paper.bib

```bibtex
@article{wishart2018drugbank,
  title={{DrugBank 5.0}: a major update to the {DrugBank} database for 2018},
  author={Wishart, David S and Feunang, Yannick D and Guo, An C and Lo, Elvis J and Marcu, Ana and Grant, Jason R and Sajed, Tanvir and Johnson, Daniel and Li, Carin and Sayeeda, Zinat and others},
  journal={Nucleic Acids Research},
  volume={46},
  number={D1},
  pages={D1074--D1082},
  year={2018},
  publisher={Oxford University Press},
  doi={10.1093/nar/gkx1037}
}

@article{tatonetti2012data,
  title={Data-driven prediction of drug effects and interactions},
  author={Tatonetti, Nicholas P and Ye, Patrick P and Daneshjou, Roxana and Altman, Russ B},
  journal={Science Translational Medicine},
  volume={4},
  number={125},
  pages={125ra31},
  year={2012},
  publisher={American Association for the Advancement of Science},
  doi={10.1126/scitranslmed.3003377}
}

@article{galeano2022onsides,
  title={{OnSIDES}: A database of drug side effects derived from {FDA} structured product labels},
  author={Galeano, Diego and Li, Sheng and Gerber, Michael and Tatonetti, Nicholas P},
  journal={medRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory Press},
  doi={10.1101/2024.03.22.24304724}
}

@article{kuhn2016sider,
  title={The {SIDER} database of drugs and side effects},
  author={Kuhn, Michael and Letunic, Ivica and Jensen, Lars Juhl and Bork, Peer},
  journal={Nucleic Acids Research},
  volume={44},
  number={D1},
  pages={D1075--D1079},
  year={2016},
  publisher={Oxford University Press},
  doi={10.1093/nar/gkv1075}
}

@article{wickham2014tidy,
  title={Tidy data},
  author={Wickham, Hadley},
  journal={Journal of Statistical Software},
  volume={59},
  number={10},
  pages={1--23},
  year={2014},
  doi={10.18637/jss.v059.i10}
}

@article{wickham2019welcome,
  title={Welcome to the Tidyverse},
  author={Wickham, Hadley and Averick, Mara and Bryan, Jennifer and Chang, Winston and McGowan, Lucy D'Agostino and Fran{\c{c}}ois, Romain and Grolemund, Garrett and Hayes, Alex and Henry, Lionel and Hester, Jim and others},
  journal={Journal of Open Source Software},
  volume={4},
  number={43},
  pages={1686},
  year={2019},
  doi={10.21105/joss.01686}
}

@article{gentleman2004bioconductor,
  title={{Bioconductor}: open software development for computational biology and bioinformatics},
  author={Gentleman, Robert C and Carey, Vincent J and Bates, Douglas M and Bolstad, Ben and Dettling, Marcel and Dudoit, Sandrine and Ellis, Byron and Gautier, Laurent and Ge, Yongchao and Gentry, Jeff and others},
  journal={Genome Biology},
  volume={5},
  number={10},
  pages={R80},
  year={2004},
  publisher={BioMed Central},
  doi={10.1186/gb-2004-5-10-r80}
}

@article{parolo2023single,
  title={Single-cell-led drug repurposing for {Alzheimer's} disease},
  author={Parolo, Silvia and Mariotti, Federica and Bora, Pranami and Carboni, Lucia and Domenici, Enrico},
  journal={Scientific Reports},
  volume={13},
  pages={8497},
  year={2023},
  publisher={Nature Publishing Group},
  doi={10.1038/s41598-023-27420-x}
}

@article{perez2021covid,
  title={A {COVID-19} drug repurposing strategy through quantitative homological similarities using a topological data analysis-based framework},
  author={P{\'e}rez-Moraga, Raquel and For{\'e}s-Martos, Jaume and Suay-Garc{\'i}a, Beatriz and Duval, Jean-Louis and Falc{\'o}, Antonio and Climent, Joan},
  journal={Pharmaceutics},
  volume={13},
  number={4},
  pages={488},
  year={2021},
  publisher={MDPI},
  doi={10.3390/pharmaceutics13040488}
}

@article{schubert2022transcriptome,
  title={Transcriptome-guided identification of drugs for repurposing to treat age-related hearing loss},
  author={Schubert, Natalie MA and van Tuinen, Marieke and Pyott, Sonja J},
  journal={Biomolecules},
  volume={12},
  number={11},
  pages={1633},
  year={2022},
  publisher={MDPI},
  doi={10.3390/biom12111633}
}

@article{mercatelli2022detection,
  title={Detection of pan-cancer surface protein biomarkers via a network-based approach on transcriptomics data},
