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<!doctype html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport"
content="width=device-width, user-scalable=no, initial-scale=1.0, maximum-scale=1.0, minimum-scale=1.0">
<meta http-equiv="X-UA-Compatible" content="ie=edge">
<link rel="stylesheet" href="static/css/bootstrap.css">
<title>Nikita Vaulin</title>
<link rel="icon" href="static/images/profile.png" type="image/png">
</head>
<body>
<!-- Here starts the header" -->
<div class="px-3 py-2 fixed-top text-bg-dark">
<div class="container-fluid">
<div class="d-flex flex-wrap align-items-center justify-content-center justify-content-lg-start">
<a href="/" class="d-flex align-items-center my-2 my-lg-0 me-lg-auto text-white text-decoration-none">
<h4> Nikita Vaulin </h4>
</a>
<ul class="nav col-12 col-lg-auto my-2 justify-content-center my-md-0 text-small">
<li><a href="#top" class="btn mx-3 btn-outline-light"> Home </a></li>
<li><a href="#education" class="btn mx-1 text-white"> Education </a></li>
<li><a href="#experience" class="btn mx-1 text-white"> Experience </a></li>
<li><a href="#skills" class="btn mx-1 text-white"> Skills </a></li>
<li><a href="#teaching" class="btn mx-1 text-white"> Teaching </a></li>
<li><a href="https://drive.google.com/drive/folders/1HmiZacANd59kWI_i4tIZESeuKJC_9VyR?usp=share_link"
class="btn mx-1 text-white"> CV </a></li>
</ul>
</div>
</div>
</div>
<!--Title Screen-->
<div class="imageContainer">
<div class="container pt-5 px-5">
<div class="row mb-2 align-items-center">
<div class="col-12 col-lg-6 mb-5 mb-lg-0 me-auto">
<div class="shadow p-3 mb-5 bg-light rounded bg-opacity-75">
<h2 class="display-3"> Hi, i am</h2>
<h1 class="display-1 fw-normal" id="name">Nikita Vaulin</h1>
<p/>
<p class="lead-15 fw-normal">Bioinformatician. Biophysicist. Molecular biologist.</p>
</div>
</div>
<div class="pt-4 col-5 col-lg-5 justify-content-center align-items-center">
<img class="img" src="static/images/nick_new_beyond_borders.png" alt="Nikita Vaulin"
style="height:120%;width:120%">
</div>
</div>
</div>
</div>
<script src="static/js/titlepage.js"></script>
<!--About-->
<div class="container pt-5 px-3">
<div class="row align-items-center">
<div class="col-8 ">
<h2 class="display-3"> About </h2>
<div class="bg-body-padding rounded-4">
<p>
I am an omics-fan bioinformatician interested in <b>cell fate decisions</b>, especially in the context of neurodevelopment.
I think (I hope) we are now on the cusp of putting together a complete picture of how the various processes together govern the life of a cell. <br/>
Transcription factors, chromatin structure, post-translational modifications, etc.
- they set the rules of the game in which the cell must go from the opening through the mittelspiel to the endgame.
Chaos plays its role, but I believe that by defining a fully-omics state space we can anticipate all possible outcomes.
</p>
<p>
You can find me struggling with this questions in the
<a style="color: rgba(var(--bs-link-color-rgb))" href="adameykolab.eu">Adameyko lab</a> and
<a style="color: rgba(var(--bs-link-color-rgb))" href="https://hic.skoltech.ru/">Khrameeva lab</a>.
And also in <a style="color: rgba(var(--bs-link-color-rgb))" href="https://bioinf.me/">Bioinformatics institute</a>,
where I teach python programming.
