Dr. Alexey K. Shaytan - Curriculum Vitae

Website:http://www.intbio.org
GitHub:molsim
Social media: follow me on facebook View Alexey Shaytan's profile on LinkedIn follow me on VK
GoogleScholar:goo.gl/6W1QKS
Pubmed:Shaytan A
ORCID:0000-0003-0312-938X
ResearcherID:D-7306-2012
Scopus ID:26635808600
ResearchGate:Alexey_Shaytan3
Istina:405377
eLibrary SPIN:6275-5481
CONTACT
E-mail:shaytan_ak@mail.bio.msu.ru
Tel/Fax:+7 495 939 57 38
Skype:alexeyshaytan
Address:Bioengineering Department, Faculty of Biology, Moscow State University, 1 Leninskie Gory, building 73, Moscow, 119991 Russia
CAREER
BIOGRAPHY
Alexey Shaytan received his diploma in condensed matter physics from Moscow State University in 2007. He then pursued PHD studies in computer simulations of synthetic and biological macromolecules under the supervision of Prof. Alexei R. Khokhlov earning PHD degree in polymer physics from Moscow State University in Russia and the University of Ulm in Germany. Fascinated by the world of biological macromolecules Dr. Shaytan became a research fellow at the Faculty of Biology of Moscow State University. At this point his interests turned towards computational and biophysical studies of chromatin through collaboration with the laboratory of Prof. Vasily Studitsky. He then received the US-Russia Collaboration in the Biomedical Sciences Fellowship Award and moved to the laboratory of Dr. Anna Panchenko at the National Center for Biotechnology Information, NIH in USA for post-doctoral training. While at NIH Dr. Shaytan worked primarily on studying histones and nucleosomes by combining molecular modeling, bioinformatics and experimental approaches. In collaboration with the laboratory of Dr. Carl Wu he developed methods of detailed structural analysis of nucleosomes from hydroxyl-radical footprinting experiments that were applied to understand the structure of centromeric nucleosomes. Together with the group of Dr. David Landsman he developed the database of histone variants "HistoneDB 2.0". In collaboration with the laboratory of Dr. Victor Zhurkin he worked on elucidating nucleosome dynamics through record-long all-atom molecular dynamics simulations. In 2017 Dr. Shaytan moved back to Moscow State University as the leader of the Integrative Biology Group at the Department of Bioengineering, Faculty of Biology.
RESEARCH
INTERESTS
Our broad aim is on integrating and applying modern concepts and approaches from physical and engineering sciences, molecular modeling, computer science and bioinformatics towards solving problems in biology and bioengineering. Particularly, our current focus is on studying chromatin structure at nucleosomal level via a combination of biophysical, modeling and bioinformatics approaches. We are interested in how nucleosome structure, positioning and dynamics affect interactions with other chromatin proteins and ultimately affect gene expression and control cell functioning at the epigenetic level.
WORK
EXPERIENCE
2017-Group LeaderIntegrative Biology Group, Department of Bioengineering, Faculty of Biology, Moscow State University
2013--2017Postdoctoral Visiting FellowNational Center for Biotechnology Information, National Institutes of Health, USA; Advisor: Dr. Anna R. Panchenko
2012-Leading researcherMoscow State University, Faculty of Biology, Department of Bioengineering
2010Scientific CoordinatorRussian Technology Platform “Supercomputers and high performance computing”
2010--2012Research fellowMoscow State University, Faculty of Biology, Department of Bioengineering; focus on computer simulations of bio and nano structures
2009--2011Research fellowUniversity of Ulm, Institute of Polymer Science, Ulm, Germany; Advisors: Prof. A.R. Khokhlov, Prof. P.G. Khalatur
2008--2010Leading engineerMoscow State University, Faculty of Biology, Department of Bioengineering; focus on IT infrastructure for computer simulations
2006--2008School teacherSchool N1326/Lyceum 1586, subjects: computer modeling (10-11 grades), computer methods in biology and physics (7-9 grades)
EDUCATION/
DEGREES
2016CertificateAdvanced Studies in Technology Transfer, FAES Graduate School at National Institues of Health, USA (15 credits, GPA 4.0, max 4.0)
2014--2016Advanced Studies in Technology Transfer, FAES Graduate School at National Institues of Health, USA
2011Dr. Rer. Nat. degree (PHD)University of Ulm, Germany; Thesis title “Computer simulations of self-assembling nanofibers from thiophene-peptide oligomers”; Magna cum laude; Advisor Prof. A.R. Khokhlov
2010PHD degree (physics and mathematics)Moscow State University, Russia; Thesis title “Computer simulations and statistical analysis of self-organizing molecular structures based on peptides”; Advisor Prof. A.R. Khokhlov
2007--2010PHD studentMoscow State University, Faculty of Physics, Chair of Physics of Polymers and Crystals
2007--2008“Innovation Studio” Entrepreneurship Study Program at Moscow State University
2007Master of Science degreeMoscow State M.V. Lomonosov University, Faculty of Physics, Chair of Physics of Polymers and Crystals, diploma with excellence (GPA 5.0, max 5.0), Master Thesis “Study of hydration and adsorption of amino acid side chains via MD simulations”; Advisors Prof. A.R. Khokhlov, Prof. V.A. Ivanov. Selected as the best thesis at the department.
