
              rare neuronal cell types corresponding to as few as one or two
              cells in the L2 worm. We integrated these profiles with
              whole-animal chromatin immunoprecipitation sequencing data to
              deconvolve the cell type--specific effects of transcription
              factors. The data generated by sci-RNA-seq constitute a powerful
              resource for nematode biology and foreshadow similar atlases for
              other organisms.",
  journal  = "Science",
  volume   =  357,
  number   =  6352,
  pages    = "661--667",
  year     =  2017,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Wills2013-nj,
  title    = "Single-cell gene expression analysis reveals genetic associations
              masked in whole-tissue experiments",
  author   = "Wills, Quin F and Livak, Kenneth J and Tipping, Alex J and Enver,
              Tariq and Goldson, Andrew J and Sexton, Darren W and Holmes,
              Chris",
  abstract = "Gene expression in multiple individual cells from a tissue or
              culture sample varies according to cell-cycle, genetic,
              epigenetic and stochastic differences between the cells. However,
              single-cell differences have been largely neglected in the
              analysis of the functional consequences of genetic variation.
              Here we measure the expression of 92 genes affected by Wnt
              signaling in 1,440 single cells from 15 individuals to associate
              single-nucleotide polymorphisms (SNPs) with gene-expression
              phenotypes, while accounting for stochastic and cell-cycle
              differences between cells. We provide evidence that many
              heritable variations in gene function--such as burst size, burst
              frequency, cell cycle-specific expression and expression
              correlation/noise between cells--are masked when expression is
              averaged over many cells. Our results demonstrate how single-cell
              analyses provide insights into the mechanistic and network
              effects of genetic variability, with improved statistical power
              to model these effects on gene expression.",
  journal  = "Nat. Biotechnol.",
  volume   =  31,
  number   =  8,
  pages    = "748--752",
  year     =  2013,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Pina2012-us,
  title    = "Inferring rules of lineage commitment in haematopoiesis",
  author   = "Pina, Cristina and Fugazza, Cristina and Tipping, Alex J and
              Brown, John and Soneji, Shamit and Teles, Jose and Peterson,
              Carsten and Enver, Tariq",
  abstract = "How the molecular programs of differentiated cells develop as
              cells transit from multipotency through lineage commitment
              remains unexplored. This reflects the inability to access cells
              undergoing commitment or located in the immediate vicinity of
              commitment boundaries. It remains unclear whether commitment
              constitutes a gradual process, or else represents a discrete
              transition. Analyses of in vitro self-renewing multipotent
              systems have revealed cellular heterogeneity with individual
              cells transiently exhibiting distinct biases for lineage
              commitment. Such systems can be used to molecularly interrogate
              early stages of lineage affiliation and infer rules of lineage
              commitment. In haematopoiesis, population-based studies have
              indicated that lineage choice is governed by global
              transcriptional noise, with self-renewing multipotent cells
              reversibly activating transcriptome-wide lineage-affiliated
              programs. We examine this hypothesis through functional and
              molecular analysis of individual blood cells captured from
              self-renewal cultures, during cytokine-driven differentiation and
              from primary stem and progenitor bone marrow compartments. We
              show dissociation between self-renewal potential and
              transcriptome-wide activation of lineage programs, and instead
              suggest that multipotent cells experience independent activation
              of individual regulators resulting in a low probability of
              transition to the committed state.",
  journal  = "Nat. Cell Biol.",
  volume   =  14,
  number   =  3,
  pages    = "287--294",
  year     =  2012,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Lang2015-sj,
  title    = "{SCExV}: A webtool for the analysis and visualisation of single
              cell {qRT-PCR} data",
  author   = "Lang, Stefan and Ugale, Amol and Erlandsson, Eva and Karlsson,
              G{\"o}ran and Bryder, David and Soneji, Shamit",
  abstract = "BACKGROUND: Single cell gene expression assays have become a
              powerful tool with which to dissect heterogeneous populations.
              While methods and software exist to interrogate such data, what
              has been lacking is a unified solution combining analysis and
              visualisation which is also accessible and intuitive for use by
              non-bioinformaticians, as well as bioinformaticians. RESULTS: We
              present the Single cell expression visualiser (SCExV), a webtool
              developed to expedite the analysis of single cell qRT-PCR data.
              SCExV is able to take any data matrix of Ct values as an input,
              but can handle files exported by the Fluidigm Biomark platform
              directly. In addition, SCExV also accepts and automatically
              integrates cell surface marker intensity values which are
              measured during index sorting. This allows the user to directly
              visualise relationships between a single cell gene expression
              profile and the immunophenotype of the interrogated cell.
              CONCLUSIONS: SCExV is a freely available webtool created to
              import, filter, analyse, and visualise single cell gene
              expression data whilst being able to simultaneously consider
              cellular immunophenotype. SCExV is designed to be intuitive to
              use whilst maintaining advanced functionality and flexibility in
              how analyses are performed.",
  journal  = "BMC Bioinformatics",
  volume   =  16,
  number   =  1,
  year     =  2015,
  keywords = "FACS; Gene expression; Index sorting; QRT-PCR; Single cells;
              Visualisation; Webtool;Mendeley Import (Feb 23)"
}

@ARTICLE{Bendall2014-dg,
  title    = "Single-cell trajectory detection uncovers progression and
              regulatory coordination in human b cell development",
  author   = "Bendall, Sean C and Davis, Kara L and Amir, El Ad David and
              Tadmor, Michelle D and Simonds, Erin F and Chen, Tiffany J and
              Shenfeld, Daniel K and Nolan, Garry P and Pe'Er, Dana",
  abstract = "Tissue regeneration is an orchestrated progression of cells from
              an immature state to a mature one, conventionally represented as
              distinctive cell subsets. A continuum of transitional cell states
              exists between these discrete stages. We combine the depth of
              single-cell mass cytometry and an algorithm developed to leverage
              this continuum by aligning single cells of a given lineage onto a
              unified trajectory that accurately predicts the developmental
              path de novo. Applied to human B cell lymphopoiesis, the
              algorithm (termed Wanderlust) constructed trajectories spanning
              from hematopoietic stem cells through to naive B cells. This
              trajectory revealed nascent fractions of B cell progenitors and
              aligned them with developmentally cued regulatory signaling
              including IL-7/STAT5 and cellular events such as immunoglobulin
              rearrangement, highlighting checkpoints across which regulatory
              signals are rewired paralleling changes in cellular state. This
              study provides a comprehensive analysis of human B lymphopoiesis,
              laying a foundation to apply this approach to other tissues and
              ``corrupted'' developmental processes including cancer.
              \copyright{} 2014 Elsevier Inc.",
  journal  = "Cell",
  volume   =  157,
  number   =  3,
  pages    = "714--725",
  year     =  2014,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Komorowska2017-ey,
  title    = "Hepatic Leukemia Factor Maintains Quiescence of Hematopoietic
              Stem Cells and Protects the Stem Cell Pool during Regeneration",
  author   = "Komorowska, Karolina and Doyle, Alexander and Wahlestedt, Martin
              and Subramaniam, Agatheeswaran and Debnath, Shubhranshu and Chen,
              Jun and Soneji, Shamit and Van Handel, Ben and Mikkola, Hanna K A
              and Miharada, Kenichi and Bryder, David and Larsson, Jonas and
              Magnusson, Mattias",
  abstract = "The transcription factor hepatic leukemia factor (HLF) is
              strongly expressed in hematopoietic stem cells (HSCs) and is
              thought to influence both HSC self-renewal and leukemogenesis.
              However, the physiological role of HLF in hematopoiesis and HSC
              function is unclear. Here, we report that mice lacking Hlf are
              viable with essentially normal hematopoietic parameters,
              including an intact HSC pool during steady-state hematopoiesis.
              In contrast, when challenged through transplantation,
              Hlf-deficient HSCs showed an impaired ability to reconstitute
              hematopoiesis and became gradually exhausted upon serial
              transplantation. Transcriptional profiling of Hlf-deficient HSCs
              revealed changes associated with enhanced cellular activation,
              and cell-cycle analysis demonstrated a significant reduction of
              quiescent HSCs. Accordingly, toxic insults targeting dividing
              cells completely eradicated the HSC pool in Hlf-deficient mice.
              In summary, our findings point to HLF as a critical regulator of
              HSC quiescence and as an essential factor for maintaining the HSC
              pool during regeneration. Komorowska et al. report that the
              transcription factor HLF is required to maintain hematopoietic
              stem cell (HSC) function during regeneration. Moreover,
              Hlf-deficient HSCs are less quiescent. In accordance with this,
              toxic insults targeting dividing cells completely eradicate the
              HSC pool in Hlf-deficient mice.",
  journal  = "Cell Rep.",
  volume   =  21,
  number   =  12,
  pages    = "3514--3523",
  year     =  2017,
  keywords = "5FU; HLF; HSC; cell cycle; quiescence; reconstitution;
              self-renewal; stress; transcription factor;
              transplantation;Mendeley Import (Feb 23)"
}

@ARTICLE{Nestorowa2016-zx,
  title    = "A single-cell resolution map of mouse hematopoietic stem and
              progenitor cell differentiation",
  author   = "Nestorowa, Sonia and Hamey, Fiona K and Pijuan Sala, Blanca and
              Diamanti, Evangelia and Shepherd, Mairi and Laurenti, Elisa and
              Wilson, Nicola K and Kent, David G and G{\"o}ttgens, Berthold",
  abstract = "Maintenance of the blood system requires balanced cell fate
              decisions by hematopoietic stem and progenitor cells (HSPCs).
              Because cell fate choices are executed at the individual cell
              level, new single-cell profiling technologies offer exciting
              possibilities for mapping the dynamic molecular changes
              underlying HSPC differentiation. Here, we have used single-cell
              RNA sequencing to profile more than 1600 single HSPCs, and deep
              sequencing has enabled detection of an average of 6558
              protein-coding genes per cell. Index sorting, in combination with
              broad sorting gates, allowed us to retrospectively assign cells
              to 12 commonly sorted HSPC phenotypes while also capturing
              intermediate cells typically excluded by conventional gating. We
              further show that independently generated single-cell data sets
              can be projected onto the single-cell resolution expression map
              to directly compare data from multiple groups and to build and
              refine new hypotheses. Reconstruction of differentiation
              trajectories reveals dynamic expression changes associated with
              early lymphoid, erythroid, and granulocyte-macrophage
              differentiation. The latter two trajectories were characterized
              by common upregulation of cell cycle and oxidative
              phosphorylation transcriptional programs. By using external
              spike-in controls, we estimate absolute messenger RNA (mRNA)
              levels per cell, showing for the first time that despite a
              general reduction in total mRNA, a subset of genes shows higher
              expression levels in immature stem cells consistent with active
              maintenance of the stem-cell state. Finally, we report the
              development of an intuitive Web interface as a new community
              resource to permit visualization of gene expression in HSPCs at
              single-cell resolution for any gene of choice.",
  journal  = "Blood",
  volume   =  128,
  number   =  8,
  pages    = "e20--e31",
  year     =  2016,
  keywords = "Mendeley Import (Feb 23)"
}

@MISC{Badman2007-rw,
  title    = "Hepatic Fibroblast Growth Factor 21 Is Regulated by {PPARalpha}
              and Is a Key Mediator of Hepatic Lipid Metabolism in Ketotic
              States",
  author   = "Badman, Michael K and Pissios, Pavlos and Kennedy, Adam R and
              Koukos, George and Flier, Jeffrey S and Maratos-Flier, Eleftheria",
  abstract = "Mice fed a high-fat, low-carbohydrate ketogenic diet (KD) exhibit
              marked changes in hepatic metabolism and energy homeostasis.
              Here, we identify liver-derived fibroblast growth factor 21
              (FGF21) as an endocrine regulator of the ketotic state. Hepatic
              expression and circulating levels of FGF21 are induced by both KD
              and fasting, are rapidly suppressed by refeeding, and are in
              large part downstream of PPAR??. Importantly, adenoviral
              knockdown of hepatic FGF21 in KD-fed mice causes fatty liver,
              lipemia, and reduced serum ketones, due at least in part to
              altered expression of key genes governing lipid and ketone
              metabolism. Hence, induction of FGF21 in liver is required for
              the normal activation of hepatic lipid oxidation, triglyceride
              clearance, and ketogenesis induced by KD. These findings identify
              hepatic FGF21 as a critical regulator of lipid homeostasis and
              identify a physiological role for this hepatic hormone. ?? 2007
              Elsevier Inc. All rights reserved.",
  journal  = "Cell Metabolism",
  volume   =  5,
  number   =  6,
  pages    = "426--437",
  year     =  2007,
  keywords = "HUMDISEASE;Mendeley Import (Feb 23)"
}

@ARTICLE{May2013-sp,
  title    = "Dynamic analysis of gene expression and genome-wide transcription
              factor binding during lineage specification of multipotent
              progenitors",
  author   = "May, Gillian and Soneji, Shamit and Tipping, Alex J and Teles,
              Jose and McGowan, Simon J and Wu, Mengchu and Guo, Yanping and
              Fugazza, Cristina and Brown, John and Karlsson, G{\"o}ran and
              Pina, Cristina and Olariu, Victor and Taylor, Stephen and Tenen,
              Daniel G and Peterson, Carsten and Enver, Tariq",
  abstract = "We used the paradigmatic GATA-PU.1 axis to explore, at the
              systems level, dynamic relationships between transcription factor
              (TF) binding and global gene expression programs as multipotent
              cells differentiate. We combined global ChIP-seq of GATA1, GATA2,
              and PU.1 with expression profiling during differentiation to
              erythroid and neutrophil lineages. Our analysis reveals (1)
              differential complexity of sequence motifs bound by GATA1, GATA2,
              and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs
              within, and during transitions between, different cell
              compartments, and the extent of their hard-wiring by DNA motifs;
              (3) the potential to predict gene expression trajectories based
              on global associations between TF-binding data and target gene
              expression; and (4) how dynamic modeling of DNA-binding and gene
              expression data can be used to infer regulatory logic of TF
              circuitry. This rubric exemplifies the utility of this
              cross-platform resource for deconvoluting the complexity of
              transcriptional programs controlling stem/progenitor cell fate in
              hematopoiesis. \copyright{} 2013 Elsevier Inc.",
  journal  = "Cell Stem Cell",
  volume   =  13,
  number   =  6,
  pages    = "754--768",
  year     =  2013,
  keywords = "Mendeley Import (Feb 23)"
}

@ARTICLE{Venkatesan2021-jr,
  title    = "Virtual and augmented reality for biomedical applications",
  author   = "Venkatesan, Mythreye and Mohan, Harini and Ryan, Justin R and
              Sch{\"u}rch, Christian M and Nolan, Garry P and Frakes, David H
              and Coskun, Ahmet F",
  abstract = "3D visualization technologies such as virtual reality (VR),
              augmented reality (AR), and mixed reality (MR) have gained
              popularity in the recent decade. Digital extended reality (XR)
              technologies have been adopted in various domains ranging from
              entertainment to education because of their accessibility and
              affordability. XR modalities create an immersive experience,
              enabling 3D visualization of the content without a conventional
              2D display constraint. Here, we provide a perspective on XR in
              current biomedical applications and demonstrate case studies
              using cell biology concepts, multiplexed proteomics images,
              surgical data for heart operations, and cardiac 3D models.
              Emerging challenges associated with XR technologies in the
              context of adverse health effects and a cost comparison of
              distinct platforms are discussed. The presented XR platforms will
              be useful for biomedical education, medical training, surgical
              guidance, and molecular data visualization to enhance trainees'
              and students' learning, medical operation accuracy, and the
              comprehensibility of complex biological systems.",
  journal  = "Cell Rep Med",
  volume   =  2,
  number   =  7,
  pages    = "100348",
  month    =  jul,
  year     =  2021,
  language = "en"
}

@ARTICLE{Mansell2020-td,
  title    = "Mitochondrial Potentiation Ameliorates {Age-Related}
              Heterogeneity in Hematopoietic Stem Cell Function",
  author   = "Mansell, Els and Sigurdsson, Valgardur and Deltcheva, Elitza and
              Brown, John and James, Chela and Miharada, Kenichi and Soneji,
              Shamit and Larsson, Jonas and Enver, Tariq",
  abstract = "Aging is associated with reduced fitness and increased myeloid
              bias of the hematopoietic stem cell (HSC) compartment, causing
              increased risk of immune compromise, anemia, and malignancy. We
              show that mitochondrial membrane potential (MMP) can be used to
              prospectively isolate chronologically old HSCs with
              transcriptional features and functional attributes characteristic
              of young HSCs, including a high rate of transcription and
              balanced lineage-affiliated programs. Strikingly, MMP is a
              stronger determinant of the quantitative and qualitative
              transcriptional state of HSCs than chronological age, and
              transcriptional consequences of manipulation of MMP in HSCs
              within their native niche suggest a causal relationship.
              Accordingly, we show that pharmacological enhancement of MMP in
              old HSCs in vivo increases engraftment potential upon
              transplantation and reverses myeloid-biased peripheral blood
              output at steady state. Our results demonstrate that MMP is a
              source of heterogeneity in old HSCs, and its pharmacological
              manipulation can alter transcriptional programs with beneficial
              consequences for function.",
  journal  = "Cell Stem Cell",
  volume   =  28,
  number   =  2,
  pages    = "241--256.e6",
  month    =  oct,
  year     =  2020,
  address  = "United States",
  keywords = "Aging; Hematopoietc Stem Cell; Lineage bias; Mitochondria;
              Mitochondrial Membrane Potential; Mitoquinol; Transcription Rate",
  language = "en"
}

@ARTICLE{Krokos2019-vz,
  title    = "Virtual memory palaces: immersion aids recall",
  author   = "Krokos, Eric and Plaisant, Catherine and Varshney, Amitabh",
  abstract = "Virtual reality displays, such as head-mounted displays (HMD),
              afford us a superior spatial awareness by leveraging our
              vestibular and proprioceptive senses, as compared to traditional
              desktop displays. Since classical times, people have used memory
              palaces as a spatial mnemonic to help remember information by
              organizing it spatially and associating it with salient features
              in that environment. In this paper, we explore whether using
              virtual memory palaces in a head-mounted display with
              head-tracking (HMD condition) would allow a user to better recall
              information than when using a traditional desktop display with a
              mouse-based interaction (desktop condition). We found that
              virtual memory palaces in HMD condition provide a superior memory
              recall ability compared to the desktop condition. We believe this
              is a first step in using virtual environments for creating more
              memorable experiences that enhance productivity through better
              recall of large amounts of information organized using the idea
              of virtual memory palaces.",
  journal  = "Virtual Real.",
  volume   =  23,
  number   =  1,
  pages    = "1--15",
  month    =  mar,
  year     =  2019
}

@ARTICLE{Buche2022-le,
  title    = "Use of virtual reality in oncology: From the state of the art to
              an integrative model",
  author   = "Buche, H{\'e}l{\`e}ne and Michel, Aude and Blanc, Nathalie",
  abstract = "Over the past 20 years, virtual reality (VR) has been the subject
              of growing interest in oncology. More and more researchers are
              studying the effects of virtual environments to contribute to
              current thinking on technologies likely to support patients
              undergoing oncological treatment. Recent research highlights how
              VR can divert attention while reducing anxiety in stressful
              healthcare situations through its multisensory and participative
              nature. VR appears to be a promising tool capable of reducing
              cancer-related anxiety symptoms, improving treatment adherence,
              and increasing satisfaction with oncology care. While the
              literature reports these positive effects in the therapeutic
              management of cancer, few studies have focused on theoretical
              models capable of explaining the psychological benefits of
              virtual immersion. This literature review provides a theoretical
              framework combining results from all relevant empirical work in
              oncology. The review can help researchers identify the optimal
              conditions for using VR in oncology and bridge the gap between
              divergent devices, modalities, and practices (e.g., headmounted
              displays, environments, interactivity, immersion time).",
  journal  = "Frontiers in Virtual Reality",
  volume   =  3,
  year     =  2022
}

@ARTICLE{Chirico2020-ic,
  title    = "Virtual reality and music therapy as distraction interventions to
              alleviate anxiety and improve mood states in breast cancer
              patients during chemotherapy",
  author   = "Chirico, Andrea and Maiorano, Patrizia and Indovina, Paola and
              Milanese, Carla and Giordano, Giovan Giacomo and Alivernini,
              Fabio and Iodice, Giovanni and Gallo, Luigi and De Pietro,
              Giuseppe and Lucidi, Fabio and Botti, Gerardo and De Laurentiis,
              Michelino and Giordano, Antonio",
  abstract = "Psychological distress is a common consequence of breast cancer
              diagnosis and treatment and could further exacerbate therapy side
              effects. Interventions increasing treatment tolerance are crucial
              to improve both patients' quality of life and adherence to
              therapies. Virtual reality (VR) has emerged as an effective
              distraction tool for different medical procedures. Here, we
              assessed the efficacy of immersive and interactive VR in
              alleviating chemotherapy-related psychological distress in a
              cohort of Italian breast cancer patients, also comparing its
              effects with those of music therapy (MT). Thirty patients were
              included in the VR group, 30 in the MT group, and 34 in the
              control group, consisting of patients receiving standard care
              during chemotherapy. Our data suggest that both VR and MT are
              useful interventions for alleviating anxiety and for improving
              mood states in breast cancer patients during chemotherapy.
              Moreover, VR seems more effective than MT in relieving anxiety,
              depression, and fatigue.",
  journal  = "J. Cell. Physiol.",
  volume   =  235,
  number   =  6,
  pages    = "5353--5362",
  month    =  jun,
  year     =  2020,
  keywords = "anxiety; breast cancer; chemotherapy; cybersickness; mood states;
              music therapy; virtual reality",
  language = "en"
}