</p>
</ol>
</div>
</div>
<div class=" col-4 justify-content-center">
<div class="lead-15 fw-normal" style="text-align: center; line-height: 2.1; margin-top: 5rem">
<p><i class="bi bi-envelope"></i> <a href="mailto:vaulin@ro.ru">vaulin@ro.ru</a></p>
<p><i class="bi bi-linkedin"></i> <a href="https://www.linkedin.com/in/nvaulin/">nvaulin</a></p>
<p><img src="static/images/telegram.svg" alt="Telegram" style="width: 24px; height: 24px;"> <a href="https://t.me/nvaulin">nvaulin</a></p>
<p><i class="bi bi-github"></i> <a href="https://github.com/nvaulin/s">nvaulin</a></p>
</div>
</div>
</div>
</div>
<!--Education-->
<div id="education" class="container pt-5 px-3">
<div class="row col-12 align-items-center">
<!-- <div class="hr-blue"></div>-->
<h2 class="display-3 text-center "> Education </h2>
<!-- <div class="hr-blue"></div>-->
<div class="bg-body-padding rounded-4 center-container">
<div class="timeline-container">
<div class="timeline">
<div class="event event-top" id="event" style="--pos: 17%; --height-vline: 50px;">
<div class="popup">
<div class="fw-bold mb-1 small"><i class="bi bi-bookmark-fill"></i> Relevant subjects</div>
<div class="popup-text">
Physics (48 ECTS) </br>
Calculus (31 ECTS) </br>
Biophysics (30 ECTS) </br>
Biostatistics (4 ECTS) </br>
Biochemistry (13 ECTS) </br>
Programming (8 ECTS) </br>
Electronics lab (6 ECTS) </br>
Molecular biology and genetics (24 ECTS) </br>
Quantum chemistry and molecular modelling (8 ECTS) </br>
</div>
</div>
<div class="event-icon">
<img src="static/images/polytech.png" alt="polytech" height="30">
</div>
<div class="event-header">
BSc in Biochemical physics
</div>
<div class="event-description">
Peter the Great St.Petersburg Polytechnic University
</div>
<div class="event-date">
Sept 2018 – Jun 2022
</div>
</div>
<div class="event event-top mt-4" id="event" style="--pos: 50%; --height-vline: 20px;">
<div class="popup">
<div class="fw-bold mb-1 small"><i class="bi bi-bookmark-fill"></i> Relevant subjects</div>
<div class="popup-text">
Python </br>
Statistics </br>
Discrete math </br>
Machine learning </br>
Bioinformatics lab </br>
Molecular phylogenetics and evolution </br>
</div>
</div>
<div class="event-icon">
<img src="static/images/BI.png" alt="polytech" height="50">
</div>
<div class="event-header">
Bioinformatics for biologists
</div>
<div class="event-description">
Bioinformatics institute qualification program
</div>
<div class="event-date">
Sept 2022 – Jun 2023
</div>
</div>
<div class="event event-top" id="event" style="--pos: 83%; --height-vline: 50px;">
<div class="popup">
<div class="fw-bold mb-1 small"><i class="bi bi-bookmark-fill"></i> Relevant subjects</div>
<div class="popup-text">
Molecular Biology (6 ECTS) </br>
Biostatistics (6 ECTS) </br>
Bioinformatics (6 ECTS) </br>
Omics Data Analysis (6 ECTS) </br>
Experimental Design in Biology (3 ECTS) </br>
Computational Methods in Genetics (6 ECTS) </br>
Introduction to Data Science (3 ECTS) </br>
CAD Modeling (1 ECTS) </br>
</div>
</div>
<div class="event-icon">
<img src="static/images/skoltech.png" alt="polytech" height="30">
</div>
<div class="event-header">
MSc in Life Sciences
</div>
<div class="event-description">
Skolkovo Institute of Science and Technology
</div>
<div class="event-date">
Sept 2022 – Jun 2024
</div>
</div>
</div>
</div>
<div class="text-center mt-2 mb-1" style="font-size: 1.1rem;"><i> and plenty of workshops and online
courses </i>...
</div>
<div>
<div class="container px-2 ">
<div class="marquee">
<span class="online">Data analysis in R |
R programming |
Python basics and applications |
Python Programming |
Statistics |
Biotechnology: gene engineering |
Molecular phylogenetics |
Machine learning |
Web-technologies |
Introduction to NGS |
Introduction to Linux |
Molecular biology and genetics |
Git/GitHub basics |
Git-game |
<i>De novo </i> assembly of the <i>Darevskia raddei</i> lizard genome |
Mathematical modeling in drug development |
Innovation workshop</span>
</div>
</div>
</div>
</div>
</div>
</div>
<!--Experience-->
<div id="experience" class="container pt-5 px-3">
<div class="row col-12 align-items-center">
<!-- <div class="hr-blue"></div>-->
<h2 class="display-3 text-center "> Experience </h2>
<!-- <div class="hr-blue"></div>-->
<div class="bg-body-padding rounded-4 center-container">
<div class="row mt-2 mb-3 mx-4 g-0 border rounded overflow-hidden flex-md-row position-relative">
<div class="col p-4 d-flex flex-column position-static">
<h3 class="mb-0">Research on human brain cells chromatin structure</h3>
<div class="mb-3 text-body-secondary">MSc student</div>
<p class="card-text mb-auto">
I analyse different omics datasets (mainly Hi-C data, single-cell Hi-C and also ChIP-seq, ATAC-seq, RNA-seq)
to study the differences in chromatin structure between neurons and glia.
