Education
Morgridge Institute for Research, Madison, WI, US
2022-present
PostDoc

Max Planck Institute of Biochemistry, Martinsried, Germany
2021-2022
PostDoc

Max Planck Institute of Biochemistry, Martinsried, Germany
Development of computational methods for the analysis of proteomics
and next generation sequencing data
2014-2020
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
2012
august

Conference
16th Human Proteome Organization World Congress, Dublin, Ireland
Poster
2017
september
9th Munich Life Science Symposium, Munich, Germany
Poster - Searching for immunopeptides resulting from somatic mutations
2016
october
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
MaxDIA enables library-based and library-free data-independent acquisition proteomics
Pavel Sinitcyn*, Hamid Hamzeiy*, Favio Soto*, Daniel Itzhak, Frank McCarthy, Christoph Wichmann, Martin Steger, Uli Ohmayer, Ute Distler, Stephanie Kaspar-Schoenefeld, Nikita Prianichnikov, Şule Yılmaz, Jan Rudolph, Stefan Tenzer, Yasset Perez-Riverol, Nagarjuna Nagaraj, Sean Humphrey, and Jürgen Cox
Nature Biotechnology, 2021
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 Shurtleff*, Daniel Itzhak*, Jeffrey Hussmann, Nicole Oakdale, Elizabeth Costa, Martin Jonikas, Jimena Weibezahn, Katerina Popova, Calvin Jan, Pavel Sinitcyn, Shruthi Vembar, Hilda Hernandez, Jürgen Cox, Alma Burlingame, Jeffrey Brodsky, Adam Frost, Georg Borner, and Jonathan Weissman
eLife 7, 2018
Computational Methods for Understanding Mass Spectrometry–Based Shotgun Proteomics Data
Pavel Sinitcyn*, Jan 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, Jürgen Cox, Matthias Mann, and Angela Krackhardt
Nature Communications 7, 2016
The Perseus computational platform for comprehensive analysis of (prote) omics data
Stefka Tyanova, Tikira Temu, Pavel Sinitcyn, Arthur Carlson, Marco Hein, Tamar Geiger, Matthias Mann, and Jürgen Cox
Nature methods 13, 2016
Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome
Niklas Grassl, Nils Kulak, Garwin Pichler, Philipp Geyer, Jette Jung, Sören Schubert, Pavel Sinitcyn, Jürgen Cox, and Matthias Mann
Genome medicine 8, 2016
Visualization of LC-MS/MS proteomics data in MaxQuant
Stefka Tyanova, Tikira Temu, Arthur Carlson, Pavel Sinitcyn, Matthias Mann, and Jürgen Cox
Proteomics 15, 2015
Three manuscripts are currently under revision
Teaching
'Introduction to Proteomics' course, Max Planck Institute of Biochemistry, Germany
2021
'Introduction to Proteomics' course, Lomonosov MSU, Moscow, Russia
2020/2021/2022
'Introduction to Proteomics' course, Bioinformatics Institute, Russia
2019/2020
'Introduction to Proteomics' course, ITMO, St.Petersburg, Russia
2019/2020
Bioinformatics Summer School, Moscow/St.Petersburg, Russia
2018/2019/2021
Courses@CRG Advanced Proteomics Course, Barcelona, Spain
2019
MaxQuant Summer School, Oxford/Berlin/Barcelona
2016/2017/2018
Awards
Morgridge Postdoctoral Fellowship Award
2021
MPIB Junior Scientists’ Publication Award
2021
Reviewer for journals
Bioinformatics, Cancer Immunology Research