@ARTICLE{Ahmad2020-oz,
  title    = "Virtual Reality Technology for Pain and Anxiety Management among
              Patients with Cancer: A Systematic Review",
  author   = "Ahmad, Muayyad and Bani Mohammad, Eslam and Anshasi, Huda A",
  abstract = "BACKGROUND: Pain and anxiety have negative effects on the
              treatment of patients with cancer. Virtual reality technology is
              a form of distraction which is still unclear in its
              methodological quality in reducing pain and anxiety. AIMS: To
              summarize and evaluate the methodological quality of primary
              studies on the virtual reality (VR) technology for the management
              of pain and anxiety among patients with cancer, and to analyze
              the effectiveness of VR in the reviewed studies. DESIGN: This
              review was reported according to the Preferred Reporting Items
              for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.
              SETTING: Multiple databases from their inception through November
              2018. METHODS: A comprehensive search was performed to identify
              studies that evaluated the effectiveness of VR in managing pain
              and anxiety among patients with cancer. The methodological
              quality of included studies was appraised using the modified
              Downs and Black checklist. RESULTS: Thirteen studies published
              between 1999 and 2018 were eligible for inclusion. These included
              studies were classified as being of good or fair quality. The
              consensus across the included studies was that compared with
              standard care, VR plus standard care were more effective in
              reducing pain and anxiety especially in children and adolescent
              patients who were undergoing painful procedures, and in adult and
              elderly patients who were undergoing anti-cancer treatments and
              during their hospitalization. CONCLUSION: Although more high-
              methodological quality studies are needed to determine whether VR
              technology is effective in controlling symptoms in patients with
              cancer, the results of this review suggested that VR intervention
              may be beneficial for the management of pain and anxiety in
              patients with cancer. Therefore, clinicians may consider VR
              technology as an adjunctive intervention for pain and anxiety
              management.",
  journal  = "Pain Manag. Nurs.",
  volume   =  21,
  number   =  6,
  pages    = "601--607",
  month    =  dec,
  year     =  2020,
  language = "en"
}

@ARTICLE{Scates2020-ap,
  title     = "Using {Nature-Inspired} Virtual Reality as a Distraction to
               Reduce Stress and Pain Among Cancer Patients",
  author    = "Scates, Diana and Dickinson, Joan I and Sullivan, Kathleen and
               Cline, Holly and Balaraman, Rama",
  abstract  = "While many cancer centers suggest treating pain with medication
               and nondrug treatment, few include the use of virtual reality
               (VR) as an alternative for stress and pain relief therapy. The
               purpose of this research was to determine whether a
               nature-inspired VR simulation reduced stress and pain levels
               among patients in a cancer treatment center. Using a repeated
               measures design, 50 patients attending their regularly scheduled
               chemotherapy infusion were measured for pain and stress during
               their intravenous (IV)/port access. At the patient?s second
               visit, they viewed a nature-inspired VR simulation while
               receiving their IV/port access and were measured for pain and
               stress again. The paired, one-tailed t tests found significant
               increases in relaxation, feelings of peace, and positive
               distractions. While patients felt significantly less frustrated,
               measures for stress and pain were not significant. Future
               research should include additional stress and pain measures to
               determine the viability of VR for chemotherapy infusions.",
  journal   = "Environ. Behav.",
  publisher = "SAGE Publications Inc",
  volume    =  52,
  number    =  8,
  pages     = "895--918",
  month     =  oct,
  year      =  2020
}

@ARTICLE{Legetth2021-nh,
  title    = "{CellexalVR}: A virtual reality platform to visualize and analyze
              single-cell omics data",
  author   = "Legetth, Oscar and Rodhe, Johan and Lang, Stefan and Dhapola,
              Parashar and Wallerg{\aa}rd, Mattias and Soneji, Shamit",
  abstract = "Single-cell RNAseq is a routinely used method to explore
              heterogeneity within cell populations. Data from these
              experiments are often visualized using dimension reduction
              methods such as UMAP and tSNE, where each cell is projected in
              two or three dimensional space. Three-dimensional projections can
              be more informative for larger and complex datasets because they
              are less prone to merging and flattening similar
              cell-types/clusters together. However, visualizing and
              cross-comparing 3D projections using current software on
              conventional flat-screen displays is far from optimal as they are
              still essentially 2D, and lack meaningful interaction between the
              user and the data. Here we present CellexalVR
              (www.cellexalvr.med.lu.se), a feature-rich, fully interactive
              virtual reality environment for the visualization and analysis of
              single-cell experiments that allows researchers to intuitively
              and collaboratively gain an understanding of their data.",
  journal  = "iScience",
  volume   =  24,
  number   =  11,
  pages    = "103251",
  month    =  nov,
  year     =  2021,
  keywords = "Bioinformatics; Computer science; Omics; Software engineering;
              Systems biology; Transcriptomics",
  language = "en"
}

@BOOK{Graham2022-pn,
  title     = "Transformative Education",
  author    = "Graham, Charlotte and Longchamps, Philippe",
  publisher = "Routledge",
  year      =  2022
}

@ARTICLE{Brooke1995-ll,
  title     = "{SUS}: A quick and dirty usability scale",
  author    = "Brooke, John",
  abstract  = "Usability does not exist in any absolute sense; it can only be
               defined with reference to particular contexts. This, in turn,
               means that there are no absolute measures of usability, since,
               if the usability of an artefact is defined by the context in
               which that artefact is used, measures of usability must of
               necessity be defined by that context too. Despite this, there is
               a need for broad general measures which can be used to compare
               usability across a range of contexts. In addition, there is a
               need for ``quick and dirty'' methods to allow low cost
               assessments of usability in industrial systems evaluation. This
               chapter describes the System Usability Scale (SUS) a reliable,
               low-cost usability scale that can be used for global assessments
               of systems usability.",
  publisher = "unknown",
  volume    =  189,
  number    =  194,
  month     =  nov,
  year      =  1995
}

@ARTICLE{Wiljen2022-of,
  title    = "The Development of an mHealth Tool for Children With Long-term
              Illness to Enable {Person-Centered} Communication:
              {User-Centered} Design Approach",
  author   = "Wilj{\'e}n, Angelica and Chaplin, John Eric and Crine, Vanessa
              and Jobe, William and Johnson, Ensa and Karlsson, Katarina and
              Lindroth, Tomas and Schwarz, Anneli and Stenmarker, Margaretha
              and Thunberg, Gunilla and {\"O}hl{\'e}n, Joakim and Nilsson,
              Stefan",
  abstract = "BACKGROUND: Children with long-term illnesses frequently
              experience symptoms that could negatively affect their daily
              lives. These symptoms are often underreported in health care.
              Despite a large number of mobile health (mHealth) tools, few are
              based on a theoretical framework or supported by scientific
              knowledge. Incorporating universal design when developing a
              product can promote accessibility and facilitate person-centered
              communication. OBJECTIVE: The aim of this study is to identify
              the symptom-reporting needs of children with cancer and
              congenital heart defects that could be satisfied by using a
              mobile app. Another aim is to evaluate how the child might
              interact with the app by considering universal design principles
              and to identify parents' views and health care professionals'
              expectations and requirements for an mHealth tool. METHODS:
              User-centered design is an iterative process that focuses on an
              understanding of the users. The adapted user-centered design
              process includes 2 phases with 4 stages. Phase 1 involved
              interviews with 7 children with long-term illnesses, 8 parents,
              and 19 health care professionals to determine their needs and
              wishes for support; a workshop with 19 researchers to deepen our
              understanding of the needs; and a workshop with developers to
              establish a preliminary tool to further investigate needs and
              behaviors. Phase 2 involved interviews with 10 children with
              long-term illnesses, 9 parents, and 21 health care professionals
              to evaluate the mock-up (prototype) of the mHealth tool. Data
              were synthesized using the interpretive description technique.
              RESULTS: A total of 4 aspects of needs emerged from the synthesis
              of the data, as follows: different perspectives on provided and
              perceived support; the need for an easy-to-use, non-clinic-based
              tool to self-report symptoms and to facilitate communication; the
              need for safety by being in control and reaching the child's
              voice; and a way of mapping the illness journey to facilitate
              recall and improve diagnostics. The children with long-term
              illnesses expressed a need to not only communicate about pain but
              also communicate about anxiety, fatigue, fear, and nausea.
              CONCLUSIONS: The findings of this study indicated that the
              PicPecc (Pictorial Support in Person-Centered Care for Children)
              app is a potential solution for providing communicative support
              to children with long-term illnesses dealing with multiple
              symptoms and conditions. The interview data also highlighted
              symptoms that are at risk of being overlooked if they are not
              included in the mobile app. Further studies are needed to include
              usability testing and evaluation in hospitals and home care
              settings.",
  journal  = "JMIR Pediatr Parent",
  volume   =  5,
  number   =  1,
  pages    = "e30364",
  month    =  mar,
  year     =  2022,
  keywords = "children; communication; long-term illness; mHealth; pediatric
              care; person-centered care; symptom assessment; universal design",
  language = "en"
}

@MISC{noauthor_undated-cs,
  title        = "{VR} alleviates pain and anxiety for patients - Stanford
                  Medicine Children's Health",
  abstract     = "Lucile Packard Children's Hospital Stanford is one of the
                  first hospitals in the country to begin implementing VR
                  therapy in every patient unit.",
  howpublished = "\url{https://www.stanfordchildrens.org/en/about/news/releases/2017/virtual-reality-alleviates-pain-anxiety}",
  note         = "Accessed: 2023-2-1"
}

@MISC{Cornell2020-as,
  title        = "{PhD} students and their careers",
  author       = "Cornell, Bethan",
  year         =  2020,
  howpublished = "\url{https://www.hepi.ac.uk/wp-content/uploads/2020/07/HEPI-Policy-Note-25_PhD-students-careers_FINAL.pdf}",
  note         = "Accessed: 2023-2-23"
}

@MISC{Woolston2022-tx,
  title        = "Lab leaders wrestle with paucity of postdocs",
  booktitle    = "Nature Publishing Group {UK}",
  author       = "Woolston, Chris",
  abstract     = "Even high-profile scientists are struggling to recruit
                  qualified postdoctoral researchers. Even high-profile
                  scientists are struggling to recruit qualified postdoctoral
                  researchers.",
  month        =  aug,
  year         =  2022,
  howpublished = "\url{http://dx.doi.org/10.1038/d41586-022-02781-x}",
  note         = "Accessed: 2023-2-23",
  language     = "en"
}

@ARTICLE{Kis2022-mp,
  title    = "Leaving academia: {PhD} attrition and unhealthy research
              environments",
  author   = "Kis, Andrea and Tur, Elena Mas and Lakens, Dani{\"e}l and Vaesen,
              Krist and Houkes, Wybo",
  abstract = "This study investigates PhD candidates' (N = 391) perceptions
              about their research environment at a Dutch university in terms
              of the research climate, (un)ethical supervisory practices, and
              questionable research practices. We assessed whether their
              perceptions are related to career considerations. We gathered
              quantitative self-report estimations of the perceptions of PhD
              candidates using an online survey tool and then conducted
              descriptive and within-subject correlation analysis of the
              results. While most PhD candidates experience fair evaluation
              processes, openness, integrity, trust, and freedom in their
              research climate, many report lack of time and support,
              insufficient supervision, and witness questionable research
              practices. Results based on Spearman correlations indicate that
              those who experience a less healthy research environment
              (including experiences with unethical supervision, questionable
              practices, and barriers to responsible research), more often
              consider leaving academia and their current PhD position.",
  journal  = "PLoS One",
  volume   =  17,
  number   =  10,
  pages    = "e0274976",
  month    =  oct,
  year     =  2022,
  language = "en"
}

@BOOK{Brodin1970-jh,
  title     = "Doctoral Supervision in Theory and Practice",
  author    = "Brodin, Eva and Lind{\'e}n, Jitka and Sonesson, Anders and
               Lindberg-Sand, {\AA}sa",
  abstract  = "This is a long-awaited book that contributes to the professional
               development of doctoral supervisors and provides an indepth
               perspective on doctoral students' learning. Well anchored in
               current research, the authors discuss the organisation of
               Swedish doctoral education, the supervisor's professional
               practice, doctoral students' learning, and the quality system of
               this education in Sweden. The connection between theory and
               practice runs throughout the entire book. Using authentic cases
               and examples from different educational environments, it is
               demonstrated how supervision is dependent on both individual and
               cultural factors. In addition, the book offers its readers
               numerous reflection exercises that can help move thinking
               forward, both individually and collegially. The book is aimed
               primarily at supervisors in doctoral education, regardless of
               the discipline within which they are active or their previous
               experience. It can also be useful for doctoral students who are
               interested in understanding their own learning process and who
               would like to know what can be expected of them in their
               education, as well as by educational leaders who wish to improve
               the quality of doctoral education.",
  publisher = "Studentlitteratur",
  year      =  1970,
  language  = "en"
}

@MISC{DeTrempe2017-ka,
  title        = "Virtual reality alleviates pain, anxiety for pediatric
                  patients",
  booktitle    = "News Center",
  author       = "DeTrempe, Kate",
  abstract     = "Lucile Packard Children's Hospital Stanford is one of the
                  first hospitals in the country to begin implementing
                  distraction-based VR therapy within every patient unit.",
  year         =  2017,
  howpublished = "\url{https://med.stanford.edu/news/all-news/2017/09/virtual-reality-alleviates-pain-anxiety-for-pediatric-patients.html}",
  note         = "Accessed: 2023-3-18",
  language     = "sm"
}

@ARTICLE{Taylor2022-tz,
  title    = "Bioinformatics and the Metaverse: Are We Ready?",
  author   = "Taylor, Stephen and Soneji, Shamit",
  abstract = "COVID-19 forced humanity to think about new ways of working
              globally without physically being present with other people, and
              eXtended Reality (XR) systems (defined as Virtual Reality,
              Augmented Reality and Mixed Reality) offer a potentially elegant
              solution. Previously seen as mainly for gaming, commercial and
              research institutions are investigating XR solutions to solve
              real world problems from training, simulation, mental health,
              data analysis, and studying disease progression. More recently
              large corporations such as Microsoft and Meta have announced they
              are developing the Metaverse as a new paradigm to interact with
              the digital world. This article will look at how visualization
              can leverage the Metaverse in bioinformatics research, the pros
              and cons of this technology, and what the future may hold.",
  journal  = "Front Bioinform",
  volume   =  2,
  pages    = "863676",
  month    =  may,
  year     =  2022,
  keywords = "augmented reality; bioinformatcs; immersive; metaverse; mixed
              reality; virtual reality; visualization",
  language = "en"
}

@ARTICLE{Rosengren2021-ca,
  title    = "Social Belonging as the Main Concern for Achieving Life
              Satisfaction When Adapting to Parkinson's Disease",
  author   = "Rosengren, Lina and Forsberg, Anna and Brog{\aa}rdh, Christina
              and Lexell, Jan",
  abstract = "Parkinson's disease (PD) is a complex, progressive neurological
              condition that impacts daily life and reduces life satisfaction
              (LS). To achieve and maintain high LS, persons with PD (PwPD)
              must go through a process of change to adapt to their new life
              situation. However, our knowledge about this process is very
              limited. The aim of this study was to investigate the process of
              change, and the main concern in this process, in PwPD. To study
              the transitional experience of PwPD, an inductive qualitative
              approach, using Grounded Theory (GT), was employed. Thirteen
              participants (9 women, 3 men and 1 non-binary), with a mean age
              of 54 years (range from 47-62 years), participated in in-depth
              interviews. Data showed that social belonging is the main concern
              in the process of change for PwPD. In this process of change,
              they use strategies to comprehend, accept, adapt, and balance in
              their strive for social belonging, which in turn can enhance LS.
              Health care professionals can use this model with an
              interdisciplinary approach to support PwPD through a successful
              process of change to achieve social belonging, and thereby
              achieving and maintaining LS.",
  journal  = "Int. J. Environ. Res. Public Health",
  volume   =  18,
  number   =  16,
  month    =  aug,
  year     =  2021,
  keywords = "Parkinson disease; adaptation; psychological; qualitative
              research; quality of life; self-management; sense of coherence",
  language = "en"
}

@ARTICLE{Guzzi2018-be,
  title    = "Pseudouridylation of {tRNA-Derived} Fragments Steers
              Translational Control in Stem Cells",
  author   = "Guzzi, Nicola and Cie{\'s}la, Maciej and Ngoc, Phuong Cao Thi and
              Lang, Stefan and Arora, Sonali and Dimitriou, Marios and
              Pimkov{\'a}, Kristyna and Sommarin, Mikael N E and Munita,
              Roberto and Lubas, Michal and Lim, Yiting and Okuyama, Kazuki and
              Soneji, Shamit and Karlsson, G{\"o}ran and Hansson, Jenny and
              J{\"o}nsson, G{\"o}ran and Lund, Anders H and Sigvardsson, Mikael
              and Hellstr{\"o}m-Lindberg, Eva and Hsieh, Andrew C and Bellodi,
              Cristian",
  abstract = "Pseudouridylation ($\Psi$) is the most abundant and widespread
              type of RNA epigenetic modification in living organisms; however,
              the biological role of $\Psi$ remains poorly understood. Here, we
              show that a $\Psi$-driven posttranscriptional program steers
              translation control to impact stem cell commitment during early
              embryogenesis. Mechanistically, the $\Psi$ ``writer'' PUS7
              modifies and activates a novel network of tRNA-derived small
              fragments (tRFs) targeting the translation initiation complex.
              PUS7 inactivation in embryonic stem cells impairs tRF-mediated
              translation regulation, leading to increased protein biosynthesis
              and defective germ layer specification. Remarkably, dysregulation
              of this posttranscriptional regulatory circuitry impairs
              hematopoietic stem cell commitment and is common to aggressive
              subtypes of human myelodysplastic syndromes. Our findings unveil
              a critical function of $\Psi$ in directing translation control in
              stem cells with important implications for development and
              disease.",
  journal  = "Cell",
  volume   =  173,
  number   =  5,
  pages    = "1204--1216.e26",
  month    =  apr,
  year     =  2018,
  address  = "United States",
  keywords = "PUS7; RNA modifications; embryogenesis; hematopoiesis;
              myelodysplastic syndromes; protein synthesis; pseudouridine; stem
              cell; tRNA fragments; translation control",
  language = "en"
}

@ARTICLE{Somasundaram2021-jz,
  title    = "{EBF1} and {PAX5} control pro-B cell expansion via opposing
              regulation of the Myc gene",
  author   = "Somasundaram, Rajesh and Jensen, Christina T and
              Tingvall-Gustafsson, Johanna and {\AA}hsberg, Josefine and
              Okuyama, Kazuki and Prasad, Mahadesh and Hagman, James R and
              Wang, Xun and Soneji, Shamit and Strid, Tobias and Ungerb{\"a}ck,
              Jonas and Sigvardsson, Mikael",
  abstract = "Genes encoding B lineage-restricted transcription factors are
              frequently mutated in B-lymphoid leukemias, suggesting a close
              link between normal and malignant B-cell development. One of
              these transcription factors is early B-cell factor 1 (EBF1), a
              protein of critical importance for lineage specification and
              survival of B-lymphoid progenitors. Here, we report that impaired
              EBF1 function in mouse B-cell progenitors results in reduced
              expression of Myc. Ectopic expression of MYC partially rescued
              B-cell expansion in the absence of EBF1 both in vivo and in
              vitro. Using chromosome conformation analysis in combination with
              ATAC-sequencing, chromatin immunoprecipitation-sequencing, and
              reporter gene assays, six EBF1-responsive enhancer elements were
              identified within the Myc locus. CRISPR-Cas9-mediated targeting
              of EBF1-binding sites identified one element of key importance
              for Myc expression and pro-B cell expansion. These data provide
              evidence that Myc is a direct target of EBF1. Furthermore,
              chromatin immunoprecipitation-sequencing analysis revealed that
              several regulatory elements in the Myc locus are targets of PAX5.
              However, ectopic expression of PAX5 in EBF1-deficient cells
              inhibits the cell cycle and reduces Myc expression, suggesting
              that EBF1 and PAX5 act in an opposing manner to regulate Myc
              levels. This hypothesis is further substantiated by the finding
              that Pax5 inactivation reduces requirements for EBF1 in
              pro-B-cell expansion. The binding of EBF1 and PAX5 to regulatory
              elements in the human MYC gene in a B-cell acute lymphoblastic
              leukemia cell line indicates that the EBF1:PAX5:MYC regulatory
              loop is conserved and may control both normal and malignant
              B-cell development.",
  journal  = "Blood",
  volume   =  137,
  number   =  22,
  pages    = "3037--3049",
  month    =  jun,
  year     =  2021,
  address  = "United States",
  language = "en"
}