As my master's project, I am focusing on those features that are related to polycomb group proteins.
However, I am globally interested in the chromatin and epigenetic changes landscape
underlying the processes of neurogenesis and the development of brain disorders
</p>
<div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> (pandas, numpy, matplotlib,
cooltools), bash, FitHic
</div>
<div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> June 2023 – current</div>
<div class="mt-0 text-body-tertiary small" style="line-height: 1;"><i class="bi bi-building"></i>
Skolkovo Institute of Science and Technology
</div>
</div>
<div class="col-auto d-md-flex"
style="background-color: white; padding: 10px; display: flex; align-items: center; justify-content: center;">
<img src="static/images/hic_sch.png" alt="HiC experience" width="400">
</div>
</div>
<div class="row mt-2 mb-3 mx-4 g-0 border rounded overflow-hidden flex-md-row position-relative">
<div class="col p-4 d-flex flex-column position-static">
<h3 class="mb-0">Phage DNA-mimic Ocr impact on the <i>E. coli</i> chromatin</h3>
<div class="mb-3 text-body-secondary"> MSc student</div>
<p class="card-text mb-auto">
I analyse Hi-C data of the <i>E. coli</i> genome and integrate it with the ChIP-seq and RNA-seq
data. We found that Ocr DNA-mimic expression is not equal to the Hu <i>E. coli</i>
DNA-structuring protein deletion (which actually made things more complicated).
</p>
<div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> python (numpy, matplotlib,
cooltools), distiller, nextflow
</div>
<div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> May 2023 – June 2023</div>
<div class="mt-0 text-body-tertiary small" style="line-height: 1;"><i class="bi bi-building"></i>
Skolkovo Institute of Science and Technology
</div>
</div>
<div class="col-auto d-md-flex"
style="background-color: white; padding: 10px; display: flex; align-items: center; justify-content: center;">
<img src="static/images/hic_omics.png" alt="HiC in bacteria experience" width="400">
</div>
</div>
<div class="row mt-2 mb-3 mx-4 g-0 border rounded overflow-hidden flex-md-row position-relative">
<div class="col p-4 d-flex flex-column position-static">
<h3 class="mb-0"><i>In silico </i>generation of metagenomic communities</h3>
<div class="mb-3 text-body-secondary">Bioinformatician intern</div>
<p class="card-text mb-auto">
I <b>develop a python tool</b> (GitHub <a href="https://github.com/nvaulin/samovar">
SAMOVAR</a>) to generate metagenomes with specified properties. It is useful
for validating the work of metagenome analysis tools.