  author={Mercatelli, Daniele and Cabrelle, Chiara and Veltri, Pierangelo and Giorgi, Federico M},
  journal={Briefings in Bioinformatics},
  volume={23},
  number={6},
  pages={bbac400},
  year={2022},
  publisher={Oxford University Press},
  doi={10.1093/bib/bbac400}
}

@article{yang2021mapping,
  title={Mapping the landscape of synthetic lethal interactions in liver cancer},
  author={Yang, Chao and Guo, Yanru and Qian, Rui and Huang, Yuqing and Zhang, Li and Hu, Yun and others},
  journal={Pharmacological Research},
  volume={166},
  pages={105481},
  year={2021},
  publisher={Elsevier},
  doi={10.1016/j.phrs.2021.105481}
}

@article{su2024multiancestry,
  title={Multi-ancestry proteome-phenome-wide {Mendelian} randomization offers a comprehensive protein-disease atlas and potential therapeutic targets},
  author={Su, Chen-Yang and van der Graaf, Adriaan and Zhang, Wei and Jang, Dong-Keun and Kavousi, Mohsen and Sijbrands, Eric JG and Ikram, M Arfan and Voortman, Trudy},
  journal={medRxiv},
  year={2024},
  publisher={Cold Spring Harbor Laboratory Press},
  doi={10.1101/2024.10.17.24315553}
}

@article{rischke2023machine,
  title={Machine learning identifies right index finger tenderness as key signal of {DAS28-CRP} based psoriatic arthritis activity},
  author={Rischke, Sarah and Poor, Susanne Maria and Gurke, Robert and Hahnefeld, Lisa and K{\"o}hm, Michaela and Behrens, Frank and Geisslinger, Gerd and Schiffmann, Susanne},
  journal={Scientific Reports},
  volume={13},
  pages={10965},
  year={2023},
  publisher={Nature Publishing Group},
  doi={10.1038/s41598-023-49574-4}
}

@article{namiot2023international,
  title={The international clinical trials registry platform ({ICTRP}): data integrity and the trends in clinical trials, diseases, and drugs},
  author={Namiot, Evgeny D and Smirnovov{\'a}, Dagmar and Sokolov, Andrey V and Kel, Alexander E},
  journal={Frontiers in Pharmacology},
  volume={14},
  pages={1106591},
  year={2023},
  publisher={Frontiers Media SA},
  doi={10.3389/fphar.2023.1228148}
}

@article{hammoud2020multipath,
  title={{Multipath}: an {R} package to generate integrated reproducible pathway models},
  author={Hammoud, Zaynab and Kramer, Frank},
  journal={Biology},
  volume={9},
  number={12},
  pages={483},
  year={2020},
  publisher={MDPI},
  doi={10.3390/biology9120483}
}

@article{hammoud2025multipath2,
  title={{Multipath2.0}: Extending multilayer reproducible pathway models with omics data},
  author={Hammoud, Zaynab and Al Maaz, Mhaned and D'Angelo, Antonia and Kramer, Frank},
  journal={Computer Methods and Programs in Biomedicine},
  volume={244},
  pages={107958},
  year={2025},
  publisher={Elsevier},
  doi={10.1016/j.cmpb.2023.107958}
}

@article{garcia2012anticoagulant,
  title={Parenteral anticoagulants: antithrombotic therapy and prevention of thrombosis: {American College of Chest Physicians} evidence-based clinical practice guidelines},
  author={Garcia, David A and Baglin, Trevor P and Weitz, Jeffrey I and Samama, Meyer Michel},
  journal={Chest},
  volume={141},
  number={2},
  pages={e24S--e43S},
  year={2012},
  publisher={Elsevier},
  doi={10.1378/chest.11-2291}
}

@manual{dowle2023datatable,
  title={{data.table}: Extension of `data.frame`},
  author={Dowle, Matt and Srinivasan, Arun},
  year={2023},
  note={R package version 1.14.8},
  url={https://CRAN.R-project.org/package=data.table}
}

@manual{wickham2023xml2,
  title={{xml2}: Parse {XML}},
  author={Wickham, Hadley and Hester, Jim and Ooms, Jeroen},
  year={2023},
  note={R package version 1.3.5},
  url={https://CRAN.R-project.org/package=xml2}
}

@manual{dbdataset,
  title={{dbdataset}: {DrugBank} dataset files in {R} dataframes},
  author={Ali, Mohammed},
  year={2024},
  note={R package version 5.1.11},
  url={https://github.com/interstellar-egypt/dbdataset}
}

@manual{covid19dbcand,
  title={{covid19dbcand}: {Covid 19 DrugBank} selected possible drugs},
  author={Ali, Mohammed},
  year={2022},
  note={R package version 0.1.1},
  url={https://github.com/interstellar-egypt/covid19dbcand}
}
```