@ARTICLE{Mansell2020-ns,
  title    = "Mitochondrial Potentiation Ameliorates {Age-Related}
              Heterogeneity in Hematopoietic Stem Cell Function",
  author   = "Mansell, Els and Sigurdsson, Valgardur and Deltcheva, Elitza and
              Brown, John and James, Chela and Miharada, Kenichi and Soneji,
              Shamit and Larsson, Jonas and Enver, Tariq",
  abstract = "Aging is associated with reduced fitness and increased myeloid
              bias of the hematopoietic stem cell (HSC) compartment, causing
              increased risk of immune compromise, anemia, and malignancy. We
              show that mitochondrial membrane potential (MMP) can be used to
              prospectively isolate chronologically old HSCs with
              transcriptional features and functional attributes characteristic
              of young HSCs, including a high rate of transcription and
              balanced lineage-affiliated programs. Strikingly, MMP is a
              stronger determinant of the quantitative and qualitative
              transcriptional state of HSCs than chronological age, and
              transcriptional consequences of manipulation of MMP in HSCs
              within their native niche suggest a causal relationship.
              Accordingly, we show that pharmacological enhancement of MMP in
              old HSCs in vivo increases engraftment potential upon
              transplantation and reverses myeloid-biased peripheral blood
              output at steady state. Our results demonstrate that MMP is a
              source of heterogeneity in old HSCs, and its pharmacological
              manipulation can alter transcriptional programs with beneficial
              consequences for function.",
  journal  = "Cell Stem Cell",
  volume   =  28,
  number   =  2,
  pages    = "241--256.e6",
  month    =  oct,
  year     =  2020,
  address  = "United States",
  keywords = "Aging; Hematopoietc Stem Cell; Lineage bias; Mitochondria;
              Mitochondrial Membrane Potential; Mitoquinol; Transcription
              Rate;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Guzzi2018-hj,
  title    = "Pseudouridylation of {tRNA-Derived} Fragments Steers
              Translational Control in Stem Cells",
  author   = "Guzzi, Nicola and Cie{\'s}la, Maciej and Ngoc, Phuong Cao Thi and
              Lang, Stefan and Arora, Sonali and Dimitriou, Marios and
              Pimkov{\'a}, Kristyna and Sommarin, Mikael N E and Munita,
              Roberto and Lubas, Michal and Lim, Yiting and Okuyama, Kazuki and
              Soneji, Shamit and Karlsson, G{\"o}ran and Hansson, Jenny and
              J{\"o}nsson, G{\"o}ran and Lund, Anders H and Sigvardsson, Mikael
              and Hellstr{\"o}m-Lindberg, Eva and Hsieh, Andrew C and Bellodi,
              Cristian",
  abstract = "Pseudouridylation ($\Psi$) is the most abundant and widespread
              type of RNA epigenetic modification in living organisms; however,
              the biological role of $\Psi$ remains poorly understood. Here, we
              show that a $\Psi$-driven posttranscriptional program steers
              translation control to impact stem cell commitment during early
              embryogenesis. Mechanistically, the $\Psi$ ``writer'' PUS7
              modifies and activates a novel network of tRNA-derived small
              fragments (tRFs) targeting the translation initiation complex.
              PUS7 inactivation in embryonic stem cells impairs tRF-mediated
              translation regulation, leading to increased protein biosynthesis
              and defective germ layer specification. Remarkably, dysregulation
              of this posttranscriptional regulatory circuitry impairs
              hematopoietic stem cell commitment and is common to aggressive
              subtypes of human myelodysplastic syndromes. Our findings unveil
              a critical function of $\Psi$ in directing translation control in
              stem cells with important implications for development and
              disease.",
  journal  = "Cell",
  volume   =  173,
  number   =  5,
  pages    = "1204--1216.e26",
  month    =  apr,
  year     =  2018,
  address  = "United States",
  keywords = "PUS7; RNA modifications; embryogenesis; hematopoiesis;
              myelodysplastic syndromes; protein synthesis; pseudouridine; stem
              cell; tRNA fragments; translation control;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Somasundaram2021-ll,
  title    = "{EBF1} and {PAX5} control pro-B cell expansion via opposing
              regulation of the Myc gene",
  author   = "Somasundaram, Rajesh and Jensen, Christina T and
              Tingvall-Gustafsson, Johanna and {\AA}hsberg, Josefine and
              Okuyama, Kazuki and Prasad, Mahadesh and Hagman, James R and
              Wang, Xun and Soneji, Shamit and Strid, Tobias and Ungerb{\"a}ck,
              Jonas and Sigvardsson, Mikael",
  abstract = "Genes encoding B lineage-restricted transcription factors are
              frequently mutated in B-lymphoid leukemias, suggesting a close
              link between normal and malignant B-cell development. One of
              these transcription factors is early B-cell factor 1 (EBF1), a
              protein of critical importance for lineage specification and
              survival of B-lymphoid progenitors. Here, we report that impaired
              EBF1 function in mouse B-cell progenitors results in reduced
              expression of Myc. Ectopic expression of MYC partially rescued
              B-cell expansion in the absence of EBF1 both in vivo and in
              vitro. Using chromosome conformation analysis in combination with
              ATAC-sequencing, chromatin immunoprecipitation-sequencing, and
              reporter gene assays, six EBF1-responsive enhancer elements were
              identified within the Myc locus. CRISPR-Cas9-mediated targeting
              of EBF1-binding sites identified one element of key importance
              for Myc expression and pro-B cell expansion. These data provide
              evidence that Myc is a direct target of EBF1. Furthermore,
              chromatin immunoprecipitation-sequencing analysis revealed that
              several regulatory elements in the Myc locus are targets of PAX5.
              However, ectopic expression of PAX5 in EBF1-deficient cells
              inhibits the cell cycle and reduces Myc expression, suggesting
              that EBF1 and PAX5 act in an opposing manner to regulate Myc
              levels. This hypothesis is further substantiated by the finding
              that Pax5 inactivation reduces requirements for EBF1 in
              pro-B-cell expansion. The binding of EBF1 and PAX5 to regulatory
              elements in the human MYC gene in a B-cell acute lymphoblastic
              leukemia cell line indicates that the EBF1:PAX5:MYC regulatory
              loop is conserved and may control both normal and malignant
              B-cell development.",
  journal  = "Blood",
  volume   =  137,
  number   =  22,
  pages    = "3037--3049",
  month    =  jun,
  year     =  2021,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Taylor2022-yk,
  title    = "Bioinformatics and the Metaverse: Are We Ready?",
  author   = "Taylor, Stephen and Soneji, Shamit",
  abstract = "COVID-19 forced humanity to think about new ways of working
              globally without physically being present with other people, and
              eXtended Reality (XR) systems (defined as Virtual Reality,
              Augmented Reality and Mixed Reality) offer a potentially elegant
              solution. Previously seen as mainly for gaming, commercial and
              research institutions are investigating XR solutions to solve
              real world problems from training, simulation, mental health,
              data analysis, and studying disease progression. More recently
              large corporations such as Microsoft and Meta have announced they
              are developing the Metaverse as a new paradigm to interact with
              the digital world. This article will look at how visualization
              can leverage the Metaverse in bioinformatics research, the pros
              and cons of this technology, and what the future may hold.",
  journal  = "Front Bioinform",
  volume   =  2,
  pages    = "863676",
  month    =  may,
  year     =  2022,
  address  = "Switzerland",
  keywords = "augmented reality; bioinformatcs; immersive; metaverse; mixed
              reality; virtual reality; visualization;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Oburoglu2021-bh,
  title    = "Pyruvate metabolism guides definitive lineage specification
              during hematopoietic emergence",
  author   = "Oburoglu, Leal and Mansell, Els and Canals, Isaac and Sigurdsson,
              Valgardur and Guibentif, Carolina and Soneji, Shamit and Woods,
              Niels-Bjarne",
  abstract = "During embryonic development, hematopoiesis occurs through
              primitive and definitive waves, giving rise to distinct blood
              lineages. Hematopoietic stem cells (HSCs) emerge from hemogenic
              endothelial (HE) cells, through endothelial-to-hematopoietic
              transition (EHT). In the adult, HSC quiescence, maintenance, and
              differentiation are closely linked to changes in metabolism.
              However, metabolic processes underlying the emergence of HSCs
              from HE cells remain unclear. Here, we show that the emergence of
              blood is regulated by multiple metabolic pathways that induce or
              modulate the differentiation toward specific hematopoietic
              lineages during human EHT. In both in vitro and in vivo settings,
              steering pyruvate use toward glycolysis or OXPHOS differentially
              skews the hematopoietic output of HE cells toward either an
              erythroid fate with primitive phenotype, or a definitive lymphoid
              fate, respectively. We demonstrate that glycolysis-mediated
              differentiation of HE toward primitive erythroid hematopoiesis is
              dependent on the epigenetic regulator LSD1. In contrast,
              OXPHOS-mediated differentiation of HE toward definitive
              hematopoiesis is dependent on cholesterol metabolism. Our
              findings reveal that during EHT, metabolism is a major regulator
              of primitive versus definitive hematopoietic differentiation.",
  journal  = "EMBO Rep.",
  volume   =  23,
  number   =  2,
  pages    = "e54384",
  month    =  dec,
  year     =  2021,
  address  = "England",
  keywords = "OXPHOS; endothelial-to-hematopoietic transition; glycolysis;
              hematopoiesis; pyruvate metabolism;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Dhapola2022-bp,
  title    = "Scarf enables a highly memory-efficient analysis of large-scale
              single-cell genomics data",
  author   = "Dhapola, Parashar and Rodhe, Johan and Olofzon, Rasmus and
              Bonald, Thomas and Erlandsson, Eva and Soneji, Shamit and
              Karlsson, G{\"o}ran",
  abstract = "As the scale of single-cell genomics experiments grows into the
              millions, the computational requirements to process this data are
              beyond the reach of many. Herein we present Scarf, a modularly
              designed Python package that seamlessly interoperates with other
              single-cell toolkits and allows for memory-efficient single-cell
              analysis of millions of cells on a laptop or low-cost devices
              like single-board computers. We demonstrate Scarf's memory and
              compute-time efficiency by applying it to the largest existing
              single-cell RNA-Seq and ATAC-Seq datasets. Scarf wraps
              memory-efficient implementations of a graph-based t-stochastic
              neighbour embedding and hierarchical clustering algorithm.
              Moreover, Scarf performs accurate reference-anchored mapping of
              datasets while maintaining memory efficiency. By implementing a
              subsampling algorithm, Scarf additionally has the capacity to
              generate representative sampling of cells from a given dataset
              wherein rare cell populations and lineage differentiation
              trajectories are conserved. Together, Scarf provides a framework
              wherein any researcher can perform advanced processing,
              subsampling, reanalysis, and integration of atlas-scale datasets
              on standard laptop computers. Scarf is available on Github:
              https://github.com/parashardhapola/scarf .",
  journal  = "Nat. Commun.",
  volume   =  13,
  number   =  1,
  pages    = "4616",
  month    =  aug,
  year     =  2022,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Soneji2007-rm,
  title    = "Inference, validation, and dynamic modeling of transcription
              networks in multipotent hematopoietic cells",
  author   = "Soneji, Shamit and Huang, Sui and Loose, Matthew and Donaldson,
              Ian John and Patient, Roger and G{\"o}ttgens, Berthold and Enver,
              Tariq and May, Gillian",
  abstract = "Identifying the transcription factor interactions that are
              responsible for cell-specific gene expression programs is key to
              understanding the regulation of cell behaviors, such as
              self-renewal, proliferation, differentiation, and death. The
              rapidly increasing availability of microarray-derived global gene
              expression data sets, coupled with genome sequence information
              from multiple species, has driven the development of
              computational methods to reverse engineer and dynamically model
              genetic regulatory networks. An understanding of the architecture
              and behavior of transcriptional networks should lend insight into
              how the huge number of potential gene expression programs is
              constrained and facilitates efforts to direct or redirect cell
              fate.",
  journal  = "Ann. N. Y. Acad. Sci.",
  volume   =  1106,
  pages    = "30--40",
  month    =  apr,
  year     =  2007,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Warsi2022-dz,
  title    = "Schlafen2 is a regulator of quiescence in adult murine
              hematopoietic stem cells",
  author   = "Warsi, Sarah and Dahl, Maria and Smith, Emma M K and Rydstrom,
              Anna and Mansell, Els and Sigurdsson, Valgardur and Sjoberg,
              Julia and Soneji, Shamit and Rorby, Emma and Siva, Kavitha and
              Grahn, Tan H M and Liu, Yang and Blank, Ulrika and Karlsson,
              Goran and Karlsson, Stefan",
  abstract = "Even though hematopoietic stem cells (HSC) are characterized by
              their ability to self-renew and differentiate, they primarily
              reside in quiescence. Despite the immense importance of this
              quiescent state, its maintenance and regulation is still
              incompletely understood. Schlafen2 (Slfn2) is a cytoplasmic
              protein known to be involved in cell proliferation,
              differentiation, quiescence, interferon response, and regulation
              of the immune system. Interestingly, Slfn2 is highly expressed in
              primitive hematopoietic cells. In order to investigate the role
              of Slfn2 in the regulation of HSC we have studied HSC function in
              the elektra mouse model, where the elektra allele of the Slfn2
              gene contains a point mutation causing loss of function of the
              Slfn2 protein. We found that homozygosity for the elektra allele
              caused a decrease of primitive hematopoietic compartments in
              murine bone marrow. We further found that transplantation of
              elektra bone marrow and purified HSC resulted in a significantly
              reduced regenerative capacity of HSC in competitive
              transplantation settings. Importantly, we found that a
              significantly higher fraction of elektra HSC (as compared to
              wild-type HSC) were actively cycling, suggesting that the
              mutation in Slfn2 increases HSC proliferation. This additionally
              caused an increased amount of apoptotic stem and progenitor
              cells. Taken together, our findings demonstrate that
              dysregulation of Slfn2 results in a functional deficiency of
              primitive hematopoietic cells, which is particularly reflected by
              a drastically impaired ability to reconstitute the hematopoietic
              system following transplantation and an increase in HSC
              proliferation. This study thus identifies Slfn2 as a novel and
              critical regulator of adult HSC and HSC quiescence.",
  journal  = "Haematologica",
  volume   =  107,
  number   =  12,
  pages    = "2884--2896",
  month    =  dec,
  year     =  2022,
  address  = "Italy",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sjogren2021-yr,
  title    = "Targeting elevated heme levels to treat a mouse model for
              {Diamond-Blackfan} Anemia",
  author   = "Sj{\"o}gren, Sara E and Chen, Jun and Mattebo, Alexander and
              Alattar, Abdul G and Karlsson, Helena and Siva, Kavitha and
              Soneji, Shamit and Tedg{\aa}rd, Ulf and Chen, Jane-Jane and Gram,
              Magnus and Flygare, Johan",
  abstract = "Diamond-Blackfan anemia (DBA) is a rare genetic disorder in which
              patients present a scarcity of erythroid precursors in an
              otherwise normocellular bone marrow. Most, but not all, patients
              carry mutations in ribosomal proteins such as RPS19, suggesting
              that compromised mRNA translation and ribosomal stress are
              pathogenic mechanisms causing depletion of erythroid precursors.
              To gain further insight to disease mechanisms in DBA, we
              performed a custom short hairpin RNA (shRNA) based screen against
              750 genes hypothesized to affect DBA pathophysiology. Among the
              hits were two shRNAs against the erythroid specific
              heme-regulated eIF2$\alpha$ kinase (HRI), which is a negative
              regulator of mRNA translation. This study shows that
              shRNA-mediated HRI silencing or loss of one HRI allele improves
              expansion of Rps19-deficient erythroid precursors, as well as
              improves the anemic phenotype in Rps19-deficient animals. We
              found that Rps19-deficient erythroblasts have elevated levels of
              unbound intracellular heme, which is normalized by HRI
              heterozygosity. Additionally, targeting elevated heme levels by
              treating cells with the heme scavenger alpha-1-microglobulin
              (A1M), increased proliferation of Rps19-deficient erythroid
              precursors and decreased heme levels in a disease-specific
              manner. HRI heterozygosity, but not A1M treatment, also decreased
              the elevated p53 activity observed in Rps19-deficient cells,
              indicating that p53 activation is caused by ribosomal stress and
              aberrant mRNA translation and not heme overload in
              Rps19-deficiency. Together, these findings suggest that targeting
              elevated heme levels is a promising new treatment strategy for
              DBA.",
  journal  = "Exp. Hematol.",
  volume   =  105,
  pages    = "50--61",
  month    =  oct,
  year     =  2021,
  address  = "Netherlands",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Canals-Hamann2013-sh,
  title    = "A biophysical model for transcription factories",
  author   = "Canals-Hamann, Ana Z and das Neves, Ricardo Pires and Reittie,
              Joyce E and I{\~n}iguez, Carlos and Soneji, Shamit and Enver,
              Tariq and Buckle, Veronica J and Iborra, Francisco J",
  abstract = "Transcription factories are nuclear domains where gene
              transcription takes place although the molecular basis for their
              formation and maintenance are unknown. In this study, we explored
              how the properties of chromatin as a polymer may contribute to
              the structure of transcription factories. We found that
              transcriptional active chromatin contains modifications like
              histone H4 acetylated at Lysine 16 (H4K16ac). Single fibre
              analysis showed that this modification spans the entire body of
              the gene. Furthermore, H4K16ac genes cluster in regions up to 500
              Kb alternating active and inactive chromatin. The introduction of
              H4K16ac in chromatin induces stiffness in the chromatin fibre.
              The result of this change in flexibility is that chromatin could
              behave like a multi-block copolymer with repetitions of
              stiff-flexible (active-inactive chromatin) components. Copolymers
              with such structure self-organize through spontaneous phase
              separation into microdomains. Consistent with such model H4K16ac
              chromatin form foci that associates with nascent transcripts. We
              propose that transcription factories are the result of the
              spontaneous concentration of H4K16ac chromatin that are in
              proximity, mainly in cis.",
  journal  = "BMC Biophys.",
  volume   =  6,
  pages    = "2",
  month    =  feb,
  year     =  2013,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Koide2021-xp,
  title    = "{CD244} expression represents functional decline of murine
              hematopoietic stem cells after in vitro culture",
  author   = "Koide, Shuhei and Sigurdsson, Valgardur and Radulovic, Visnja and
              Saito, Kiyoka and Zheng, Zhiqian and Lang, Stefan and Soneji,
              Shamit and Iwama, Atsushi and Miharada, Kenichi",
  abstract = "Isolation of long-term hematopoietic stem cell (HSC) is possible
              by utilizing flow cytometry with multiple cell surface markers.
              However, those cell surface phenotypes do not represent
              functional HSCs after in vitro culture. Here we show that
              cultured HSCs express mast cell-related genes including Cd244.
              After in vitro culture, phenotypic HSCs were divided into
              CD244(-) and CD244(+) subpopulations, and only CD244(-) cells
              that have low mast cell gene expression and maintain HSC-related
              genes sustain reconstitution potential. The result was same when
              HSCs were cultured in an efficient expansion medium containing
              polyvinyl alcohol. Chemically induced endoplasmic reticulum (ER)
              stress signal increased the CD244(+) subpopulation, whereas ER
              stress suppression using a molecular chaperone, TUDCA, decreased
              CD244(+) population, which was correlated to improved
              reconstitution output. These data suggest CD244 is a potent
              marker to exclude non-functional HSCs after in vitro culture
              thereby useful to elucidate mechanism of functional decline of
              HSCs during ex vivo treatment.",
  journal  = "iScience",
  volume   =  25,
  number   =  1,
  pages    = "103603",
  month    =  dec,
  year     =  2021,
  address  = "United States",
  keywords = "Biological sciences; Cell biology; Immunology; Stem cells
              research;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Legetth2021-qk,
  title    = "{CellexalVR}: A virtual reality platform to visualize and analyze
              single-cell omics data",
  author   = "Legetth, Oscar and Rodhe, Johan and Lang, Stefan and Dhapola,
              Parashar and Wallerg{\aa}rd, Mattias and Soneji, Shamit",
  abstract = "Single-cell RNAseq is a routinely used method to explore
              heterogeneity within cell populations. Data from these
              experiments are often visualized using dimension reduction
              methods such as UMAP and tSNE, where each cell is projected in
              two or three dimensional space. Three-dimensional projections can
              be more informative for larger and complex datasets because they
              are less prone to merging and flattening similar
              cell-types/clusters together. However, visualizing and
              cross-comparing 3D projections using current software on
              conventional flat-screen displays is far from optimal as they are
              still essentially 2D, and lack meaningful interaction between the
              user and the data. Here we present CellexalVR
              (www.cellexalvr.med.lu.se), a feature-rich, fully interactive
              virtual reality environment for the visualization and analysis of
              single-cell experiments that allows researchers to intuitively
              and collaboratively gain an understanding of their data.",
  journal  = "iScience",
  volume   =  24,
  number   =  11,
  pages    = "103251",
  month    =  oct,
  year     =  2021,
  address  = "United States",
  keywords = "Bioinformatics; Computer science; Omics; Software engineering;
              Systems biology; Transcriptomics;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Malmevik2015-iu,
  title    = "Identification of the {miRNA} targetome in hippocampal neurons
              using {RIP-seq}",
  author   = "Malmevik, Josephine and Petri, Rebecca and Klussendorf, Thies and
              Knauff, Pina and {\AA}kerblom, Malin and Johansson, Jenny and
              Soneji, Shamit and Jakobsson, Johan",
  abstract = "MicroRNAs (miRNAs) are key players in the regulation of neuronal
              processes by targeting a large network of target messenger RNAs
              (mRNAs). However, the identity and function of mRNAs targeted by
              miRNAs in specific cells of the brain are largely unknown. Here,
              we established an adeno-associated viral vector (AAV)-based
              neuron-specific Argonaute2:GFP-RNA immunoprecipitation followed
              by high-throughput sequencing to analyse the regulatory role of
              miRNAs in mouse hippocampal neurons. Using this approach, we
              identified more than two thousand miRNA targets in hippocampal
              neurons, regulating essential neuronal features such as cell
              signalling, transcription and axon guidance. Furthermore, we
              found that stable inhibition of the highly expressed miR-124 and
              miR-125 in hippocampal neurons led to significant but distinct
              changes in the AGO2 binding of target mRNAs, resulting in
              subsequent upregulation of numerous miRNA target genes. These
              findings greatly enhance our understanding of the miRNA targetome
              in hippocampal neurons.",
  journal  = "Sci. Rep.",
  volume   =  5,
  pages    = "12609",
  month    =  jul,
  year     =  2015,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Jensen2018-le,
  title    = "Dissection of progenitor compartments resolves developmental
              trajectories in B-lymphopoiesis",
  author   = "Jensen, Christina T and {\AA}hsberg, Josefine and Sommarin,
              Mikael N E and Strid, Tobias and Somasundaram, Rajesh and
              Okuyama, Kazuki and Ungerb{\"a}ck, Jonas and Kupari, Jussi and
              Airaksinen, Matti S and Lang, Stefan and Bryder, David and
              Soneji, Shamit and Karlsson, G{\"o}ran and Sigvardsson, Mikael",
  abstract = "To understand the developmental trajectories in early lymphocyte
              differentiation, we identified differentially expressed surface
              markers on lineage-negative lymphoid progenitors (LPs).
              Single-cell polymerase chain reaction experiments allowed us to
              link surface marker expression to that of lineage-associated
              transcription factors (TFs) and identify GFRA2 and BST1 as
              markers of early B cells. Functional analyses in vitro and in
              vivo as well as single-cell gene expression analyses supported
              that surface expression of these proteins defined distinct
              subpopulations that include cells from both the classical common
              LPs (CLPs) and Fraction A compartments. The formation of the
              GFRA2-expressing stages of development depended on the TF EBF1,
              critical both for the activation of stage-specific target genes
              and modulation of the epigenetic landscape. Our data show that
              consecutive expression of Ly6D, GFRA2, and BST1 defines a
              developmental trajectory linking the CLP to the CD19(+)
              progenitor compartment.",
  journal  = "J. Exp. Med.",
  volume   =  215,
  number   =  7,
  pages    = "1947--1963",
  month    =  jun,
  year     =  2018,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Pina2012-fa,
  title    = "Inferring rules of lineage commitment in haematopoiesis",
  author   = "Pina, Cristina and Fugazza, Cristina and Tipping, Alex J and
              Brown, John and Soneji, Shamit and Teles, Jose and Peterson,
              Carsten and Enver, Tariq",
  abstract = "How the molecular programs of differentiated cells develop as
              cells transit from multipotency through lineage commitment
              remains unexplored. This reflects the inability to access cells
              undergoing commitment or located in the immediate vicinity of
              commitment boundaries. It remains unclear whether commitment
              constitutes a gradual process, or else represents a discrete
              transition. Analyses of in vitro self-renewing multipotent
              systems have revealed cellular heterogeneity with individual
              cells transiently exhibiting distinct biases for lineage
              commitment. Such systems can be used to molecularly interrogate
              early stages of lineage affiliation and infer rules of lineage
              commitment. In haematopoiesis, population-based studies have
              indicated that lineage choice is governed by global
              transcriptional noise, with self-renewing multipotent cells
              reversibly activating transcriptome-wide lineage-affiliated
              programs. We examine this hypothesis through functional and
              molecular analysis of individual blood cells captured from
              self-renewal cultures, during cytokine-driven differentiation and
              from primary stem and progenitor bone marrow compartments. We
              show dissociation between self-renewal potential and
              transcriptome-wide activation of lineage programs, and instead
              suggest that multipotent cells experience independent activation
              of individual regulators resulting in a low probability of
              transition to the committed state.",
  journal  = "Nat. Cell Biol.",
  volume   =  14,
  number   =  3,
  pages    = "287--294",
  month    =  feb,
  year     =  2012,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Guibentif2017-gi,
  title    = "{Single-Cell} Analysis Identifies Distinct Stages of Human
              {Endothelial-to-Hematopoietic} Transition",
  author   = "Guibentif, Carolina and R{\"o}nn, Roger Emanuel and B{\"o}iers,
              Charlotta and Lang, Stefan and Saxena, Shobhit and Soneji, Shamit
              and Enver, Tariq and Karlsson, G{\"o}ran and Woods, Niels-Bjarne",
  abstract = "During development, hematopoietic cells originate from
              endothelium in a process known as endothelial-to-hematopoietic
              transition (EHT). To study human EHT, we coupled flow cytometry
              and single-cell transcriptional analyses of human pluripotent
              stem cell-derived CD34(+) cells. The resulting transcriptional
              hierarchy showed a continuum of endothelial and hematopoietic
              signatures. At the interface of these two signatures, a unique
              group of cells displayed both an endothelial signature and high
              levels of key hematopoietic stem cell-associated genes. This
              interphase group was validated via sort and subculture as an
              immediate precursor to hematopoietic cells. Differential
              expression analyses further divided this population into
              subgroups, which, upon subculture, showed distinct hematopoietic
              lineage differentiation potentials. We therefore propose that
              immediate precursors to hematopoietic cells already have their
              hematopoietic lineage restrictions defined prior to complete
              downregulation of the endothelial signature. These findings
              increase our understanding of the processes of de novo
              hematopoietic cell generation in the human developmental context.",
  journal  = "Cell Rep.",
  volume   =  19,
  number   =  1,
  pages    = "10--19",
  month    =  apr,
  year     =  2017,
  address  = "United States",
  keywords = "developmental hematopoiesis; endothelial-to-hematopoietic
              transition; hematopoietic stem cell; human induced pluripotent
              stem cells; single cell analysis;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Strid2021-ig,
  title    = "{B} Lymphocyte Specification Is Preceded by Extensive Epigenetic
              Priming in Multipotent Progenitors",
  author   = "Strid, Tobias and Okuyama, Kazuki and Tingvall-Gustafsson,
              Johanna and Kuruvilla, Jacob and Jensen, Christina T and Lang,
              Stefan and Prasad, Mahadesh and Somasundaram, Rajesh and
              {\AA}hsberg, Josefine and Cristobal, Susana and Soneji, Shamit
              and Ungerb{\"a}ck, Jonas and Sigvardsson, Mikael",
  abstract = "B lymphocyte development is dependent on the interplay between
              the chromatin landscape and lineage-specific transcription
              factors. It has been suggested that B lineage commitment is
              associated with major changes in the nuclear chromatin
              environment, proposing a critical role for lineage-specific
              transcription factors in the formation of the epigenetic
              landscape. In this report, we have used chromosome conformation
              capture in combination with assay for transposase-accessible
              chromatin sequencing analysis to enable highly efficient
              annotation of both proximal and distal transcriptional control
              elements to genes activated in B lineage specification in mice. A
              large majority of these genes were annotated to at least one
              regulatory element with an accessible chromatin configuration in
              multipotent progenitors. Furthermore, the majority of binding
              sites for the key regulators of B lineage specification, EBF1 and
              PAX5, occurred in already accessible regions. EBF1 did, however,
              cause a dynamic change in assay for transposase-accessible
              chromatin accessibility and was critical for an increase in
              distal promoter-enhancer interactions. Our data unravel an
              extensive epigenetic priming at regulatory elements annotated to
              lineage-restricted genes and provide insight into the interplay
              between the epigenetic landscape and transcription factors in
              cell specification.",
  journal  = "J. Immunol.",
  volume   =  206,
  number   =  11,
  pages    = "2700--2713",
  month    =  may,
  year     =  2021,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Rydstrom2023-vf,
  title    = "{MAC-1} marks a quiescent and functionally superior {HSC} subset
              during regeneration",
  author   = "Rydstr{\"o}m, Anna and Mansell, Els and Sigurdsson, Valgardur and
              Sj{\"o}berg, Julia and Soneji, Shamit and Miharada, Kenichi and
              Larsson, Jonas",
  abstract = "Mouse hematopoietic stem cells (HSCs) have been extensively
              defined both molecularly and functionally at steady state, while
              regenerative stress induces immunophenotypical changes that limit
              high purity isolation and analysis. It is therefore important to
              identify markers that specifically label activated HSCs to gain
              further knowledge about their molecular and functional
              properties. Here, we assessed the expression of macrophage-1
              antigen (MAC-1) on HSCs during regeneration following
              transplantation and observed a transient increase in MAC-1
              expression during the early reconstitution phase. Serial
              transplantation experiments demonstrated that reconstitution
              potential was highly enriched in the MAC-1(+) portion of the HSC
              pool. Moreover, in contrast to previous reports, we found that
              MAC-1 expression inversely correlates with cell cycling, and
              global transcriptome analysis showed that regenerating MAC-1(+)
              HSCs share molecular features with stem cells with low mitotic
              history. Taken together, our results suggest that MAC-1
              expression marks predominantly quiescent and functionally
              superior HSCs during early regeneration.",
  journal  = "Stem Cell Reports",
  volume   =  18,
  number   =  3,
  pages    = "736--748",
  month    =  mar,
  year     =  2023,
  address  = "United States",
  keywords = "MAC-1; hematopoietic stem cells; regeneration;
              transplantation;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Jensen2023-oa,
  title    = "B-lineage acute lymphoblastic leukemia causes cell autonomous
              defects in long-term hematopoietic stem cell function",
  author   = "Jensen, Christina T and {\AA}hsberg, Josefine and
              Tingvall-Gustafsson, Johanna and Somasundaram, Rajesh and Lang,
              Stefan and Ungerb{\"a}ck, Jonas and Porwit, Anna and Soneji,
              Shamit and Sigvardsson, Mikael",
  abstract = "Not available.",
  journal  = "Haematologica",
  month    =  mar,
  year     =  2023,
  address  = "Italy",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Capellera-Garcia2016-vj,
  title    = "Defining the Minimal Factors Required for Erythropoiesis through
              Direct Lineage Conversion",
  author   = "Capellera-Garcia, Sandra and Pulecio, Julian and Dhulipala,
              Kishori and Siva, Kavitha and Rayon-Estrada, Violeta and
              Singbrant, Sofie and Sommarin, Mikael N E and Walkley, Carl R and
              Soneji, Shamit and Karlsson, G{\"o}ran and Raya, {\'A}ngel and
              Sankaran, Vijay G and Flygare, Johan",
  abstract = "Erythroid cell commitment and differentiation proceed through
              activation of a lineage-restricted transcriptional network
              orchestrated by a group of well characterized genes. However, the
              minimal set of factors necessary for instructing red blood cell
              (RBC) development remains undefined. We employed a screen for
              transcription factors allowing direct lineage reprograming from
              fibroblasts to induced erythroid progenitors/precursors (iEPs).
              We show that Gata1, Tal1, Lmo2, and c-Myc (GTLM) can rapidly
              convert murine and human fibroblasts directly to iEPs. The
              transcriptional signature of murine iEPs resembled mainly that of
              primitive erythroid progenitors in the yolk sac, whereas addition
              of Klf1 or Myb to the GTLM cocktail resulted in iEPs with a more
              adult-type globin expression pattern. Our results demonstrate
              that direct lineage conversion is a suitable platform for
              defining and studying the core factors inducing the different
              waves of erythroid development.",
  journal  = "Cell Rep.",
  volume   =  15,
  number   =  11,
  pages    = "2550--2562",
  month    =  jun,
  year     =  2016,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Singh2018-yl,
  title    = "{MafA} Expression Preserves Immune Homeostasis in Human and Mouse
              Islets",
  author   = "Singh, Tania and Sarmiento, Luis and Luan, Cheng and Prasad,
              Rashmi B and Johansson, Jenny and Cataldo, Luis R and
              Renstr{\"o}m, Erik and Soneji, Shamit and Cilio, Corrado and
              Artner, Isabella",
  abstract = "Type 1 (T1D) and type 2 (T2D) diabetes are triggered by a
              combination of environmental and/or genetic factors. Maf
              transcription factors regulate pancreatic beta ($\beta$)-cell
              function, and have also been implicated in the regulation of
              immunomodulatory cytokines like interferon-$\beta$ (IFN$\beta$1).
              In this study, we assessed MAFA and MAFB co-expression with
              pro-inflammatory cytokine signaling genes in RNA-seq data from
              human pancreatic islets. Interestingly, MAFA expression was
              strongly negatively correlated with cytokine-induced signaling
              (such as IFNAR1, DDX58) and T1D susceptibility genes (IFIH1),
              whereas correlation of these genes with MAFB was weaker. In order
              to evaluate if the loss of MafA altered the immune status of
              islets, MafA deficient mouse islets (MafA(-/-)) were assessed for
              inherent anti-viral response and susceptibility to enterovirus
              infection. MafA deficient mouse islets had elevated basal levels
              of Ifn$\beta$1, Rig1 (DDX58 in humans), and Mda5 (IFIH1) which
              resulted in reduced virus propagation in response to
              coxsackievirus B3 (CVB3) infection. Moreover, an acute knockdown
              of MafA in $\beta$-cell lines also enhanced Rig1 and Mda5 protein
              levels. Our results suggest that precise regulation of MAFA
              levels is critical for islet cell-specific cytokine production,
              which is a critical parameter for the inflammatory status of
              pancreatic islets.",
  journal  = "Genes",
  volume   =  9,
  number   =  12,
  month    =  dec,
  year     =  2018,
  address  = "Switzerland",
  keywords = "MafA transcription factor; interferon-induced genes; interferons;
              islet inflammatory microenvironment; islet of
              Langerhans;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Nimmo2013-wt,
  title    = "{MiR-142-3p} controls the specification of definitive
              hemangioblasts during ontogeny",
  author   = "Nimmo, Rachael and Ciau-Uitz, Aldo and Ruiz-Herguido, Cristina
              and Soneji, Shamit and Bigas, Anna and Patient, Roger and Enver,
              Tariq",
  abstract = "Hematopoietic stem cells (HSCs) emerge during embryogenesis from
              hemogenic endothelium, but it remains unclear how the HSC lineage
              is initially established from mesoderm during ontogeny. In
              Xenopus, the definitive hemangioblast precursors of the HSC
              lineage have been identified in dorsal lateral plate (DLP)
              mesoderm, and a transcriptional gene regulatory network (GRN)
              controlling hemangioblast programming has been elucidated.
              Herein, we identify an essential role for microRNAs (miRNAs) in
              establishing the mesodermal lineage leading to both HSC emergence
              and vasculogenesis and determine that a single miRNA, miR-142-3p,
              is primarily responsible for initiation of definitive
              hemangioblast specification. miR-142-3p forms a double-negative
              gate unlocking entry into the hemangioblast program, in part by
              inhibiting TGF$\beta$ signaling. Our results table miR-142-3p as
              a master regulator of HSC lineage specification, sitting at the
              apex of the hierarchy programming the adult hemangioblast, thus
              illustrating that miRNAs can act as instructive determinants of
              cell fate during development.",
  journal  = "Dev. Cell",
  volume   =  26,
  number   =  3,
  pages    = "237--249",
  month    =  aug,
  year     =  2013,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Pfisterer2016-ab,
  title    = "Small molecules increase direct neural conversion of human
              fibroblasts",
  author   = "Pfisterer, Ulrich and Ek, Fredrik and Lang, Stefan and Soneji,
              Shamit and Olsson, Roger and Parmar, Malin",
  abstract = "The generation of human induced neurons (hiNs) via exogenous
              delivery of neural transcription factors represents a novel
              technique to obtain disease and patient specific neurons. These
              cells have the potential to be used for disease modeling,
              diagnostics and drug screening, and also to be further developed
              for brain repair. In the present study, we utilized hiNs to
              develop an unbiased screening assay for small molecules that
              increase the conversion efficiency. Using this assay, we screened
              307 compounds from five annotated libraries and identified six
              compounds that were very potent in potentiating the reprogramming
              process. When combined in an optimal combination and dose, these
              compounds increased the reprogramming efficiency of human
              fibroblasts more than 6-fold. Global gene expression and CellNet
              analysis at different timepoints during the reprogramming process
              revealed that neuron-specific genes and gene regulatory networks
              (GRNs) became progressively more activated while converting cells
              shut down fibroblast-specific GRNs. Further bioinformatics
              analysis revealed that the addition of the six compound resulted
              in the accelerated upregulation of a subset of neuronal genes,
              and also increased expression of genes associated with
              transcriptional activity and mediation of cellular stress
              response.",
  journal  = "Sci. Rep.",
  volume   =  6,
  pages    = "38290",
  month    =  dec,
  year     =  2016,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sawen2016-ox,
  title    = "Mitotic History Reveals Distinct Stem Cell Populations and Their
              Contributions to Hematopoiesis",
  author   = "S{\"a}w{\'e}n, Petter and Lang, Stefan and Mandal, Pankaj and
              Rossi, Derrick J and Soneji, Shamit and Bryder, David",
  abstract = "Homeostasis of short-lived blood cells is dependent on rapid
              proliferation of immature precursors. Using a conditional histone
              2B-mCherry-labeling mouse model, we characterize hematopoietic
              stem cell (HSC) and progenitor proliferation dynamics in steady
              state and following several types of induced stress. HSC
              proliferation following HSC transplantation into lethally
              irradiated mice is fundamentally different not only from native
              hematopoiesis but also from other stress contexts. Whereas
              transplantation promoted sustained, long-term proliferation of
              HSCs, both cytokine-induced mobilization and acute depletion of
              selected blood cell lineages elicited very limited recruitment of
              HSCs to the proliferative pool. By coupling mCherry-based
              analysis of proliferation history with multiplex gene expression
              analyses on single cells, we have found that HSCs can be
              stratified into four distinct subtypes. These subtypes have
              distinct molecular signatures and differ significantly in their
              reconstitution potentials, showcasing the power of tracking
              proliferation history when resolving functional heterogeneity of
              HSCs.",
  journal  = "Cell Rep.",
  volume   =  14,
  number   =  12,
  pages    = "2809--2818",
  month    =  mar,
  year     =  2016,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Baudet2015-fj,
  title    = "Small molecule screen identifies differentiation-promoting
              compounds targeting genetically diverse acute myeloid leukaemia",
  author   = "Baudet, Aur{\'e}lie and Ek, Fredrik and Davidsson, Josef and
              Soneji, Shamit and Olsson, Roger and Magnusson, Mattias and
              Cammenga, J{\"o}rg and Juliusson, Gunnar",
  journal  = "Br. J. Haematol.",
  volume   =  175,
  number   =  2,
  pages    = "342--346",
  month    =  nov,
  year     =  2015,
  address  = "England",
  keywords = "acute myeloid leukaemia-initiating cells; differentiation; small
              molecule screen;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sen2020-yw,
  title    = "Enhancing mitochondrial function in vivo rescues {MDS-like}
              anemia induced by pRb deficiency",
  author   = "Sen, Taha and Jain, Mayur and Gram, Magnus and Mattebo, Alexander
              and Soneji, Shamit and Walkley, Carl R and Singbrant, Sofie",
  abstract = "Erythropoiesis is intimately coupled to cell division, and
              deletion of the cell cycle regulator retinoblastoma protein (pRb)
              causes anemia in mice. Erythroid-specific deletion of pRb has
              been found to result in inefficient erythropoiesis because of
              deregulated coordination of cell cycle exit and mitochondrial
              biogenesis. However, the pathophysiology remains to be fully
              described, and further characterization of the link between cell
              cycle regulation and mitochondrial function is needed. To this
              end we further assessed conditional erythroid-specific deletion
              of pRb. This resulted in macrocytic anemia, despite elevated
              levels of erythropoietin (Epo), and an accumulation of erythroid
              progenitors in the bone marrow, a phenotype strongly resembling
              refractory anemia associated with myelodysplastic syndromes
              (MDS). Using high-fractionation fluorescence-activated cell
              sorting analysis for improved phenotypic characterization, we
              illustrate that erythroid differentiation was disrupted at the
              orthochromatic stage. Transcriptional profiling of sequential
              purified populations revealed failure to upregulate genes
              critical for mitochondrial function such as Pgc1$\beta$, Alas2,
              and Abcb7 specifically at the block, together with disturbed heme
              production and iron transport. Notably, deregulated ABCB7 causes
              ring sideroblastic anemia in MDS patients, and the mitochondrial
              co-activator PGC1$\beta$ is heterozygously lost in del5q MDS.
              Importantly, the anemia could be rescued through enhanced PPAR
              signaling in vivo via either overexpression of Pgc1$\beta$ or
              bezafibrate administration. In conclusion, lack of pRb results in
              MDS-like anemia with disrupted differentiation and impaired
              mitochondrial function at the orthochromatic erythroblast stage.
              Our findings reveal for the first time a role for pRb in heme and
              iron regulation, and indicate that pRb-induced anemia can be
              rescued in vivo through therapeutic enhancement of PPAR
              signaling.",
  journal  = "Exp. Hematol.",
  volume   =  88,
  pages    = "28--41",
  month    =  jul,
  year     =  2020,
  address  = "Netherlands",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Vanhee2019-qo,
  title    = "Lin28b controls a neonatal to adult switch in {B} cell positive
              selection",
  author   = "Vanhee, Stijn and {\AA}kerstrand, Hugo and Kristiansen, Trine Ahn
              and Datta, Sebak and Montano, Giorgia and Vergani, Stefano and
              Lang, Stefan and Ungerb{\"a}ck, Jonas and Doyle, Alexander and
              Olsson, Karin and Beneventi, Giulia and Jensen, Christina T and
              Bellodi, Cristian and Soneji, Shamit and Sigvardsson, Mikael and
              Gyllenb{\"a}ck, Elin Jaensson and Yuan, Joan",
  abstract = "The ability of B-1 cells to become positively selected into the
              mature B cell pool, despite being weakly self-reactive, has
              puzzled the field since its initial discovery. Here, we explore
              changes in B cell positive selection as a function of
              developmental time by exploiting a link between CD5 surface
              levels and the natural occurrence of self-reactive B cell
              receptors (BCRs) in BCR wild-type mice. We show that the
              heterochronic RNA binding protein Lin28b potentiates a neonatal
              mode of B cell selection characterized by enhanced overall
              positive selection in general and the developmental progression
              of CD5(+) immature B cells in particular. Lin28b achieves this by
              amplifying the CD19/PI3K/c-Myc positive feedback loop, and
              ectopic Lin28b expression restores both positive selection and
              mature B cell numbers in CD19(-/-) adult mice. Thus, the
              temporally restricted expression of Lin28b relaxes the rules for
              B cell selection during ontogeny by modulating tonic signaling.
              We propose that this neonatal mode of B cell selection represents
              a cell-intrinsic cue to accelerate the de novo establishment of
              the adaptive immune system and incorporate a layer of natural
              antibody-mediated immunity throughout life.",
  journal  = "Sci Immunol",
  volume   =  4,
  number   =  39,
  month    =  sep,
  year     =  2019,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Pina2015-eg,
  title    = "{Single-Cell} Network Analysis Identifies {DDIT3} as a Nodal
              Lineage Regulator in Hematopoiesis",
  author   = "Pina, Cristina and Teles, Jos{\'e} and Fugazza, Cristina and May,
              Gillian and Wang, Dapeng and Guo, Yanping and Soneji, Shamit and
              Brown, John and Ed{\'e}n, Patrik and Ohlsson, Mattias and
              Peterson, Carsten and Enver, Tariq",
  abstract = "We explore cell heterogeneity during spontaneous and
              transcription-factor-driven commitment for network inference in
              hematopoiesis. Since individual genes display discrete OFF states
              or a distribution of ON levels, we compute and combine pairwise
              gene associations from binary and continuous components of gene
              expression in single cells. Ddit3 emerges as a regulatory node
              with positive linkage to erythroid regulators and negative
              association with myeloid determinants. Ddit3 loss impairs
              erythroid colony output from multipotent cells, while forcing
              Ddit3 in granulo-monocytic progenitors (GMPs) enhances
              self-renewal and impedes differentiation. Network analysis of
              Ddit3-transduced GMPs reveals uncoupling of myeloid networks and
              strengthening of erythroid linkages. RNA sequencing suggests that
              Ddit3 acts through development or stabilization of a precursor
              upstream of GMPs with inherent Meg-E potential. The enrichment of
              Gata2 target genes in Ddit3-dependent transcriptional responses
              suggests that Ddit3 functions in an erythroid transcriptional
              network nucleated by Gata2.",
  journal  = "Cell Rep.",
  volume   =  11,
  number   =  10,
  pages    = "1503--1510",
  month    =  jun,
  year     =  2015,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Mattebo2021-xl,
  title    = "Yippee like 4 (Ypel4) is essential for normal mouse red blood
              cell membrane integrity",
  author   = "Mattebo, Alexander and Sen, Taha and Jassinskaja, Maria and
              Pimkov{\'a}, Krist{\'y}na and Prieto Gonz{\'a}lez-Albo, Isabel
              and Alattar, Abdul Ghani and Ramakrishnan, Ramprasad and Lang,
              Stefan and J{\"a}r{\aa}s, Marcus and Hansson, Jenny and Soneji,
              Shamit and Singbrant, Sofie and van den Akker, Emile and Flygare,
              Johan",
  abstract = "The YPEL family genes are highly conserved across a diverse range
              of eukaryotic organisms and thus potentially involved in
              essential cellular processes. Ypel4, one of five YPEL family gene
              orthologs in mouse and human, is highly and specifically
              expressed in late terminal erythroid differentiation (TED). In
              this study, we investigated the role of Ypel4 in murine
              erythropoiesis, providing for the first time an in-depth
              description of a Ypel4-null phenotype in vivo. We demonstrated
              that the Ypel4-null mice displayed a secondary polycythemia with
              macro- and reticulocytosis. While lack of Ypel4 did not affect
              steady-state TED in the bone marrow or spleen, the
              anemia-recovering capacity of Ypel4-null cells was diminished.
              Furthermore, Ypel4-null red blood cells (RBC) were cleared from
              the circulation at an increased rate, demonstrating an intrinsic
              defect of RBCs. Scanning electron micrographs revealed an
              ovalocytic morphology of Ypel4-null RBCs and functional testing
              confirmed reduced deformability. Even though Band 3 protein
              levels were shown to be reduced in Ypel4-null RBC membranes, we
              could not find support for a physical interaction between YPEL4
              and the Band 3 protein. In conclusion, our findings provide
              crucial insights into the role of Ypel4 in preserving normal red
              cell membrane integrity.",
  journal  = "Sci. Rep.",
  volume   =  11,
  number   =  1,
  pages    = "15898",
  month    =  aug,
  year     =  2021,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Lang2015-pl,
  title    = "{SCExV}: a webtool for the analysis and visualisation of single
              cell {qRT-PCR} data",
  author   = "Lang, Stefan and Ugale, Amol and Erlandsson, Eva and Karlsson,
              G{\"o}ran and Bryder, David and Soneji, Shamit",
  abstract = "BACKGROUND: Single cell gene expression assays have become a
              powerful tool with which to dissect heterogeneous populations.
              While methods and software exist to interrogate such data, what
              has been lacking is a unified solution combining analysis and
              visualisation which is also accessible and intuitive for use by
              non-bioinformaticians, as well as bioinformaticians. RESULTS: We
              present the Single cell expression visualiser (SCExV), a webtool
              developed to expedite the analysis of single cell qRT-PCR data.
              SCExV is able to take any data matrix of Ct values as an input,
              but can handle files exported by the Fluidigm Biomark platform
              directly. In addition, SCExV also accepts and automatically
              integrates cell surface marker intensity values which are
              measured during index sorting. This allows the user to directly
              visualise relationships between a single cell gene expression
              profile and the immunophenotype of the interrogated cell.
              CONCLUSIONS: SCExV is a freely available webtool created to
              import, filter, analyse, and visualise single cell gene
              expression data whilst being able to simultaneously consider
              cellular immunophenotype. SCExV is designed to be intuitive to
              use whilst maintaining advanced functionality and flexibility in
              how analyses are performed.",
  journal  = "BMC Bioinformatics",
  volume   =  16,
  pages    = "320",
  month    =  oct,
  year     =  2015,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Karlsson2013-zr,
  title    = "The tetraspanin {CD9} affords high-purity capture of all murine
              hematopoietic stem cells",
  author   = "Karlsson, G{\"o}ran and R{\"o}rby, Emma and Pina, Cristina and
              Soneji, Shamit and Reckzeh, Kristian and Miharada, Kenichi and
              Karlsson, Christine and Guo, Yanping and Fugazza, Cristina and
              Gupta, Rajeev and Martens, Joost H A and Stunnenberg, Hendrik G
              and Karlsson, Stefan and Enver, Tariq",
  abstract = "Prospective isolation is critical for understanding the cellular
              and molecular aspects of stem cell heterogeneity. Here, we
              identify the cell surface antigen CD9 as a positive marker that
              provides a simple alternative for hematopoietic stem cell
              isolation at high purity. Crucially, CD9 affords the capture of
              all hematopoietic stem cells in murine bone marrow in the absence
              of contaminating populations that lack authentic stem cell
              function. Using CD9 as a tool to subdivide hematopoietic
              stem-cell-containing populations, we provide evidence for
              heterogeneity at the cellular, functional, and molecular levels.",
  journal  = "Cell Rep.",
  volume   =  4,
  number   =  4,
  pages    = "642--648",
  month    =  aug,
  year     =  2013,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sawen2018-qp,
  title    = "Murine {HSCs} contribute actively to native hematopoiesis but
              with reduced differentiation capacity upon aging",
  author   = "S{\"a}wen, Petter and Eldeeb, Mohamed and Erlandsson, Eva and
              Kristiansen, Trine A and Laterza, Cecilia and Kokaia, Zaal and
              Karlsson, G{\"o}ran and Yuan, Joan and Soneji, Shamit and Mandal,
              Pankaj K and Rossi, Derrick J and Bryder, David",
  abstract = "A hallmark of adult hematopoiesis is the continuous replacement
              of blood cells with limited lifespans. While active hematopoietic
              stem cell (HSC) contribution to multilineage hematopoiesis is the
              foundation of clinical HSC transplantation, recent reports have
              questioned the physiological contribution of HSCs to
              normal/steady-state adult hematopoiesis. Here, we use inducible
              lineage tracing from genetically marked adult HSCs and reveal
              robust HSC-derived multilineage hematopoiesis. This commences via
              defined progenitor cells, but varies substantially in between
              different hematopoietic lineages. By contrast, adult HSC
              contribution to hematopoietic cells with proposed fetal origins
              is neglible. Finally, we establish that the HSC contribution to
              multilineage hematopoiesis declines with increasing age.
              Therefore, while HSCs are active contributors to native adult
              hematopoiesis, it appears that the numerical increase of HSCs is
              a physiologically relevant compensatory mechanism to account for
              their reduced differentiation capacity with age.",
  journal  = "Elife",
  volume   =  7,
  month    =  dec,
  year     =  2018,
  address  = "England",
  keywords = "aging; hematopoiesis; lineage tracing; mouse; regenerative
              medicine; steady state; stem cells;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Merryweather-Clarke2011-ea,
  title    = "Global gene expression analysis of human erythroid progenitors",
  author   = "Merryweather-Clarke, Alison T and Atzberger, Ann and Soneji,
              Shamit and Gray, Nicki and Clark, Kevin and Waugh, Craig and
              McGowan, Simon J and Taylor, Stephen and Nandi, Asoke K and Wood,
              William G and Roberts, David J and Higgs, Douglas R and Buckle,
              Veronica J and Robson, Kathryn J H",
  abstract = "Understanding the pattern of gene expression during
              erythropoiesis is crucial for a synthesis of erythroid
              developmental biology. Here, we isolated 4 distinct populations
              at successive erythropoietin-dependent stages of erythropoiesis,
              including the terminal, pyknotic stage. The transcriptome was
              determined using Affymetrix arrays. First, we demonstrated the
              importance of using defined cell populations to identify lineage
              and temporally specific patterns of gene expression. Cells sorted
              by surface expression profile not only express significantly
              fewer genes than unsorted cells but also demonstrate
              significantly greater differences in the expression levels of
              particular genes between stages than unsorted cells. Second,
              using standard software, we identified more than 1000 transcripts
              not previously observed to be differentially expressed during
              erythroid maturation, 13 of which are highly significantly
              terminally regulated, including RFXAP and SMARCA4. Third, using
              matched filtering, we identified 12 transcripts not previously
              reported to be continuously up-regulated in maturing human
              primary erythroblasts. Finally, using transcription factor
              binding site analysis, we identified potential transcription
              factors that may regulate gene expression during terminal
              erythropoiesis. Our stringent lists of differentially regulated
              and continuously expressed transcripts containing many genes with
              undiscovered functions in erythroblasts are a resource for future
              functional studies of erythropoiesis. Our Human Erythroid
              Maturation database is available at
              https://cellline.molbiol.ox.ac.uk/eryth/index.html. [corrected].",
  journal  = "Blood",
  volume   =  117,
  number   =  13,
  pages    = "e96--108",
  month    =  jan,
  year     =  2011,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Okuyama2019-mw,
  title    = "{PAX5} is part of a functional transcription factor network
              targeted in lymphoid leukemia",
  author   = "Okuyama, Kazuki and Strid, Tobias and Kuruvilla, Jacob and
              Somasundaram, Rajesh and Cristobal, Susana and Smith, Emma and
              Prasad, Mahadesh and Fioretos, Thoas and Lilljebj{\"o}rn, Henrik
              and Soneji, Shamit and Lang, Stefan and Ungerb{\"a}ck, Jonas and
              Sigvardsson, Mikael",
  abstract = "One of the most frequently mutated proteins in human B-lineage
              leukemia is the transcription factor PAX5. These mutations often
              result in partial rather than complete loss of function of the
              transcription factor. While the functional dose of PAX5 has a
              clear connection to human malignancy, there is limited evidence
              for that heterozygote loss of PAX5 have a dramatic effect on the
              development and function of B-cell progenitors. One possible
              explanation comes from the finding that PAX5 mutated B-ALL often
              display complex karyotypes and additional mutations. Thus, PAX5
              might be one component of a larger transcription factor network
              targeted in B-ALL. To investigate the functional network
              associated with PAX5 we used BioID technology to isolate proteins
              associated with this transcription factor in the living cell.
              This identified 239 proteins out of which several could be found
              mutated in human B-ALL. Most prominently we identified the
              commonly mutated IKZF1 and RUNX1, involved in the formation of
              ETV6-AML1 fusion protein, among the interaction partners. ChIP-
              as well as PLAC-seq analysis supported the idea that these
              factors share a multitude of target genes in human B-ALL cells.
              Gene expression analysis of mouse models and primary human
              leukemia suggested that reduced function of PAX5 increased the
              ability of an oncogenic form of IKZF1 or ETV6-AML to modulate
              gene expression. Our data reveals that PAX5 belong to a
              regulatory network frequently targeted by multiple mutations in
              B-ALL shedding light on the molecular interplay in leukemia
              cells.",
  journal  = "PLoS Genet.",
  volume   =  15,
  number   =  8,
  pages    = "e1008280",
  month    =  aug,
  year     =  2019,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Luc2012-jp,
  title    = "The earliest thymic {T} cell progenitors sustain {B} cell and
              myeloid lineage potential",
  author   = "Luc, Sidinh and Luis, Tiago C and Boukarabila, Hanane and
              Macaulay, Iain C and Buza-Vidas, Natalija and Bouriez-Jones,
              Tiphaine and Lutteropp, Michael and Woll, Petter S and Loughran,
              Stephen J and Mead, Adam J and Hultquist, Anne and Brown, John
              and Mizukami, Takuo and Matsuoka, Sahoko and Ferry, Helen and
              Anderson, Kristina and Duarte, Sara and Atkinson, Deborah and
              Soneji, Shamit and Domanski, Aniela and Farley, Alison and
              Sanjuan-Pla, Alejandra and Carella, Cintia and Patient, Roger and
              de Bruijn, Marella and Enver, Tariq and Nerlov, Claus and
              Blackburn, Clare and Godin, Isabelle and Jacobsen, Sten Eirik W",
  abstract = "The stepwise commitment from hematopoietic stem cells in the bone
              marrow to T lymphocyte-restricted progenitors in the thymus
              represents a paradigm for understanding the requirement for
              distinct extrinsic cues during different stages of lineage
              restriction from multipotent to lineage-restricted progenitors.
              However, the commitment stage at which progenitors migrate from
              the bone marrow to the thymus remains unclear. Here we provide
              functional and molecular evidence at the single-cell level that
              the earliest progenitors in the neonatal thymus had combined
              granulocyte-monocyte, T lymphocyte and B lymphocyte lineage
              potential but not megakaryocyte-erythroid lineage potential.
              These potentials were identical to those of candidate
              thymus-seeding progenitors in the bone marrow, which were closely
              related at the molecular level. Our findings establish the
              distinct lineage-restriction stage at which the T cell
              lineage-commitment process transits from the bone marrow to the
              remote thymus.",
  journal  = "Nat. Immunol.",
  volume   =  13,
  number   =  4,
  pages    = "412--419",
  month    =  feb,
  year     =  2012,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Ugale2014-sh,
  title    = "Hematopoietic stem cells are intrinsically protected against
              {MLL-ENL-mediated} transformation",
  author   = "Ugale, Amol and Norddahl, Gudmundur L and Wahlestedt, Martin and
              S{\"a}w{\'e}n, Petter and Jaako, Pekka and Pronk, Cornelis Jan
              and Soneji, Shamit and Cammenga, J{\"o}rg and Bryder, David",
  abstract = "Studies of developmental pathways of hematopoietic stem cells
              (HSCs) have defined lineage relationships throughout the blood
              system. This is relevant to acute myeloid leukemia (AML), where
              aggressiveness and therapeutic responsiveness can be influenced
              by the initial stage of transformation. To address this, we
              generated a mouse model in which the mixed-lineage
              leukemia/eleven-nineteen-leukemia (MLL-ENL) transcription factor
              can be conditionally activated in any cell type. We show that AML
              can originate from multiple hematopoietic progenitor subsets with
              granulocytic and monocytic potential, and that the normal
              developmental position of leukemia-initiating cells influences
              leukemic development. However, disease failed to arise from HSCs.
              Although it maintained or upregulated the expression of target
              genes associated with leukemic development, MLL-ENL dysregulated
              the proliferative and repopulating capacity of HSCs. Therefore,
              the permissiveness for development of AML may be associated with
              a narrower window of differentiation than was previously
              appreciated, and hijacking the self-renewal capacity of HSCs by a
              potent oncogene is insufficient for leukemic development.",
  journal  = "Cell Rep.",
  volume   =  9,
  number   =  4,
  pages    = "1246--1255",
  month    =  nov,
  year     =  2014,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Renoux2015-ym,
  title    = "Identification of a Human Natural Killer Cell
              {Lineage-Restricted} Progenitor in Fetal and Adult Tissues",
  author   = "Renoux, Virginie M and Zriwil, Alya and Peitzsch, Claudia and
              Micha{\"e}lsson, Jakob and Friberg, Danielle and Soneji, Shamit
              and Sitnicka, Ewa",
  abstract = "Natural killer (NK) cells are cytotoxic lymphocytes and play a
              vital role in controlling viral infections and cancer. In
              contrast to B and T lymphopoiesis where cellular and regulatory
              pathways have been extensively characterized, the cellular stages
              of early human NK cell commitment remain poorly understood. Here
              we demonstrate that a
              Lin(-)CD34(+)CD38(+)CD123(-)CD45RA(+)CD7(+)CD10(+)CD127(-)
              population represents a NK lineage-restricted progenitor (NKP) in
              fetal development, umbilical cord blood, and adult tissues. The
              newly identified NKP has robust NK cell potential both in vitro
              and in vivo, generates functionally cytotoxic NK cells, and lacks
              the ability to produce T cells, B cells, myeloid cells, and
              innate lymphoid-like cells (ILCs). Our findings identify an early
              step to human NK cell commitment and provide new insights into
              the human hematopoietic hierarchy.",
  journal  = "Immunity",
  volume   =  43,
  number   =  2,
  pages    = "394--407",
  month    =  aug,
  year     =  2015,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Goardon2011-ci,
  title    = "Coexistence of {LMPP-like} and {GMP-like} leukemia stem cells in
              acute myeloid leukemia",
  author   = "Goardon, Nicolas and Marchi, Emanuele and Atzberger, Ann and
              Quek, Lynn and Schuh, Anna and Soneji, Shamit and Woll, Petter
              and Mead, Adam and Alford, Kate A and Rout, Raj and Chaudhury,
              Salma and Gilkes, Amanda and Knapper, Steve and Beldjord, Kheira
              and Begum, Suriya and Rose, Susan and Geddes, Nicola and
              Griffiths, Mike and Standen, Graham and Sternberg, Alexander and
              Cavenagh, Jamie and Hunter, Hannah and Bowen, David and Killick,
              Sally and Robinson, Lisa and Price, Andrew and Macintyre,
              Elizabeth and Virgo, Paul and Burnett, Alan and Craddock, Charles
              and Enver, Tariq and Jacobsen, Sten Eirik W and Porcher,
              Catherine and Vyas, Paresh",
  abstract = "The relationships between normal and leukemic stem/progenitor
              cells are unclear. We show that in ∼80\% of primary human CD34+
              acute myeloid leukemia (AML), two expanded populations with
              hemopoietic progenitor immunophenotype coexist in most patients.
              Both populations have leukemic stem cell (LSC) activity and are
              hierarchically ordered; one LSC population gives rise to the
              other. Global gene expression profiling shows the LSC populations
              are molecularly distinct and resemble normal progenitors but not
              stem cells. The more mature LSC population most closely mirrors
              normal granulocyte-macrophage progenitors (GMP) and the immature
              LSC population a previously uncharacterized progenitor
              functionally similar to lymphoid-primed multipotential
              progenitors (LMPPs). This suggests that in most cases primary
              CD34+ AML is a progenitor disease where LSCs acquire abnormal
              self-renewal potential.",
  journal  = "Cancer Cell",
  volume   =  19,
  number   =  1,
  pages    = "138--152",
  month    =  jan,
  year     =  2011,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Velasco-Hernandez2018-nt,
  title    = "{Hif-1$\alpha$} Deletion May Lead to Adverse Treatment Effect in
              a Mouse Model of {MLL-AF9-Driven} {AML}",
  author   = "Velasco-Hernandez, Talia and Soneji, Shamit and Hidalgo, Isabel
              and Erlandsson, Eva and Cammenga, J{\"o}rg and Bryder, David",
  abstract = "Relapse of acute myeloid leukemia (AML) remains a significant
              clinical challenge due to limited therapeutic options and poor
              prognosis. Leukemic stem cells (LSCs) are the cellular units
              responsible for relapse in AML, and strategies that target LSCs
              are thus critical. One proposed potential strategy to this end is
              to break the quiescent state of LSCs, thereby sensitizing LSCs to
              conventional cytostatics. The hypoxia-inducible factor (HIF)
              pathway is a main driver of cellular quiescence and a potential
              therapeutic target, with precedence from both solid cancers and
              leukemias. Here, we used a conditional knockout Hif-1$\alpha$
              mouse model together with a standard chemotherapy regimen to
              evaluate LSC targeting in AML. Contrary to expectation, our
              studies revealed that Hif-1$\alpha$-deleted-leukemias displayed a
              faster disease progression after chemotherapy. Our studies
              thereby challenge the general notion of cancer stem cell
              sensitization by inhibition of the HIF pathway, and warrant
              caution when applying HIF inhibition in combination with
              chemotherapy in AML.",
  journal  = "Stem Cell Reports",
  volume   =  12,
  number   =  1,
  pages    = "112--121",
  month    =  dec,
  year     =  2018,
  address  = "United States",
  keywords = "HIF-1$\alpha$; acute myeloid leukemia; chemotherapy; hypoxia;
              mouse model; single-cell transcriptional
              analysis;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Hong2008-fx,
  title    = "Initiating and cancer-propagating cells in {TEL-AML1-associated}
              childhood leukemia",
  author   = "Hong, Dengli and Gupta, Rajeev and Ancliff, Philip and Atzberger,
              Ann and Brown, John and Soneji, Shamit and Green, Joanne and
              Colman, Sue and Piacibello, Wanda and Buckle, Veronica and
              Tsuzuki, Shinobu and Greaves, Mel and Enver, Tariq",
  abstract = "Understanding cancer pathogenesis requires knowledge of not only
              the specific contributory genetic mutations but also the cellular
              framework in which they arise and function. Here we explore the
              clonal evolution of a form of childhood precursor-B cell acute
              lymphoblastic leukemia that is characterized by a chromosomal
              translocation generating a TEL-AML1 fusion gene. We identify a
              cell compartment in leukemic children that can propagate leukemia
              when transplanted in mice. By studying a monochorionic twin pair,
              one preleukemic and one with frank leukemia, we establish the
              lineal relationship between these ``cancer-propagating'' cells
              and the preleukemic cell in which the TEL-AML1 fusion first
              arises or has functional impact. Analysis of TEL-AML1-transduced
              cord blood cells suggests that TEL-AML1 functions as a first-hit
              mutation by endowing this preleukemic cell with altered
              self-renewal and survival properties.",
  journal  = "Science",
  volume   =  319,
  number   =  5861,
  pages    = "336--339",
  month    =  jan,
  year     =  2008,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Galeev2016-pc,
  title    = "Genome-wide {RNAi} Screen Identifies Cohesin Genes as Modifiers
              of Renewal and Differentiation in Human {HSCs}",
  author   = "Galeev, Roman and Baudet, Aur{\'e}lie and Kumar, Praveen and
              Rundberg Nilsson, Alexandra and Nilsson, Bj{\"o}rn and Soneji,
              Shamit and T{\"o}rngren, Therese and Borg, {\AA}ke and Kvist,
              Anders and Larsson, Jonas",
  abstract = "To gain insights into the regulatory mechanisms of hematopoietic
              stem cells (HSCs), we employed a genome-wide RNAi screen in human
              cord-blood derived cells and identified candidate genes whose
              knockdown maintained the HSC phenotype during culture. A striking
              finding was the identification of members of the cohesin complex
              (STAG2, RAD21, STAG1, and SMC3) among the top 20 genes from the
              screen. Upon individual validation of these cohesin genes, we
              found that their knockdown led to an immediate expansion of cells
              with an HSC phenotype in vitro. A similar expansion was observed
              in vivo following transplantation to immunodeficient mice.
              Transcriptome analysis of cohesin-deficient CD34(+) cells showed
              an upregulation of HSC-specific genes, demonstrating an immediate
              shift toward a more stem-cell-like gene expression signature upon
              cohesin deficiency. Our findings implicate cohesin as a major
              regulator of HSCs and illustrate the power of global RNAi screens
              to identify modifiers of cell fate.",
  journal  = "Cell Rep.",
  volume   =  14,
  number   =  12,
  pages    = "2988--3000",
  month    =  mar,
  year     =  2016,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Lim2021-fa,
  title    = "Development of acoustically isolated extracellular plasma
              vesicles for biomarker discovery in allogeneic hematopoietic stem
              cell transplantation",
  author   = "Lim, Hooi Ching and Soneji, Shamit and P{\'a}lmason, R{\'o}bert
              and Lenhoff, Stig and Laurell, Thomas and Scheding, Stefan",
  abstract = "BACKGROUND: Infection and graft-versus-host disease (GvHD) are
              the major causes for mortality and morbidity of allogeneic
              hematopoietic stem cell transplantation (allo-HSCT).
              Plasma-derived extracellular vesicles (EVs) contain
              disease-related proteins, DNAs and RNAs, and have recently been
              suggested as potential biomarker candidates for transplantation
              complications. However, EV isolation from small plasma volumes in
              clinical biomarker studies using conventional methods is
              challenging. We therefore investigated if EVs isolated by novel
              automated acoustic trapping could be developed as potential
              biomarkers for allo-HSCT complications by performing a clinical
              proof-of-principle study. RESULTS: Plasma samples were collected
              from twenty consecutive patients with high-risk/relapsed
              hematologic malignancies undergoing allo-HSCT before
              transplantation and post-transplant up to 12 weeks. EVs were
              isolated from small plasma sample volumes (150 $\mu$l) by an
              automated, acoustofluidic-based particle trapping device, which
              utilizes a local $\lambda$/2 ultrasonic standing wave in a
              borosilicate glass capillary to capture plasma EVs among
              pre-seeded polystyrene microbeads through sound scatter
              interactions. We found that EVs could be reliably isolated from
              all plasma samples (n = 173) and that EV numbers increased more
              than 2-fold in the majority of patients after transplantation.
              Also, sufficient quantities of RNA for downstream microRNA
              (miRNA) analysis were obtained from all samples and EV miRNA
              profiles were found to differ from whole plasma profiles. As a
              proof of principle, expression of platelet-specific miR-142-3p in
              EVs was shown to correlate with platelet count kinetics after
              transplantation as expected. Importantly, we identified plasma EV
              miRNAs that were consistently positively correlated with
              infection and GvHD, respectively, as well as miRNAs that were
              consistently negatively correlated with these complications.
              CONCLUSIONS: This study demonstrates that acoustic enrichment of
              EVs in a clinical biomarker study setting is feasible and that
              downstream analysis of acoustically-enriched EVs presents a
              promising tool for biomarker development in allo-HSCT. Certainly,
              these findings warrant further exploration in larger studies,
              which will have significant implications not only for biomarker
              studies in transplantation but also for the broad field of
              EV-based biomarker discovery.",
  journal  = "Biomark Res",
  volume   =  9,
  number   =  1,
  pages    = "6",
  month    =  jan,
  year     =  2021,
  address  = "England",
  keywords = "Acoustic trapping; Allo-HSCT; Allogeneic hematopoietic stem cell
              transplantation; Biomarker development; EVs; Graft-versus host
              disease; GvHD; Infection; Plasma extracellular vesicles;
              Transplantation;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{De_Gobbi2011-lw,
  title    = "Generation of bivalent chromatin domains during cell fate
              decisions",
  author   = "De Gobbi, Marco and Garrick, David and Lynch, Magnus and
              Vernimmen, Douglas and Hughes, Jim R and Goardon, Nicolas and
              Luc, Sidinh and Lower, Karen M and Sloane-Stanley, Jacqueline A
              and Pina, Cristina and Soneji, Shamit and Renella, Raffaele and
              Enver, Tariq and Taylor, Stephen and Jacobsen, Sten Eirik W and
              Vyas, Paresh and Gibbons, Richard J and Higgs, Douglas R",
  abstract = "BACKGROUND: In self-renewing, pluripotent cells, bivalent
              chromatin modification is thought to silence (H3K27me3) lineage
              control genes while 'poising' (H3K4me3) them for subsequent
              activation during differentiation, implying an important role for
              epigenetic modification in directing cell fate decisions.
              However, rather than representing an equivalently balanced
              epigenetic mark, the patterns and levels of histone modifications
              at bivalent genes can vary widely and the criteria for
              identifying this chromatin signature are poorly defined. RESULTS:
              Here, we initially show how chromatin status alters during
              lineage commitment and differentiation at a single well
              characterised bivalent locus. In addition we have determined how
              chromatin modifications at this locus change with gene expression
              in both ensemble and single cell analyses. We also show, on a
              global scale, how mRNA expression may be reflected in the ratio
              of H3K4me3/H3K27me3. CONCLUSIONS: While truly 'poised' bivalently
              modified genes may exist, the original hypothesis that all
              bivalent genes are epigenetically premarked for subsequent
              expression might be oversimplistic. In fact, from the data
              presented in the present work, it is equally possible that many
              genes that appear to be bivalent in pluripotent and multipotent
              cells may simply be stochastically expressed at low levels in the
              process of multilineage priming. Although both situations could
              be considered to be forms of 'poising', the underlying mechanisms
              and the associated implications are clearly different.",
  journal  = "Epigenetics Chromatin",
  volume   =  4,
  number   =  1,
  pages    = "9",
  month    =  jun,
  year     =  2011,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Billing2016-tz,
  title    = "A network including {TGF$\beta$/Smad4}, Gata2, and p57 regulates
              proliferation of mouse hematopoietic progenitor cells",
  author   = "Billing, Matilda and R{\"o}rby, Emma and May, Gillian and
              Tipping, Alex J and Soneji, Shamit and Brown, John and Salminen,
              Marjo and Karlsson, G{\"o}ran and Enver, Tariq and Karlsson,
              Stefan",
  abstract = "Transforming growth factor $\beta$ (TGF$\beta$) is a potent
              inhibitor of hematopoietic stem and progenitor cell
              proliferation. However, the precise mechanism for this effect is
              unknown. Here, we have identified the transcription factor Gata2,
              previously described as an important regulator of hematopoietic
              stem cell function, as an early and direct target gene for
              TGF$\beta$-induced Smad signaling in hematopoietic progenitor
              cells. We also report that Gata2 is involved in mediating a
              significant part of the TGF$\beta$ response in primitive
              hematopoietic cells. Interestingly, the cell cycle regulator and
              TGF$\beta$ signaling effector molecule p57 was found to be
              upregulated as a secondary response to TGF$\beta$. We observed
              Gata2 binding upstream of the p57 genomic locus, and importantly,
              loss of Gata2 abolished TGF$\beta$-stimulated induction of p57 as
              well as the resulting growth arrest of hematopoietic progenitors.
              Our results connect key molecules involved in hematopoietic stem
              cell self-renewal and reveal a functionally relevant network,
              regulating proliferation of primitive hematopoietic cells.",
  journal  = "Exp. Hematol.",
  volume   =  44,
  number   =  5,
  pages    = "399--409.e5",
  month    =  feb,
  year     =  2016,
  address  = "Netherlands",
  keywords = "SonejiS\_Publications",
  language = "en"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Bochukova2009-jx,
  title    = "Scalp fibroblasts have a shared expression profile in monogenic
              craniosynostosis",
  author   = "Bochukova, Elena G and Soneji, Shamit and Wall, Steven A and
              Wilkie, Andrew O M",
  abstract = "BACKGROUND: Craniosynostosis can be caused by both genetic and
              environmental factors, the relative contributions of which vary
              between patients. Genetic testing identifies a pathogenic
              mutation or chromosomal abnormality in ∼ 21\% of cases, but it is
              likely that further causative mutations remain to be discovered.
              OBJECTIVE: To identify a shared signature of genetically
              determined craniosynostosis by comparing the expression patterns
              in three monogenic syndromes with a control group of patients
              with non-syndromic sagittal synostosis. METHODS: Fibroblasts from
              10 individuals each with Apert syndrome (FGFR2 substitution
              S252W), Muenke syndrome (FGFR3 substitution P250R),
              Saethre-Chotzen syndrome (various mutations in TWIST1) and
              non-syndromic sagittal synostosis (no mutation detected) were
              cultured. The relative expression of ∼ 47,000 transcripts was
              quantified on Affymetrix arrays. RESULTS: 435, 45 and 46
              transcripts were identified in the Apert, Muenke and
              Saethre-Chotzen groups, respectively, that differed significantly
              from the controls. Forty-six of these transcripts were shared
              between two or more syndromes and, in all but one instance,
              showed the same direction of altered expression level compared
              with controls. Pathway analysis showed over-representation of the
              shared transcripts in core modules involving cell-to-cell
              communication and signal transduction. Individual samples from
              the Apert syndrome cases could be reliably distinguished from
              non-syndromic samples based on the gene expression profile, but
              this was not possible for samples from patients with Muenke and
              Saethre-Chotzen syndromes. CONCLUSIONS: Common modules of altered
              gene expression shared by genetically distinct forms of
              craniosynostosis were identified. Although the expression
              profiles cannot currently be used to classify individual
              patients, this may be overcome by using more sensitive assays and
              sampling additional tissues.",
  journal  = "J. Med. Genet.",
  volume   =  47,
  number   =  12,
  pages    = "803--808",
  month    =  sep,
  year     =  2009,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Pina2008-dx,
  title    = "{MLLT3} regulates early human erythroid and megakaryocytic cell
              fate",
  author   = "Pina, Cristina and May, Gillian and Soneji, Shamit and Hong,
              Dengli and Enver, Tariq",
  abstract = "Regulatory mechanisms of human hematopoiesis remain largely
              uncharacterized. Through expression profiling of prospectively
              isolated stem and primitive progenitor cells as well as committed
              progenitors from cord blood (CB), we identified MLLT3 as a
              candidate regulator of erythroid/megakaryocytic (E/Meg) lineage
              decisions. Through the analysis of the hematopoietic potential of
              primitive cord blood cells in which MLLT3 expression has been
              knocked down, we identify a requirement for MLLT3 in the
              elaboration of the erythroid and megakaryocytic lineages.
              Conversely, forced expression of MLLT3 promotes the output of
              erythroid and megakaryocytic progenitors, and analysis of MLLT3
              mutants suggests that this capacity of MLLT3 depends on its
              transcriptional regulatory activity. Gene expression and
              cis-regulatory element analyses reveal crossregulatory
              interactions between MLLT3 and E/Meg-affiliated transcription
              factor GATA-1. Taken together, the data identify MLLT3 as a
              regulator of early erythroid and megakaryocytic cell fate in the
              human system.",
  journal  = "Cell Stem Cell",
  volume   =  2,
  number   =  3,
  pages    = "264--273",
  month    =  mar,
  year     =  2008,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Warfvinge2017-hq,
  title    = "Single-cell molecular analysis defines therapy response and
              immunophenotype of stem cell subpopulations in {CML}",
  author   = "Warfvinge, Rebecca and Geironson, Linda and Sommarin, Mikael N E
              and Lang, Stefan and Karlsson, Christine and Roschupkina, Teona
              and Stenke, Leif and Stentoft, Jesper and Olsson-Str{\"o}mberg,
              Ulla and Hjorth-Hansen, Henrik and Mustjoki, Satu and Soneji,
              Shamit and Richter, Johan and Karlsson, G{\"o}ran",
  abstract = "Understanding leukemia heterogeneity is critical for the
              development of curative treatments as the failure to eliminate
              therapy-persistent leukemic stem cells (LSCs) may result in
              disease relapse. Here we have combined high-throughput
              immunophenotypic screens with large-scale single-cell gene
              expression analysis to define the heterogeneity within the LSC
              population in chronic phase chronic myeloid leukemia (CML)
              patients at diagnosis and following conventional tyrosine kinase
              inhibitor (TKI) treatment. Our results reveal substantial
              heterogeneity within the putative LSC population in CML at
              diagnosis and demonstrate differences in response to subsequent
              TKI treatment between distinct subpopulations. Importantly, LSC
              subpopulations with myeloid and proliferative molecular
              signatures are proportionally reduced at a higher extent in
              response to TKI therapy compared with subfractions displaying
              primitive and quiescent signatures. Additionally, cell surface
              expression of the CML stem cell markers CD25, CD26, and IL1RAP is
              high in all subpopulations at diagnosis but downregulated and
              unevenly distributed across subpopulations in response to TKI
              treatment. The most TKI-insensitive cells of the LSC compartment
              can be captured within the CD45RA(-) fraction and further defined
              as positive for CD26 in combination with an aberrant lack of cKIT
              expression. Together, our results expose a considerable
              heterogeneity of the CML stem cell population and propose a
              Lin(-)CD34(+)CD38(-/low)CD45RA(-)cKIT(-)CD26(+) population as a
              potential therapeutic target for improved therapy response.",
  journal  = "Blood",
  volume   =  129,
  number   =  17,
  pages    = "2384--2394",
  month    =  jan,
  year     =  2017,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Karlsson2013-nq,
  title    = "Identification of the chemokine {CCL28} as a growth and survival
              factor for human hematopoietic stem and progenitor cells",
  author   = "Karlsson, Christine and Baudet, Aur{\'e}lie and Miharada, Natsumi
              and Soneji, Shamit and Gupta, Rajeev and Magnusson, Mattias and
              Enver, Tariq and Karlsson, G{\"o}ran and Larsson, Jonas",
  abstract = "In an attempt to discover novel growth factors for hematopoietic
              stem and progenitor cells (HSPCs), we have assessed cytokine
              responses of cord blood (CB)-derived CD34(+) cells in a
              high-content growth factor screen. We identify the
              immunoregulatory chemokine (C-C motif) ligand 28 (CCL28) as a
              novel growth factor that directly stimulates proliferation of
              primitive hematopoietic cells from different ontogenetic origins.
              CCL28 enhances the functional progenitor cell content of cultured
              cells by stimulating cell cycling and induces gene expression
              changes associated with survival. Importantly, addition of CCL28
              to cultures of purified putative hematopoietic stem cells (HSCs)
              significantly increases the ability of the cells to long-term
              repopulate immunodeficient mice compared with equivalent input
              numbers of fresh cells. Together, our findings identify CCL28 as
              a potent growth-promoting factor with the ability to support the
              in vitro and in vivo functional properties of cultured human
              hematopoietic cells.",
  journal  = "Blood",
  volume   =  121,
  number   =  19,
  pages    = "3838--42, S1--15",
  month    =  mar,
  year     =  2013,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Morrison2008-qy,
  title    = "Anterior definitive endoderm from {ESCs} reveals a role for {FGF}
              signaling",
  author   = "Morrison, Gillian M and Oikonomopoulou, Ifigenia and Migueles,
              Rosa Portero and Soneji, Shamit and Livigni, Alessandra and
              Enver, Tariq and Brickman, Joshua M",
  abstract = "The use of embryonic stem cell (ESC) differentiation to generate
              functional hepatic or pancreatic progenitors and as a tool for
              developmental biology is limited by an inability to isolate in
              vitro equivalents of regionally specified anterior definitive
              endoderm (ADE). To address this, we devised a strategy using a
              fluorescent reporter gene under the transcriptional control of
              the anterior endoderm marker Hex alongside the definitive
              mesendoderm marker Cxcr4. Isolation of Hex(+)Cxcr4(+)
              differentiating ESCs yielded a population expressing ADE markers
              that both can be expanded and is competent to undergo
              differentiation toward liver and pancreatic fates. Hex reporter
              ESCs were also used to define conditions for ADE specification in
              serum-free adherent culture and revealed an unexpected role for
              FGF signaling in the generation of ADE. Our findings in defined
              monolayer differentiation suggest FGF signaling is an important
              regulator of early anterior mesendoderm differentiation rather
              than merely a mediator of morphogenetic movement.",
  journal  = "Cell Stem Cell",
  volume   =  3,
  number   =  4,
  pages    = "402--415",
  month    =  oct,
  year     =  2008,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Komorowska2017-zt,
  title    = "Hepatic Leukemia Factor Maintains Quiescence of Hematopoietic
              Stem Cells and Protects the Stem Cell Pool during Regeneration",
  author   = "Komorowska, Karolina and Doyle, Alexander and Wahlestedt, Martin
              and Subramaniam, Agatheeswaran and Debnath, Shubhranshu and Chen,
              Jun and Soneji, Shamit and Van Handel, Ben and Mikkola, Hanna K A
              and Miharada, Kenichi and Bryder, David and Larsson, Jonas and
              Magnusson, Mattias",
  abstract = "The transcription factor hepatic leukemia factor (HLF) is
              strongly expressed in hematopoietic stem cells (HSCs) and is
              thought to influence both HSC self-renewal and leukemogenesis.
              However, the physiological role of HLF in hematopoiesis and HSC
              function is unclear. Here, we report that mice lacking Hlf are
              viable with essentially normal hematopoietic parameters,
              including an intact HSC pool during steady-state hematopoiesis.
              In contrast, when challenged through transplantation,
              Hlf-deficient HSCs showed an impaired ability to reconstitute
              hematopoiesis and became gradually exhausted upon serial
              transplantation. Transcriptional profiling of Hlf-deficient HSCs
              revealed changes associated with enhanced cellular activation,
              and cell-cycle analysis demonstrated a significant reduction of
              quiescent HSCs. Accordingly, toxic insults targeting dividing
              cells completely eradicated the HSC pool in Hlf-deficient mice.
              In summary, our findings point to HLF as a critical regulator of
              HSC quiescence and as an essential factor for maintaining the HSC
              pool during regeneration.",
  journal  = "Cell Rep.",
  volume   =  21,
  number   =  12,
  pages    = "3514--3523",
  month    =  dec,
  year     =  2017,
  address  = "United States",
  keywords = "5FU; HLF; HSC; cell cycle; quiescence; reconstitution;
              self-renewal; stress; transcription factor;
              transplantation;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sjogren2015-wh,
  title    = "Glucocorticoids improve erythroid progenitor maintenance and
              dampen Trp53 response in a mouse model of {Diamond-Blackfan}
              anaemia",
  author   = "Sj{\"o}gren, Sara E and Siva, Kavitha and Soneji, Shamit and
              George, Amee J and Winkler, Marcus and Jaako, Pekka and
              Wlodarski, Marcin and Karlsson, Stefan and Hannan, Ross D and
              Flygare, Johan",
  abstract = "Diamond-Blackfan anaemia (DBA) is a rare congenital disease
              causing severe anaemia and progressive bone marrow failure. The
              majority of patients carry mutations in ribosomal proteins, which
              leads to depletion of erythroid progenitors in the bone marrow.
              As many as 40\% of all DBA patients receive glucocorticoids to
              alleviate their anaemia. However, despite their use in DBA
              treatment for more than half a century, the therapeutic
              mechanisms of glucocorticoids remain largely unknown. Therefore
              we sought to study disease specific effects of glucocorticoid
              treatment using a ribosomal protein s19 (Rps19) deficient mouse
              model of DBA. This study determines for the first time that a
              mouse model of DBA can respond to glucocorticoid treatment,
              similar to DBA patients. Our results demonstrate that
              glucocorticoid treatment reduces apoptosis, rescues erythroid
              progenitor depletion and premature differentiation of erythroid
              cells. Furthermore, glucocorticoids prevent Trp53 activation in
              Rps19-deficient cells- in a disease-specific manner. Dissecting
              the therapeutic mechanisms behind glucocorticoid treatment of DBA
              provides indispensible insight into DBA pathogenesis. Identifying
              mechanisms important for DBA treatment also enables development
              of more disease-specific treatments of DBA.",
  journal  = "Br. J. Haematol.",
  volume   =  171,
  number   =  4,
  pages    = "517--529",
  month    =  aug,
  year     =  2015,
  address  = "England",
  keywords = "Diamond-Blackfan anaemia; Trp53; erythroid differentiation;
              erythroid progenitor; glucocorticoid
              therapy;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Gokhale2015-du,
  title    = "Culture adaptation alters transcriptional hierarchies among
              single human embryonic stem cells reflecting altered patterns of
              differentiation",
  author   = "Gokhale, Paul J and Au-Young, Janice K and Dadi, Srividya and
              Keys, David N and Harrison, Neil J and Jones, Mark and Soneji,
              Shamit and Enver, Tariq and Sherlock, Jon K and Andrews, Peter W",
  abstract = "We have used single cell transcriptome analysis to re-examine the
              substates of early passage, karyotypically Normal, and late
              passage, karyotypically Abnormal ('Culture Adapted') human
              embryonic stem cells characterized by differential expression of
              the cell surface marker antigen, SSEA3. The results confirmed
              that culture adaptation is associated with alterations to the
              dynamics of the SSEA3(+) and SSEA3(-) substates of these cells,
              with SSEA3(-) Adapted cells remaining within the stem cell
              compartment whereas the SSEA3(-) Normal cells appear to have
              differentiated. However, the single cell data reveal that these
              substates are characterized by further heterogeneity that changes
              on culture adaptation. Notably the Adapted population includes
              cells with a transcriptome substate suggestive of a shift to a
              more na{\"\i}ve-like phenotype in contrast to the cells of the
              Normal population. Further, a subset of the Normal SSEA3(+) cells
              expresses genes typical of endoderm differentiation, despite also
              expressing the undifferentiated stem cell genes, POU5F1 (OCT4)
              and NANOG, whereas such apparently lineage-primed cells are
              absent from the Adapted population. These results suggest that
              the selective growth advantage gained by genetically variant,
              culture adapted human embryonic stem cells may derive in part
              from a changed substate structure that influences their
              propensity for differentiation.",
  journal  = "PLoS One",
  volume   =  10,
  number   =  4,
  pages    = "e0123467",
  month    =  apr,
  year     =  2015,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{May2013-bu,
  title    = "Dynamic analysis of gene expression and genome-wide transcription
              factor binding during lineage specification of multipotent
              progenitors",
  author   = "May, Gillian and Soneji, Shamit and Tipping, Alex J and Teles,
              Jose and McGowan, Simon J and Wu, Mengchu and Guo, Yanping and
              Fugazza, Cristina and Brown, John and Karlsson, G{\"o}ran and
              Pina, Cristina and Olariu, Victor and Taylor, Stephen and Tenen,
              Daniel G and Peterson, Carsten and Enver, Tariq",
  abstract = "We used the paradigmatic GATA-PU.1 axis to explore, at the
              systems level, dynamic relationships between transcription factor
              (TF) binding and global gene expression programs as multipotent
              cells differentiate. We combined global ChIP-seq of GATA1, GATA2,
              and PU.1 with expression profiling during differentiation to
              erythroid and neutrophil lineages. Our analysis reveals (1)
              differential complexity of sequence motifs bound by GATA1, GATA2,
              and PU.1; (2) the scope and interplay of GATA1 and GATA2 programs
              within, and during transitions between, different cell
              compartments, and the extent of their hard-wiring by DNA motifs;
              (3) the potential to predict gene expression trajectories based
              on global associations between TF-binding data and target gene
              expression; and (4) how dynamic modeling of DNA-binding and gene
              expression data can be used to infer regulatory logic of TF
              circuitry. This rubric exemplifies the utility of this
              cross-platform resource for deconvoluting the complexity of
              transcriptional programs controlling stem/progenitor cell fate in
              hematopoiesis.",
  journal  = "Cell Stem Cell",
  volume   =  13,
  number   =  6,
  pages    = "754--768",
  month    =  oct,
  year     =  2013,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Rundberg_Nilsson2016-xx,
  title    = "Human and Murine Hematopoietic Stem Cell Aging Is Associated with
              Functional Impairments and Intrinsic {Megakaryocytic/Erythroid}
              Bias",
  author   = "Rundberg Nilsson, Alexandra and Soneji, Shamit and Adolfsson,
              Sofia and Bryder, David and Pronk, Cornelis Jan",
  abstract = "Aging within the human hematopoietic system associates with
              various deficiencies and disease states, including anemia,
              myeloid neoplasms and reduced adaptive immune responses. Similar
              phenotypes are observed in mice and have been linked to
              alterations arising at the hematopoietic stem cell (HSC) level.
              Such an association is, however, less established in human
              hematopoiesis and prompted us here to detail characteristics of
              the most primitive human hematopoietic compartments throughout
              ontogeny. In addition, we also attempted to interrogate
              similarities between aging human and murine hematopoiesis.
              Coupled to the transition from human cord blood (CB) to young and
              aged bone marrow (BM), we observed a gradual increase in
              frequency of candidate HSCs. This was accompanied by functional
              impairments, including decreased lymphoid output and reduced
              proliferative potential. Downstream of human HSCs, we observed
              decreasing levels of common lymphoid progenitors (CLPs), and
              increasing frequencies of megakaryocyte/erythrocyte progenitors
              (MEPs) with age, which could be linked to changes in
              lineage-affiliated gene expression patterns in aged human HSCs.
              These findings were paralleled in mice. Therefore, our data
              support the notion that age-related changes also in human
              hematopoiesis involve the HSC pool, with a prominent skewing
              towards the megakaryocytic/erythroid lineages, and suggests
              conserved mechanisms underlying aging of the blood cell system.",
  journal  = "PLoS One",
  volume   =  11,
  number   =  7,
  pages    = "e0158369",
  month    =  jul,
  year     =  2016,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Ghazanfari2017-xu,
  title    = "Human Primary Bone Marrow Mesenchymal Stromal Cells and Their in
              vitro Progenies Display Distinct Transcriptional Profile
              Signatures",
  author   = "Ghazanfari, Roshanak and Zacharaki, Dimitra and Li, Hongzhe and
              Ching Lim, Hooi and Soneji, Shamit and Scheding, Stefan",
  abstract = "Bone marrow mesenchymal stromal cells (BM-MSCs) are a rare
              population of cells that gives rise to skeletal tissues and the
              hematopoietic stroma in vivo. Recently, we have demonstrated that
              BM-MSCs fulfill stringent in vivo stem cell criteria when
              propagated as non-adherent mesenspheres but not as
              adherent-cultured cells. Motivated by these profound functional
              differences, the current study aimed to identify potential
              important MSC regulators by investigating global gene expression
              profiles of adherent and non-adherent culture-derived BM-MSCs in
              comparison with primary BM-MSCs. A substantial number of genes
              were differentially expressed between primary and
              culture-expanded cells already early upon culture, and numerous
              genes were found to be different when comparing adherent and
              non-adherent BM-MSCs. Cluster analysis identified 16 sets of
              genes of which two displayed comparable gene expression levels in
              primary and non-adherent cultured cells, but not in adherent
              cultured cells. This pattern suggested that these clusters
              contained candidate regulators of BM-MSCs. Gene expression
              differences were confirmed for selected genes and BM-MSC
              transcription factors by protein analysis and RT-PCR,
              respectively. Taken together, these data demonstrated profound
              gene expression changes upon culture of primary BM-MSCs.
              Moreover, gene cluster differences provide the basis to uncover
              the regulatory mechanisms that control primary and cultured
              BM-MSCs.",
  journal  = "Sci. Rep.",
  volume   =  7,
  number   =  1,
  pages    = "10338",
  month    =  sep,
  year     =  2017,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Jensen2016-jt,
  title    = "Identification of {Stage-Specific} Surface Markers in Early {B}
              Cell Development Provides Novel Tools for Identification of
              Progenitor Populations",
  author   = "Jensen, Christina T and Lang, Stefan and Somasundaram, Rajesh and
              Soneji, Shamit and Sigvardsson, Mikael",
  abstract = "Whereas the characterization of B lymphoid progenitors has been
              facilitated by the identification of lineage- and stage-specific
              surface markers, the continued identification of differentially
              expressed proteins increases our capacity to explore normal and
              malignant B cell development. To identify novel surface markers
              with stage-specific expression patterns, we explored the
              reactivity of CD19(+) B cell progenitor cells to Abs targeted to
              176 surface proteins. Markers with stage-specific expression were
              identified using a transgenic reporter gene system subdividing
              the B cell progenitors into four surface IgM(-) stages. This
              approach affirmed the utility of known stage-specific markers, as
              well as identifying additional proteins that selectively marked
              defined stages of B cell development. Among the stage-specific
              markers were the cell adhesion proteins CD49E, CD11A, and CD54
              that are highly expressed selectively on the most immature
              progenitors. This work identifies a set of novel stage-specific
              surface markers that can be used as a complement to the classical
              staining protocols to explore B lymphocyte development.",
  journal  = "J. Immunol.",
  volume   =  197,
  number   =  5,
  pages    = "1937--1944",
  month    =  jul,
  year     =  2016,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Wernisch2003-bb,
  title    = "Analysis of whole-genome microarray replicates using mixed models",
  author   = "Wernisch, Lorenz and Kendall, Sharon L and Soneji, Shamit and
              Wietzorrek, Andreas and Parish, Tanya and Hinds, Jason and
              Butcher, Philip D and Stoker, Neil G",
  abstract = "MOTIVATION: Microarray experiments are inherently noisy.
              Replication is the key to estimating realistic fold-changes
              despite such noise. In the analysis of the various sources of
              noise the dependency structure of the replication needs to be
              taken into account. RESULTS: We analyzed replicate data sets from
              a Mycobacterium tuberculosis trcS mutant in order to identify
              differentially expressed genes and suggest new methods for
              filtering and normalizing raw array data and for imputing missing
              values. Mixed ANOVA models are applied to quantify the various
              sources of error. Such analysis also allows us to determine the
              optimal number of samples and arrays. Significance values for
              differential expression are obtained by a hierarchical
              bootstrapping scheme on scaled residuals. Four highly upregulated
              genes, including bfrB, were analyzed further. We observed an
              artefact, where transcriptional readthrough from these genes led
              to apparent upregulation of adjacent genes. AVAILABILITY: All
              methods and data discussed are available in the package
              YASMAhttp://www.cryst.bbk.ac.uk/wernisch/yasma.html for the
              statistical data analysis system R (http://www.R-project.org).",
  journal  = "Bioinformatics",
  volume   =  19,
  number   =  1,
  pages    = "53--61",
  month    =  jan,
  year     =  2003,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Kristiansen2016-wf,
  title    = "Cellular Barcoding Links B-1a {B} Cell Potential to a Fetal
              Hematopoietic Stem Cell State at the {Single-Cell} Level",
  author   = "Kristiansen, Trine A and Jaensson Gyllenb{\"a}ck, Elin and
              Zriwil, Alya and Bj{\"o}rklund, Tomas and Daniel, Jeremy A and
              Sitnicka, Ewa and Soneji, Shamit and Bryder, David and Yuan, Joan",
  abstract = "Hematopoietic stem cells (HSCs) undergo a functional switch in
              neonatal mice hallmarked by a decrease in self-renewing divisions
              and entry into quiescence. Here, we investigated whether the
              developmental attenuation of B-1a cell output is a consequence of
              a shift in stem cell state during ontogeny. Using cellular
              barcoding for in vivo single-cell fate analyses, we found that
              fetal liver definitive HSCs gave rise to both B-1a and B-2 cells.
              Whereas B-1a potential diminished in all HSCs with time, B-2
              output was maintained. B-1a and B-2 plasticity could be
              reinitiated in a subset of adult HSCs by ectopic expression of
              the RNA binding protein LIN28B, a key regulator of fetal
              hematopoiesis, and this coincided with the clonal reversal to
              fetal-like elevated self-renewal and repopulation potential.
              These results anchor the attenuation of B-1a cell output to fetal
              HSC behavior and demonstrate that the developmental decline in
              regenerative potential represents a reversible HSC state.",
  journal  = "Immunity",
  volume   =  45,
  number   =  2,
  pages    = "346--357",
  month    =  aug,
  year     =  2016,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Kassouf2010-ms,
  title    = "Genome-wide identification of {TAL1's} functional targets:
              insights into its mechanisms of action in primary erythroid cells",
  author   = "Kassouf, Mira T and Hughes, Jim R and Taylor, Stephen and
              McGowan, Simon J and Soneji, Shamit and Green, Angela L and Vyas,
              Paresh and Porcher, Catherine",
  abstract = "Coordination of cellular processes through the establishment of
              tissue-specific gene expression programs is essential for lineage
              maturation. The basic helix-loop-helix hemopoietic
              transcriptional regulator TAL1 (formerly SCL) is required for
              terminal differentiation of red blood cells. To gain insight into
              TAL1 function and mechanisms of action in erythropoiesis, we
              performed ChIP-sequencing and gene expression analyses from
              primary fetal liver erythroid cells. We show that TAL1
              coordinates expression of genes in most known red cell-specific
              processes. The majority of TAL1's genomic targets require direct
              DNA-binding activity. However, one-fifth of TAL1's target
              sequences, mainly among those showing high affinity for TAL1, can
              recruit the factor independently of its DNA binding activity. An
              unbiased DNA motif search of sequences bound by TAL1 identified
              CAGNTG as TAL1-preferred E-box motif in erythroid cells. Novel
              motifs were also characterized that may help distinguish
              activated from repressed genes and suggest a new mechanism by
              which TAL1 may be recruited to DNA. Finally, analysis of
              recruitment of GATA1, a protein partner of TAL1, to sequences
              occupied by TAL1 suggests that TAL1's binding is necessary prior
              or simultaneous to that of GATA1. This work provides the
              framework to study regulatory networks leading to erythroid
              terminal maturation and to model mechanisms of action of
              tissue-specific transcription factors.",
  journal  = "Genome Res.",
  volume   =  20,
  number   =  8,
  pages    = "1064--1083",
  month    =  jun,
  year     =  2010,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Halvarsson2019-aw,
  title    = "Putative Role of Nuclear {Factor-Kappa} {B} But Not
              {Hypoxia-Inducible} {Factor-1$\alpha$} in {Hypoxia-Dependent}
              Regulation of Oxidative Stress in Hematopoietic Stem and
              Progenitor Cells",
  author   = "Halvarsson, Camilla and R{\"o}rby, Emma and Eliasson, Pernilla
              and Lang, Stefan and Soneji, Shamit and J{\"o}nsson, Jan-Ingvar",
  abstract = "Aims: Adaptation to low oxygen of hematopoietic stem cells (HSCs)
              in the bone marrow has been demonstrated to depend on the
              activation of hypoxia-inducible factor (HIF)-1$\alpha$ as well as
              the limited production of reactive oxygen species (ROS). In this
              study, we aimed at determining whether HIF-1$\alpha$ is involved
              in protecting HSCs from ROS. Results: Oxidative stress was
              induced by DL-buthionine-(S,R)-sulfoximine (BSO)-treatment, which
              increases the mitochondrial ROS level. Hypoxia rescued
              Lineage-Sca-1(+)c-kit(+) (LSK) cells from BSO-induced apoptosis,
              whereas cells succumbed to apoptosis in normoxia. Apoptosis in
              normoxia was inhibited with the antioxidant N-acetyl-L-cysteine
              or by overexpression of anti-apoptotic BCL-2. Moreover,
              stabilized expression of oxygen-insensitive HIFs could not
              protect LSK cells from oxidative stress-induced apoptosis at
              normoxia, neither could short hairpin RNA to Hif-1$\alpha$
              inhibit the protective effects by hypoxia in LSK cells. Likewise,
              BSO treatment of LSK cells from Hif-1$\alpha$ knockout mice did
              not suppress the effects seen in hypoxia. Microarray analysis
              identified the nuclear factor-kappa B (NF-$\kappa$B) pathway as a
              pathway induced by hypoxia. By using NF-$\kappa$B lentiviral
              construct and DNA-binding assay, we found increased NF-$\kappa$B
              activity in cells cultured in hypoxia compared with normoxia.
              Using an inhibitor against NF-$\kappa$B activation, we could
              confirm the involvement of NF-$\kappa$B signaling as BSO-mediated
              cell death was significantly increased in hypoxia after adding
              the inhibitor. Innovation: HIF-1$\alpha$ is not involved in
              protecting HSCs and progenitors to elevated levels of ROS on
              glutathione depletion during hypoxic conditions. Conclusion: The
              study proposes a putative role of NF-$\kappa$B signaling as a
              hypoxia-induced regulator in early hematopoietic cells.",
  journal  = "Antioxid. Redox Signal.",
  volume   =  31,
  number   =  3,
  pages    = "211--226",
  month    =  apr,
  year     =  2019,
  address  = "United States",
  keywords = "NF-$\kappa$B; glutathione; hematopoiesis; hypoxia; mitochondria;
              oxidative stress;SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Rosario2010-qv,
  title    = "Safety and immunogenicity of novel recombinant {BCG} and modified
              vaccinia virus Ankara vaccines in neonate rhesus macaques",
  author   = "Rosario, Maximillian and Fulkerson, John and Soneji, Shamit and
              Parker, Joe and Im, Eung-Jun and Borthwick, Nicola and Bridgeman,
              Anne and Bourne, Charles and Joseph, Joan and Sadoff, Jerald C
              and Hanke, Tom{\'a}s",
  abstract = "Although major inroads into making antiretroviral therapy
              available in resource-poor countries have been made, there is an
              urgent need for an effective vaccine administered shortly after
              birth, which would protect infants from acquiring human
              immunodeficiency virus type 1 (HIV-1) through breast-feeding.
              Bacillus Calmette-Gu{\'e}rin (BCG) is given to most infants at
              birth, and its recombinant form could be used to prime
              HIV-1-specific responses for a later boost by heterologous
              vectors delivering the same HIV-1-derived immunogen. Here, two
              groups of neonate Indian rhesus macaques were immunized with
              either novel candidate vaccine BCG.HIVA(401) or its parental
              strain AERAS-401, followed by two doses of recombinant modified
              vaccinia virus Ankara MVA.HIVA. The HIVA immunogen is derived
              from African clade A HIV-1. All vaccines were safe, giving local
              reactions consistent with the expected response at the injection
              site. No systemic adverse events or gross abnormality was seen at
              necropsy. Both AERAS-401 and BCG.HIVA(401) induced high
              frequencies of BCG-specific IFN-gamma-secreting lymphocytes that
              declined over 23 weeks, but the latter failed to induce
              detectable HIV-1-specific IFN-gamma responses. MVA.HIVA elicited
              HIV-1-specific IFN-gamma responses in all eight animals, but,
              except for one animal, these responses were weak. The
              HIV-1-specific responses induced in infants were lower compared
              to historic data generated by the two HIVA vaccines in adult
              animals but similar to other recombinant poxviruses tested in
              this model. This is the first time these vaccines were tested in
              newborn monkeys. These results inform further infant vaccine
              development and provide comparative data for two human infant
              vaccine trials of MVA.HIVA.",
  journal  = "J. Virol.",
  volume   =  84,
  number   =  15,
  pages    = "7815--7821",
  month    =  may,
  year     =  2010,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Mansson2007-ik,
  title    = "Molecular evidence for hierarchical transcriptional lineage
              priming in fetal and adult stem cells and multipotent progenitors",
  author   = "M{\aa}nsson, Robert and Hultquist, Anne and Luc, Sidinh and Yang,
              Liping and Anderson, Kristina and Kharazi, Shabnam and Al-Hashmi,
              Suleiman and Liuba, Karina and Thor{\'e}n, Lina and Adolfsson,
              J{\"o}rgen and Buza-Vidas, Natalija and Qian, Hong and Soneji,
              Shamit and Enver, Tariq and Sigvardsson, Mikael and Jacobsen,
              Sten Eirik W",
  abstract = "Recent studies implicated the existence of adult lymphoid-primed
              multipotent progenitors (LMPPs) with little or no
              megakaryocyte-erythroid potential, questioning common myeloid and
              lymphoid progenitors as obligate intermediates in hematopoietic
              stem cell (HSC) lineage commitment. However, the existence of
              LMPPs remains contentious. Herein, global and single-cell
              analyses revealed a hierarchical organization of transcriptional
              lineage programs, with downregulation of megakaryocyte-erythroid
              genes from HSCs to LMPPs, sustained granulocyte-monocyte priming,
              and upregulation of common lymphoid (but not B and T
              cell-specific) genes. These biological and molecular
              relationships, implicating almost mutual exclusion of
              megakaryocyte-erythroid and lymphoid pathways, are established
              already in fetal hematopoiesis, as evidenced by existence of
              LMPPs in fetal liver. The identification of LMPPs and
              hierarchically ordered transcriptional activation and
              downregulation of distinct lineage programs is compatible with a
              model for HSC lineage commitment in which the probability for
              undergoing different lineage commitment fates changes gradually
              when progressing from HSCs to LMPPs.",
  journal  = "Immunity",
  volume   =  26,
  number   =  4,
  pages    = "407--419",
  month    =  apr,
  year     =  2007,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sternberg2005-ye,
  title    = "Evidence for reduced B-cell progenitors in early (low-risk)
              myelodysplastic syndrome",
  author   = "Sternberg, Alexander and Killick, Sally and Littlewood, Tim and
              Hatton, Chris and Peniket, Andy and Seidl, Thomas and Soneji,
              Shamit and Leach, Joanne and Bowen, David and Chapman, Claire and
              Standen, Graham and Massey, Edwin and Robinson, Lisa and Vadher,
              Bipin and Kaczmarski, Richard and Janmohammed, Riaz and Clipsham,
              Kim and Carr, Andrew and Vyas, Paresh",
  abstract = "Early, low-risk International Prognostic Scoring System (IPSS)
              myelodysplastic syndrome (MDS) is a heterogeneous disorder where
              the molecular and cellular hematopoietic defects are poorly
              understood. To gain insight into this condition, we analyzed gene
              expression profiles of marrow CD34+ progenitor cells from
              normal-karyotype, low-blast-count MDS patients, age-matched
              controls, and patients with non-MDS anemia. Given the
              heterogeneity of early MDS, a surprisingly consistent finding was
              decreased expression of B-cell lineage-affiliated genes in MDS
              patients compared with healthy controls and 3 of 5 samples with
              non-MDS anemia. Both patients with non-MDS anemia with reduced
              B-cell gene expression were on chemotherapy. In 25 of 27 of the
              original samples and 9 further MDS samples, Taqman real-time
              polymerase chain reaction (PCR) confirmed these data. Flow
              cytometry on unfractionated marrow from independent samples also
              demonstrated reduced B-cell progenitors in MDS patients compared
              with healthy controls. These novel findings suggest a common
              perturbation in early MDS hematopoiesis. They also provide the
              rationale for a larger study to evaluate the diagnostic utility
              of reduced B-cell progenitor number as a diagnostic biomarker of
              early low-risk MDS, which can pose a diagnostic challenge.",
  journal  = "Blood",
  volume   =  106,
  number   =  9,
  pages    = "2982--2991",
  month    =  aug,
  year     =  2005,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Enver2005-nj,
  title    = "Cellular differentiation hierarchies in normal and
              culture-adapted human embryonic stem cells",
  author   = "Enver, Tariq and Soneji, Shamit and Joshi, Chirag and Brown, John
              and Iborra, Francisco and Orntoft, Torben and Thykjaer, Thomas
              and Maltby, Edna and Smith, Kath and Abu Dawud, Raed and Jones,
              Mark and Matin, Maryam and Gokhale, Paul and Draper, Jonathan and
              Andrews, Peter W",
  abstract = "Human embryonic stem cell (HESC) lines vary in their
              characteristics and behaviour not only because they are derived
              from genetically outbred populations, but also because they may
              undergo progressive adaptation upon long-term culture in vitro.
              Such adaptation may reflect selection of variants with altered
              propensity for survival and retention of an undifferentiated
              phenotype. Elucidating the mechanisms involved will be important
              for understanding normal self-renewal and commitment to
              differentiation and for validating the safety of HESC-based
              therapy. We have investigated this process of adaptation at the
              cellular and molecular levels through a comparison of early
              passage (normal) and late passage (adapted) sublines of a single
              HESC line, H7. To account for spontaneous differentiation that
              occurs in HESC cultures, we sorted cells for SSEA3, which marks
              undifferentiated HESC. We show that the gene expression
              programmes of the adapted cells partially reflected their
              aberrant karyotype, but also resulted from a failure in
              X-inactivation, emphasizing the importance in adaptation of
              karyotypically silent epigenetic changes. On the basis of growth
              potential, ability to re-initiate ES cultures and global
              transcription profiles, we propose a cellular differentiation
              hierarchy for maintenance cultures of HESC: normal SSEA3+ cells
              represent pluripotent stem cells. Normal SSEA3- cells have exited
              this compartment, but retain multilineage differentiation
              potential. However, adapted SSEA3+ and SSEA3- cells co-segregate
              within the stem cell territory, implying that adaptation reflects
              an alteration in the balance between self-renewal and
              differentiation. As this balance is also an essential feature of
              cancer, the mechanisms of culture adaptation may mirror those of
              oncogenesis and tumour progression.",
  journal  = "Hum. Mol. Genet.",
  volume   =  14,
  number   =  21,
  pages    = "3129--3140",
  month    =  sep,
  year     =  2005,
  address  = "England",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Lawrie2007-lr,
  title    = "{MicroRNA} expression distinguishes between germinal center {B}
              cell-like and activated {B} cell-like subtypes of diffuse large
              {B} cell lymphoma",
  author   = "Lawrie, Charles H and Soneji, Shamit and Marafioti, Teresa and
              Cooper, Christopher D O and Palazzo, Stefano and Paterson,
              Jennifer C and Cattan, Helen and Enver, Tariq and Mager, Rachel
              and Boultwood, Jacqueline and Wainscoat, James S and Hatton,
              Christian S R",
  abstract = "Diffuse large B cell lymphoma (DLBCL) is an aggressive malignancy
              that accounts for nearly 40\% of all lymphoid tumors. This
              heterogeneous disease can be divided into germinal center B
              cell-like (GCB) and activated B cell-like (ABC) subtypes by gene
              expression and immunohistochemical profiling. Using microarray
              analysis on prototypic cell lines, we identified microRNAs
              (miR-155, miR-21 and miR-221) that were more highly expressed in
              ABC-type than GCB-type cell lines. These microRNAs were
              over-expressed in de novo DLBCL (n = 35), transformed DLBCL (n =
              14) and follicular center lymphoma cases (n = 27) compared to
              normal B cells. Consistent with the cell line model, expression
              levels were higher in DLBCL cases with an ABC-type
              immunophenotype than those that were GCB-type (p < 0.05).
              Moreover, using multivariate analysis we found that expression of
              miR-21 was an independent prognostic indicator in de novo DLBCL
              (p < 0.05). Interestingly, expression levels of both miR-155 and
              miR-21 were also higher in nonmalignant ABC than in GCB cells. As
              we also demonstrate that expression of microRNAs can be measured
              reliably from routine paraffin-embedded biopsies of more than
              8-years-old (p < 0.001), we suggest that microRNAs could be
              clinically useful molecular markers for DLBCL as well as other
              cancers.",
  journal  = "Int. J. Cancer",
  volume   =  121,
  number   =  5,
  pages    = "1156--1161",
  month    =  sep,
  year     =  2007,
  address  = "United States",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Hampshire2004-id,
  title    = "Stationary phase gene expression of Mycobacterium tuberculosis
              following a progressive nutrient depletion: a model for
              persistent organisms?",
  author   = "Hampshire, Tobias and Soneji, Shamit and Bacon, Joanna and James,
              Brian W and Hinds, Jason and Laing, Ken and Stabler, Richard A
              and Marsh, Philip D and Butcher, Philip D",
  abstract = "The majority of individuals infected with TB develop a latent
              infection, in which organisms survive within the body while
              evading the host immune system. Such persistent bacilli are
              capable of surviving several months of combinatorial antibiotic
              treatment. Evidence suggests that stationary phase bacteria adapt
              to increase their tolerance to environmental stresses. We have
              developed a unique in vitro model of dormancy based on the
              characterization of a single, large volume fermenter culture of
              M. tuberculosis, as it adapts to stationary phase. Cells are
              maintained in controlled and defined aerobic conditions (50\%
              dissolved oxygen tension), using probes that measure dissolved
              oxygen tension, temperature, and pH. Microarray analysis has been
              used in conjunction with viability and nutrient depletion assays
              to dissect differential gene expression. Following exponential
              phase growth the gradual depletion of glucose/glycerol resulted
              in a small population of survivors that were characterized for
              periods in excess of 100 days. Bacilli adapting to nutrient
              depletion displayed characteristics associated with persistence
              in vivo, including entry into a non-replicative state and the
              up-regulation of genes involved in beta-oxidation of fatty acids
              and virulence. A reduced population of non-replicating bacilli
              went on to adapt sufficiently to re-initiate cellular division.",
  journal  = "Tuberculosis",
  volume   =  84,
  number   = "3-4",
  pages    = "228--238",
  year     =  2004,
  address  = "Scotland",
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Bhatia2012-oo,
  title    = "Nonadherence to oral mercaptopurine and risk of relapse in
              Hispanic and non-Hispanic white children with acute lymphoblastic
              leukemia: a report from the children's oncology group",
  author   = "Bhatia, Smita and Landier, Wendy and Shangguan, Muyun and
              Hageman, Lindsey and Schaible, Alexandra N and Carter, Andrea R
              and Hanby, Cara L and Leisenring, Wendy and Yasui, Yutaka and
              Kornegay, Nancy M and Mascarenhas, Leo and Ritchey, A Kim and
              Casillas, Jacqueline N and Dickens, David S and Meza, Jane and
              Carroll, William L and Relling, Mary V and Wong, F Lennie",
  abstract = "PURPOSE: Systemic exposure to mercaptopurine (MP) is critical for
              durable remissions in children with acute lymphoblastic leukemia
              (ALL). Nonadherence to oral MP could increase relapse risk and
              also contribute to inferior outcome in Hispanics. This study
              identified determinants of adherence and described impact of
              adherence on relapse, both overall and by ethnicity. PATIENTS AND
              METHODS: A total of 327 children with ALL (169 Hispanic; 158
              non-Hispanic white) participated. Medication event-monitoring
              system caps recorded date and time of MP bottle openings.
              Adherence rate, calculated monthly, was defined as ratio of days
              of MP bottle opening to days when MP was prescribed. RESULTS:
              After 53,394 person-days of monitoring, adherence declined from
              94.7\% (month 1) to 90.2\% (month 6; P < .001). Mean adherence
              over 6 months was significantly lower among Hispanics (88.4\% v
              94.8\%; P < .001), patients age $\geq$ 12 years (85.8\% v 93.1\%;
              P < .001), and patients from single-mother households (80.6\% v
              93.1\%; P = .001). A progressive increase in relapse was observed
              with decreasing adherence (reference: adherence $\geq$ 95\%;
              94.9\% to 90\%: hazard ratio [HR], 4.1; 95\% CI,1.2 to 13.5; P =
              .02; 89.9\% to 85\%: HR, 4.0; 95\% CI, 1.0 to 15.5; P = .04; <
              85\%: HR. 5.7; 95\% CI, 1.9 to 16.8; P = .002). Cumulative
              incidence of relapse ($\pm$ standard deviation) was higher among
              Hispanics (16.5\% $\pm$ 4.0\% v 6.3\% $\pm$ 2.2\%; P = .02).
              Association between Hispanic ethnicity and relapse (HR, 2.6; 95\%
              CI, 1.1 to 6.1; P = .02) became nonsignificant (HR, 1.8; 95\% CI,
              0.6 to 5.2; P = .26) after adjusting for adherence and
              socioeconomic status. At adherence rates $\geq$ 90\%, Hispanics
              continued to demonstrate higher relapse, whereas at rates < 90\%,
              relapse risk was comparable to that of non-Hispanic whites.
              CONCLUSION: Lower adherence to oral MP increases relapse risk.
              Ethnic difference in relapse risk differs by level of
              adherence-an observation currently under investigation.",
  journal  = "J. Clin. Oncol.",
  volume   =  30,
  number   =  17,
  pages    = "2094--2101",
  month    =  jun,
  year     =  2012,
  language = "en"
}