I implemented part of the algorithm for selecting the required species based on SAT-solvers as
well as interaction with the NCBI database
</p>
<div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> Git, NCBI, conda, python (pandas,
biopython, pysat)
</div>
<div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> Jan 2023 – current</div>
<div class="mt-0 text-body-tertiary small" style="line-height: 1;"><i class="bi bi-building"></i>
ITMO & Bioinformatics institute
</div>
</div>
<div class="col-auto d-md-flex"
style="background-color: white; padding: 10px; display: flex; align-items: center; justify-content: center;">
<img src="static/images/pipeline.png" alt="Metagenomics experience" width="400">
</div>
</div>
<!-- <div class="row mt-2 mb-3 mx-4 g-0 border rounded overflow-hidden flex-md-row position-relative">-->
<!-- <div class="col p-4 d-flex flex-column position-static">-->
<!-- <h3 class="mb-0">Research on type I CRISPR-Cas systems</h3>-->
<!-- <div class="mb-3 text-body-secondary">Laboratory assistant, BSc and MSc student</div>-->
<!-- <p class="card-text mb-auto">-->
<!-- I perform all stages of the work from <b>conducting experiments</b> and-->
<!-- Illumina libraries preparation to <b>NGS data processing</b>. My key research topics are:-->
<!-- </p>-->
<!-- <ol>-->
<!-- <li>-->
<!-- Study of functioning of the Cas3 helicase-nuclease-->
<!-- </li>-->
<!-- <li>-->
<!-- Studying the role of cellular nucleases in the operation of CRISPR-Cas systems-->
<!-- </li>-->
<!-- </ol>-->
<!-- <div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> R (ggplot2, statistics), bash-->
<!-- (scripts, sam-tools, bwa), UGENE, ChIP-seq, 3-C, CorelDraw-->
<!-- </div>-->
<!-- <div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> Oct 2020 – May 2023</div>-->
<!-- <div class="mt-0 text-body-tertiary small" style="line-height: 1;"><i class="bi bi-building"></i>-->
<!-- Skolkovo Institute of Science and Technology & «NanoBio» research center, SPbPU & <br> -->
<!-- Institute of Molecular Genetics, National Research Centre «Kurchatov Institute»-->
<!-- </div>-->
<!-- </div>-->
<!-- <div class="col-auto d-md-flex"-->
<!-- style="background-color: white; padding: 10px; display: flex; align-items: center; justify-content: center;">-->
<!-- <img src="static/images/exp_crispr.png" alt="CRISPR-Cas experience" width="400">-->
<!-- </div>-->
<!-- </div>-->
<div class="center-container row">
<a href="experience/index.html" class="more-info btn btn-primary ">
Want to learn more about my experience? Check out the
<b class="my-a">Research Experience</b> page!
</a>
</div>
</div>
</div>
</div>
<!--Skills-->
<div id="skills" class="container pt-5 px-3">
<div class="row col-12 align-items-center">
<h2 class="display-3 text-center "> Skills </h2>
<div class="bg-body-padding rounded-4 center-container">
<div class="image-container">
<img src="static/images/Evidence_board_website.png" alt="Skills" width="100%">
<h3 class="image-text"
style="top: 14.9%; left: 29.8%; transform: translate(-50%, -50%) rotate(10.9deg);">
Programming</h3>
<p class="image-text"
style="top: 55%; left: 14.75%; transform: translate(-50%, -50%) rotate(-3deg);">
<b>Python</b> (Pandas, NumPy, Scikit-learn) </br>
<b>R</b> (ggplot2, tidyverse, knitr, emo) </br>
<b>Bash</b> (scripts), Git </br>
Classical ML, basic C++
</p>
<h3 class="image-text"
style="top: 65.7%; left: 14.9%; transform: translate(-50%, -50%) rotate(-3deg);">Bioinf</h3>
<p class="image-text"
style="top: 77%; left: 14.8%; transform: translate(-50%, -50%) rotate(-3deg);">
<b>NGS</b> data processing</br>
<b>ChIP-seq, Hi-C, GWAS, RNA-seq</b></br>
variant calling, genome assembly</br>
biostatistics and visualization
</p>
<h3 class="image-text"
style="top: 15.6%; left: 72.5%; transform: translate(-50%, -50%) rotate(-7deg);">Lab</h3>
<p class="image-text" style="top: 54%; left: 81%; transform: translate(-20%, -50%) rotate(-2deg);">
NGS libraries preparation</br>
ChIP-seq 3C</br>
gene knock-out</br>
work with <i>E. coli</i> and P1 phage</br>
</p>
<h3 class="image-text"
style="top: 78.9%; left: 41.3%; transform: translate(-50%, -50%) rotate(6deg);">Teaching</h3>
<p class="image-text"
style="top: 86.7%; left: 71.1%; transform: translate(-50%, -50%) rotate(29deg); font-size: 50;">
laser cutter</p>
</div>
</div>
</div>
</div>
<!-- Teaching Experience-->
<div id="teaching" class="container pt-5 px-3">
<div class="row col-12 align-items-center">
<!-- <div class="hr-blue"></div>-->
<h2 class="display-3 text-center "> Teaching experience </h2>
<!-- <div class="hr-blue"></div>-->
<div class="bg-body-padding rounded-4 center-container">
<div class="row mt-2 mb-3 mx-4 g-0 border rounded overflow-hidden flex-md-row position-relative">
<div class="col p-4 d-flex flex-column position-static">
<h3 class="mb-0">Workspace and workflow management in biology</h3>
<div class="mb-3 text-body-secondary">My own short course</div>
<p class="card-text mb-auto">
I developed a Skoltech ISP (indepenent study period) course for 16 hours. In this course we
practiced with some tools and shared each other experice. This course were <b>awarded</b> as a
best
student ISP 2023 course!
