Education
Max Planck Institute of Biochemistry, Martinsried, Germany
topic - Algorithm development in computational proteomics
2014-present
PhD

Lomonosov Moscow State University, Russia
speciality - Bioengineering and Bioinformatics
2009-2014
master

Research
Experience
Lomonosov Moscow State University, Russia
Research of harringtonine action
Research of UTR's structure evolution in prokaryotes
Advisor: Mironov AA, Laboratory of Bioinformatics
2012-2014
Lomonosov Moscow State University, Russia
Research of physiological function of eIF2D
Advisor: Dmitriev SE, Laboratory of Protein Synthesis Regulation
2010-2012
Exchange Programs
Leiden University, The Netherlands
Study of heterogeneity of repeat regions in the human genome
Advisor: Pulyakhina I, Hoen Peter-Bram 't, Human Genetics Department
final report
2012
august

Conference
16th Human Proteome Organization World Congress, Dublin, Ireland
Poster
2017
september
9th MaxQuant Summer School, Berlin, Germany
Talk - "Next Generation Sequencing in MaxQuant" and "Perseus plug-in programming"
2017
july
9th Munich Life Science Symposium, Munich, Germany
Poster - Searching for immunopeptides resulting from somatic mutations
2016
october
8th MaxQuant Summer School, Oxford, UK
Talk - "Next Generation Sequencing in MaxQuant" and "Perseus plug-in programming"
2016
july
MCCMB, MoBiLe 10Y symposium, Moscow, Russia
Talk - Peptide search engine approach for detection of translated mutations
2015
july
63rd ASMS Conference on Mass Spectrometry and Allied Topics, St.Louis, USA
Talk - Peptide search engine approach for the detection of translated mutations
based on sequencing data, mutation databases and exhaustive codon changes
2015
may
Information Technology and Systems, Russia
Poster - New insight to harringtonine action
2013
september
Publications
MaxQuant goes Linux
Pavel Sinitcyn, Shivani Tiwary, Jan Rudolph, Petra Gutenbrunner, Christoph Wichmann, Şule Yılmaz, Hamid Hamzeiy, Favio Salinas, and Jürgen Cox
Nature Methods 15, 2018
The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins
Matthew J Shurtleff, Daniel N Itzhak, Jeffrey A Hussmann, Nicole T Schirle Oakdale, Elizabeth A Costa, Martin Jonikas, Jimena Weibezahn, Katerina D Popova, Calvin H Jan, Pavel Sinitcyn, Shruthi S Vembar, Hilda Hernandez, Jürgen Cox, Alma L Burlingame, Jeffrey Brodsky, Adam Frost, Georg HH Borner, Jonathan S Weissman
eLife 7, 2018
Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data
Pavel Sinitcyn*, Jan Daniel Rudolph*, and Jürgen Cox
Annual Review of Biomedical Data Science 1, 2018
Direct identification of clinically relevant neoepitopes presented on native human melanoma tissue by mass spectrometry
Michal Bassani-Sternberg, Eva Braeunlein, Richard Klar, Thomas Engleitner, Pavel Sinitcyn, Stefan Audehm, Melanie Straub, Julia Weber, Julia Slotta-Huspenina, Katja Specht, Marc Martignoni, Angelika Werner, Ruediger Hein, Dirk Busch, Christian Peschel, Roland Rad, Juergen Cox, Matthias Mann, and Angela Krackhardt
Nature Communications 7, 2016
The Perseus computational platform for comprehensive analysis of (prote) omics data
Tyanova, Stefka, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Y. Hein, Tamar Geiger, Matthias Mann, and Jürgen Cox
Nature methods 13, 2016
Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome
Grassl, Niklas, Nils Alexander Kulak, Garwin Pichler, Philipp Emanuel Geyer, Jette Jung, Sören Schubert, Pavel Sinitcyn, Juergen Cox, and Matthias Mann
Genome medicine 8, 2016
Visualization of LC-MS/MS proteomics data in MaxQuant
Tyanova, Stefka, Tikira Temu, Arthur Carlson, Pavel Sinitcyn, Matthias Mann, and Juergen Cox
Proteomics 15, 2015
Statements
Machine Learning
Andrew Ng, Stanford University
2017
Introduction to LaTeX
Higher School of Economics
result - 99%
2014
Computation molecular evolution
University of Denmark
result - 88.2%
2014
8.01x: Physics I (Classical Mechanics)
Massachusetts Institute of Technology
result - 91%
2014
Algorithms: Design and Analysis, Part 2
Stanford University
result - 85.9%
2013
Algorithms: Design and Analysis, Part 1
Stanford University
result - 88.3%
2012
Calculus Two: Sequence and Series
Ohio State University
result - 87.3%
2013
Computing for Data Analysis
Johns Hopkins University
result - 92.0%
2013
UNIX Basics
Lomonosov Moscow State University
result
2011
Skills
Programming
C#, Python, R, bash, SQL
Bioinformatic experience
Alignment, Hide Markov Model, Motif discovery (MEME, MAST), Genome assembly, RNA structure prediction, PCA, ANOVA, Phylogenetic algorithms, High-throughput data processing