@ARTICLE{Gold2006-yb,
  title    = "Approaches to patient education: emphasizing the long-term value
              of compliance and persistence",
  author   = "Gold, Deborah T and McClung, Betsy",
  abstract = "Approximately 50\% of patients with chronic disease do not obtain
              optimal clinical benefit from treatment because of poor
              compliance with medication regimens. Lack of compliance is
              associated with poor clinical outcomes, increased
              hospitalizations, lower quality of life, and higher overall
              healthcare costs. Although poor compliance and persistence are
              common across many disease states, they may be particularly poor
              in treatment for asymptomatic chronic diseases such as
              osteoporosis. Patient education has been demonstrated to
              significantly improve compliance with medication across a broad
              range of conditions and disease severities. In a study in which
              patients received educational materials, referral for bone
              densitometry, and physician consultation, 67\% were compliant
              with treatment after 6 months. Patient satisfaction with
              treatment has been linked to compliance with therapy; by
              improving patient care through fulfilling expectations for
              physician visits and providing frequent feedback, the healthcare
              provider can dramatically improve compliance. Self-management
              programs focusing on day-to-day management of chronic diseases
              have been shown to significantly improve heath behaviors and
              health status. Regardless of the strategy used, attention must be
              directed to identifying the patients least likely to persist with
              treatment and to providing the education and support these
              patients need to adhere to osteoporosis therapy.",
  journal  = "Am. J. Med.",
  volume   =  119,
  number   = "4 Suppl 1",
  pages    = "S32--7",
  month    =  apr,
  year     =  2006,
  language = "en"
}