</p>
<div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> Git, GitHub, Snakemake, Bash
scripts
</div>
<div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> Jan 2023</div>
<div class="mt-0 text-body-tertiary small" style="line-height: 1;"><i class="bi bi-building"></i>
Skolkovo Institute of Science and Technology
</div>
</div>
<div class="col-auto d-md-flex"
style=" display: flex; align-items: center; justify-content: center;">
<img src="static/images/isp2.jpg" alt="My course!" width="400">
</div>
</div>
<div class="row mt-2 mb-3 mx-4 g-0 border rounded overflow-hidden flex-md-row position-relative">
<div class="col p-4 d-flex flex-column position-static">
<h3 class="mb-0">Python programming for biologists</h3>
<div class="mb-3 text-body-secondary">Teacher</div>
<p class="card-text mb-auto">
I teach a year-long programming course.
We start with the basics of python and then move on may interesting and advanced things
which are widely used in computational biology.
</p>
<div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> python (pandas and matplotlib, OOP and FP, biopython)
</div>
<div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> Sep 2023 - current</div>
<div class="mt-0 text-body-tertiary small" style="line-height: 1;"><i class="bi bi-building"></i>
Bioinformatics institute
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<h3 class="mb-0">3D genomics and Hi-C data analysis</h3>
<div class="mb-3 text-body-secondary">Teacher</div>
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I teach a Hi-C data analysis as a part of the <a style="color: rgba(var(--bs-link-color-rgb))" href="https://bioinf.me/education/workshops/ngs">NGS data analysis</a> workshop in BI.
Also I give public lectures on the 3D genomics (<a style="color: rgba(var(--bs-link-color-rgb))" href="https://www.youtube.com/live/VlshGnJXe2o?si=trpDT5DCOPdKWl0l">example in russian</a>).
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Bioinformatics institute
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<img src="static/images/bi_hic.png" alt="Working with Hi-C matrix" width="400">
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<h3 class="mb-0">Bioinformatics club</h3>
<div class="mb-3 text-body-secondary">My own club</div>
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I managed club meetings, gave short lectures on some topics, demonstrate solutions to some
problems from the
<a href="https://rosalind.info/problems/list-view/">Rosalind website </a>
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<div class="mt-2 text-body-secondary"><i class="bi bi-gear"></i> python
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<div class="mt-2 text-body-tertiary"><i class="bi bi-calendar-week"></i> Oct - Dec 2022</div>
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Skolkovo Institute of Science and Technology
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<h3 class="mb-0">More teaching:</h3>
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<ul>
<li>
Intro to bioinformatics for school students, <i>Secondary school 179 named after N. Konstantinov</i>
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Python programmming, <i>blastim</i>
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<b>Teaching assistant:</b>
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<li>
Metagenome analysis workshops, <i>Skoltech</i>
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<li>
NGS data analysis, <i>Bioinformatics institute</i>
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<li>
Machine learning, <i>Bioinformatics institute</i>
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<div class="fw-bold mx-1"> Skoltech Triple Point X Startup Village</div>
<div class="mt-2 mb-3"><i class="bi bi-geo-alt-fill"></i> May 2023; Skolkovo Institute of Science and
Technology
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<div class="fw-bold mx-1"> Donor’s Day SPbPU</div>
<div class="mt-2 mb-3"><i class="bi bi-geo-alt-fill"></i> 2019; Peter the Great St.Petersburg Polytechnic
University
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<div class="fw-bold mx-1"> «Scientists Against Myths», «Science Station»</div>
<div class="mt-2 mb-3"><i class="bi bi-geo-alt-fill"></i> 2018 - 2019; «SciTeam» Center for the Science
Promotion
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<div class="fw-bold mx-1"> Eco-festival</div>
<div class="mt-2 mb-3"><i class="bi bi-geo-alt-fill"></i> 2019; Dubki, Sestroretsk</div>
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<div class="fw-bold mx-1"> North-West Public Organization of the Russian Federation of Cosmonautics</div>
<div class="mt-2 mb-3"><i class="bi bi-geo-alt-fill"></i> 2018 - 2019; Saint-Petersburg</div>
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