@ARTICLE{Zeng2023-pd,
  title    = "Adherence to Oral Chemotherapy in Acute Lymphoblastic Leukemia
              during Maintenance Therapy in Children, Adolescents, and Young
              Adults: A Systematic Review",
  author   = "Zeng, Xiaopei L and Heneghan, Mallorie B and Badawy, Sherif M",
  abstract = "Acute lymphoblastic leukemia (ALL) is the most common malignancy
              in children and young adults. Treatment is long and involves 2-3
              years of a prolonged maintenance phase composed of oral
              chemotherapies. Adherence to these medications is critical to
              achieving good outcomes. However, adherence is difficult to
              determine, as there is currently no consensus on measures of
              adherence or criteria to determine nonadherence. Furthermore,
              there have been few studies in pediatric B-ALL describing factors
              associated with nonadherence. Thus, we performed a systematic
              review of literature on oral chemotherapy adherence during
              maintenance therapy in ALL following PRISMA guidelines. Published
              studies demonstrated various objective and subjective methods of
              assessing adherence without generalizable definitions of
              nonadherence. However, the results of these studies suggested
              that nonadherence to oral maintenance chemotherapy was associated
              with increased risk of relapse. Future studies of B-ALL therapy
              should utilize a uniform assessment of adherence and definitions
              of nonadherence to better determine the impact of nonadherence on
              B-ALL outcomes and identify predictors of nonadherence that could
              yield targets for adherence improving interventions.",
  journal  = "Curr. Oncol.",
  volume   =  30,
  number   =  1,
  pages    = "720--748",
  month    =  jan,
  year     =  2023,
  keywords = "ALL; AYA; acute lymphoblastic leukemia; adherence; adolescents;
              cancer; children; compliance; leukemia; lymphoblastic leukemia;
              oral chemotherapy; pediatric; young adults",
  language = "en"
}

@ARTICLE{Ridout2021-os,
  title    = "Effectiveness of Virtual Reality Interventions for Adolescent
              Patients in Hospital Settings: Systematic Review",
  author   = "Ridout, Brad and Kelson, Joshua and Campbell, Andrew and
              Steinbeck, Kate",
  abstract = "BACKGROUND: Given the high level of interest and increasing
              familiarity with virtual reality among adolescents, there is
              great potential to use virtual reality to address adolescents'
              unique health care delivery needs while in hospital. While there
              have been reviews on the use of virtual reality for specific
              health conditions and procedures, none to date have reviewed the
              full scope of virtual reality hospital interventions for
              adolescents who are often combined with children as a homogenous
              group, despite the fact that adolescents experience virtual
              environments different from children. OBJECTIVE: The aim of this
              review was to systematically identify available evidence
              regarding the use of virtual reality interventions for adolescent
              patients in hospital settings to evaluate effectiveness,
              suitability, and safety and identify opportunities for future
              research. METHODS: PubMed, PsycINFO, Medline, and Scopus
              databases were searched using keywords and phrases. Retrieved
              abstracts (n=1525) were double screened, yielding 276 articles
              for full-text screening. Of these, 8 articles met inclusion
              criteria. Data were extracted to a standardized coding sheet, and
              a narrative synthesis was performed due to the heterogeneity of
              the studies. RESULTS: Four RCTs and 4 single-case reports were
              identified for inclusion, all of which aimed to reduce pain or
              anxiety. The scenarios targeted were burn pain, venipuncture,
              chemotherapy, preoperative anxiety, and palliative care. Three
              out of 4 RCTs found significant reductions in pain or anxiety
              outcomes measures when using virtual reality compared to standard
              care or other distraction techniques; however, only 1 study
              combined self-reported experiences of pain or anxiety with any
              physiological measures. Single-case reports relied primarily upon
              qualitative feedback, with patients reporting reduced pain or
              anxiety and a preference for virtual reality to no virtual
              reality. CONCLUSIONS: Virtual reality can provide a safe and
              engaging way to reduce pain and anxiety in adolescents while in
              hospital, particularly when virtual reality software is highly
              immersive and specifically designed for therapeutic purposes. As
              VR becomes more accessible and affordable for use in hospitals,
              larger and more diverse studies that capitalize on adolescents'
              interest in and aptitude for virtual reality, and on the full
              range of capabilities of this emerging technology, are needed to
              build on these promising results. TRIAL REGISTRATION: PROSPERO
              International Prospective Register of Systematic Reviews
              CRD42020198760;
              https://www.crd.york.ac.uk/prospero/display\_record.php?ID=CRD42020198760.",
  journal  = "J. Med. Internet Res.",
  volume   =  23,
  number   =  6,
  pages    = "e24967",
  month    =  jun,
  year     =  2021,
  keywords = "adolescents; anxiety; hospital; pain; virtual reality",
  language = "en"
}

% The entry below contains non-ASCII chars that could not be converted
% to a LaTeX equivalent.
@ARTICLE{Vo2024-vc,
  title    = "A {TEMPORAL} {DEVELOPMENTAL} {MAP} {SEPARATES} {HUMAN} {NK}
              {CELLS} {FROM} {NON-CYTOTOXIC} {ILCS} {THROUGH} {CLONAL} {AND}
              {SINGLE-CELL} {ANALYSIS}",
  author   = "Vo, Dang Nghiem and Yuan, Ouyang and Kanaya, Minoru and
              Telliam-Dushime, Gladys and Li, Hongzhe and Kotova, Olga and
              Caglar, Emel and de Lichtenberg, Kristian Honnens and Rahman,
              Shamim Herbert and Soneji, Shamit and Scheding, Stefan and
              Bryder, David and Malmberg, Karl-Johan and Sitnicka, Ewa",
  abstract = "Natural Killer (NK) cells represent the cytotoxic member within
              the innate lymphoid cell (ILC) family that are important against
              viral infections and cancer. While the NK cell emergence from
              hematopoietic stem and progenitor cells through multiple
              intermediate stages and the underlying regulatory gene network
              has been extensively studied in mouse, this process is not well
              characterized in human. Here, using a temporal in vitro model to
              reconstruct the developmental trajectory of NK lineage, we
              identified an ILC-restricted oligo-potent Stage 3a
              CD34-CD117+CD161+CD45RA+CD56- progenitor population, that
              exclusively gave rise to CD56-expressing ILCs in vitro. We also
              further investigated a previously non-appreciated heterogeneity
              within the CD56+CD94-NKp44+ subset, phenotypically equivalent to
              Stage 3b population containing both group-1 ILC and RORt+ ILC3
              cells, that could be further separated based on their
              differential expression of DNAM-1 and CD161 receptors. We
              confirmed that DNAM-1hi S3b and CD161hiCD117hi ILC3 populations
              distinctively differed in their expression of effector molecules,
              cytokine secretion, and cytotoxic activity. Furthermore, analysis
              of lineage output using DNA-barcode tracing across these stages
              supported a close developmental relationship between S3b-NK and
              S4 (CD56+CD94+) cells, while distant to ILC3 subset.
              Cross-referencing gene signatures of culture derived NK cells and
              other non-cytotoxic ILCs with publicly available datasets
              validated that these in vitro stages highly resemble
              transcriptional profiles of respective in vivo ILC counterparts.
              Finally, by integrating RNA-velocity and gene-network analysis
              through SCENIC we unravel a network of coordinated and highly
              dynamic regulons driving the cytotoxic NK cell program, as a
              guide map for future studies on NK cell regulation.",
  journal  = "Blood Adv",
  month    =  mar,
  year     =  2024,
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Rydstrom2023-em,
  title    = "Functional and molecular profiling of hematopoietic stem cells
              during regeneration",
  author   = "Rydstr{\"o}m, Anna and Grahn, Tan H M and Niroula, Abhishek and
              Mansell, Els and van der Garde, Mark and Pertesi, Maroulio and
              Subramaniam, Agatheeswaran and Soneji, Shamit and Zubarev, Roman
              and Enver, Tariq and Nilsson, Bj{\"o}rn and Miharada, Kenichi and
              Larsson, Jonas and Karlsson, Stefan",
  abstract = "Hematopoietic stem cells (HSCs) enable hematopoietic stem cell
              transplantation (HCT) through their ability to replenish the
              entire blood system. Proliferation of HSCs is linked to decreased
              reconstitution potential, and a precise regulation of actively
              dividing HSCs is thus essential to ensure long-term
              functionality. This regulation becomes important in the
              transplantation setting where HSCs undergo proliferation followed
              by a gradual transition to quiescence and homeostasis. Although
              mouse HSCs have been well studied under homeostatic conditions,
              the mechanisms regulating HSC activation under stress remain
              unclear. Here, we analyzed the different phases of regeneration
              after transplantation. We isolated bone marrow from mice at 8
              time points after transplantation and examined the reconstitution
              dynamics and transcriptional profiles of stem and progenitor
              populations. We found that regenerating HSCs initially produced
              rapidly expanding progenitors and displayed distinct changes in
              fatty acid metabolism and glycolysis. Moreover, we observed
              molecular changes in cell cycle, MYC and mTOR signaling in both
              HSCs, and progenitor subsets. We used a decay rate model to fit
              the temporal transcription profiles of regenerating HSCs and
              identified genes with progressively decreased or increased
              expression after transplantation. These genes overlapped to a
              large extent with published gene sets associated with key aspects
              of HSC function, demonstrating the potential of this data set as
              a resource for identification of novel HSC regulators. Taken
              together, our study provides a detailed functional and molecular
              characterization of HSCs at different phases of regeneration and
              identifies a gene set associated with the transition from
              proliferation to quiescence.",
  journal  = "Exp. Hematol.",
  volume   =  127,
  pages    = "40--51",
  month    =  nov,
  year     =  2023,
  keywords = "SonejiS\_Publications",
  language = "en"
}

@ARTICLE{Sommarin2023-cl,
  title    = "Single-cell multiomics of human fetal hematopoiesis define a
              developmental-specific population and a fetal signature",
  author   = "Sommarin, Mikael N E and Olofzon, Rasmus and Palo, Sara and
              Dhapola, Parashar and Soneji, Shamit and Karlsson, G{\"o}ran and
              B{\"o}iers, Charlotta",
  abstract = "Knowledge of human fetal blood development and how it differs
              from adult blood is highly relevant to our understanding of
              congenital blood and immune disorders and childhood leukemia, of
              which the latter can originate in utero. Blood formation occurs
              in waves that overlap in time and space, adding to heterogeneity,
              which necessitates single-cell approaches. Here, a combined
              single-cell immunophenotypic and transcriptional map of first
              trimester primitive blood development is presented. Using
              CITE-seq (cellular indexing of transcriptomes and epitopes by
              sequencing), the molecular profile of established
              immunophenotype-gated progenitors was analyzed in the fetal liver
              (FL). Classical markers for hematopoietic stem cells (HSCs), such
              as CD90 and CD49F, were largely preserved, whereas CD135 (FLT3)
              and CD123 (IL3R) had a ubiquitous expression pattern capturing
              heterogenous populations. Direct molecular comparison with an
              adult bone marrow data set revealed that the HSC state was less
              frequent in FL, whereas cells with a lymphomyeloid signature were
              more abundant. An erythromyeloid-primed multipotent progenitor
              cluster was identified, potentially representing a transient,
              fetal-specific population. Furthermore, differentially expressed
              genes between fetal and adult counterparts were specifically
              analyzed, and a fetal core signature was identified. The core
              gene set could separate subgroups of acute lymphoblastic leukemia
              by age, suggesting that a fetal program may be partially retained
              in specific subgroups of pediatric leukemia. Our detailed
              single-cell map presented herein emphasizes molecular and
              immunophenotypic differences between fetal and adult blood cells,
              which are of significance for future studies of pediatric
              leukemia and blood development in general.",
  journal  = "Blood Adv",
  volume   =  7,
  number   =  18,
  pages    = "5325--5340",
  month    =  sep,
  year     =  2023,
  language = "en"
}

@ARTICLE{Sommarin2023-uv,
  title    = "Single-cell multiomics of human fetal hematopoiesis define a
              developmental-specific population and a fetal signature",
  author   = "Sommarin, Mikael N E and Olofzon, Rasmus and Palo, Sara and
              Dhapola, Parashar and Soneji, Shamit and Karlsson, G{\"o}ran and
              B{\"o}iers, Charlotta",
  abstract = "Knowledge of human fetal blood development and how it differs
              from adult blood is highly relevant to our understanding of
              congenital blood and immune disorders and childhood leukemia, of
              which the latter can originate in utero. Blood formation occurs
              in waves that overlap in time and space, adding to heterogeneity,
              which necessitates single-cell approaches. Here, a combined
              single-cell immunophenotypic and transcriptional map of first
              trimester primitive blood development is presented. Using
              CITE-seq (cellular indexing of transcriptomes and epitopes by
              sequencing), the molecular profile of established
              immunophenotype-gated progenitors was analyzed in the fetal liver
              (FL). Classical markers for hematopoietic stem cells (HSCs), such
              as CD90 and CD49F, were largely preserved, whereas CD135 (FLT3)
              and CD123 (IL3R) had a ubiquitous expression pattern capturing
              heterogenous populations. Direct molecular comparison with an
              adult bone marrow data set revealed that the HSC state was less
              frequent in FL, whereas cells with a lymphomyeloid signature were
              more abundant. An erythromyeloid-primed multipotent progenitor
              cluster was identified, potentially representing a transient,
              fetal-specific population. Furthermore, differentially expressed
              genes between fetal and adult counterparts were specifically
              analyzed, and a fetal core signature was identified. The core
              gene set could separate subgroups of acute lymphoblastic leukemia
              by age, suggesting that a fetal program may be partially retained
              in specific subgroups of pediatric leukemia. Our detailed
              single-cell map presented herein emphasizes molecular and
              immunophenotypic differences between fetal and adult blood cells,
              which are of significance for future studies of pediatric
              leukemia and blood development in general.",
  journal  = "Blood Adv",
  volume   =  7,
  number   =  18,
  pages    = "5325--5340",
  month    =  sep,
  year     =  2023,
  keywords = "SonejiS\_Publications",
  language = "en"
}