2001--2007StudentMoscow State M.V. Lomonosov University, Faculty of Physics
2002--2005Russian-German Institute of Science and Culture at MSU
1991--2001School studentMoscow Comprehensive School No. 1260 with advanced studies of English language. School-leaving certificate with gold medal (GPA 5.0, max 5.0)
AWARDS
SCHOLARSHIPS
2013Scholarship of US-Russia Collaboration in the Biomedical Sciences NIH Visiting Fellows Program
2013Finalist of the 37-th competition of scientific works by young scientists of Lomonosov Moscow state University
2012Finalist of the contest of works by talented students, graduates and young scientists of Lomonosov Moscow State University established by O.V. Deripaska
2008BioCamp 2008, Novartis International Biotechnology Leadership Camp, Hong Kong: leader of the best Best Performing Team, 2nd Runner Up Best Performing Student
2008Russian Innovation Contest, participant of the 2nd round
2005Scholarship of Vladimir Potanin Foundation
2005Scholarship “Grant of Moscow”
PUBLICATIONS
GoogleScholar Pubmed Complete list of publications with PDFs
Selected papers
2018Shaytan AK*, Xiao H, Armeev G, et al. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROIDNature Protocols 2018; in press
2017Xiao H, Wang F*, Wisniewski J*, Shaytan AK*, Ghirlando R, FitzGerald PC, et al. Molecular basis of CENP-C association with the CENP-A nucleosome at yeast centromeres. Genes Dev. 2017; doi:10.1101/gad.304782.117; *-equal contribution
2017Shaytan AK*, Xiao H*, Armeev GA, Wu C, Landsman D, Panchenko AR. Hydroxyl-radical footprinting combined with molecular modeling identifies unique features of DNA conformation and nucleosome positioning. Nucleic Acids Res. 2017;45: 9229–9243. doi:10.1093/nar/gkx616; *-equal contribution
2017El Kennani S, Adrait A, Shaytan AK, Khochbin S, Bruley C, Panchenko AR, et al. MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones. Epigenetics Chromatin. 2017;10: 2. doi:10.1186/s13072-016-0109-x
2016Draizen EJ*, Shaytan AK*, Marino-Ramirez L, Talbert PB, Landsman D, Panchenko AR. HistoneDB 2.0: a histone database with variants--an integrated resource to explore histones and their variants. Database-the Journal of Biological Databases and Curation. 2016;2016. doi:10.1093/database/baw014; *-equal contribution
2016Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions. J Mol Biol. 2016;428: 221–237. doi:10.1016/j.jmb.2015.12.004
2016Valieva ME, Armeev GA, Kudryashova KS, Gerasimova NS, Shaytan AK, Kulaeva OI, et al. Large-scale ATP-independent nucleosome unfolding by a histone chaperone. Nat Struct Mol Biol. 2016;23: 1111–1116. doi:10.1038/nsmb.3321
2015Shaytan AK, Landsman D, Panchenko AR. Nucleosome adaptability conferred by sequence and structural variations in histone H2A–H2B dimers. Curr Opin Struct Biol. Elsevier; 2015;32C: 48–57. doi:10.1016/j.sbi.2015.02.004
2014Nishi H, Shaytan A, Panchenko AR. Physicochemical mechanisms of protein regulation by phosphorylation. Front Genet. 2014;5: 270. doi:10.3389/fgene.2014.00270
2013Yolamanova M, Meier C, Shaytan AK, Vas V, Bertoncini CW, Arnold F, et al. Peptide nanofibrils boost retroviral gene transfer and provide a rapid means for concentrating viruses. Nat Nanotechnol. 2013;8: 130–136. doi:10.1038/nnano.2012.248
2011Shaytan AK, Schillinger E-K, Khalatur PG, Mena-Osteritz E, Hentschel J, Börner HG, et al. Self-assembling nanofibers from thiophene-peptide diblock oligomers: a combined experimental and computer simulations study. ACS Nano. ACS Publications; 2011;5: 6894–6909. doi:10.1021/nn2011943
2010Shaytan AK, Ivanov VA, Shaitan KV, Khokhlov AR. Free energy profiles of amino acid side chain analogs near water-vapor interface obtained via MD simulations. J Comput Chem. Wiley Online Library; 2010;31: 204–216. doi:10.1002/jcc.21267
2009Shaytan AK, Shaitan KV, Khokhlov AR. Solvent accessible surface area of amino acid residues in globular proteins: correlation of apparent transfer free energies with experimental hydrophobicity scales. Biomacromolecules. 2009;10: 1224–1237. doi:10.1021/bm8015169
Theses/Dissertations
2011Shaytan AK. Computer simulations of self-assembling nanofibers from thiophene-peptide oligomers. PHD thesis. Universität Ulm. 2012. doi:10.18725/OPARU-1936
2010Shaytan AK. Computer simulations and statistical analysis of self-organizing molecular structures based on peptides (in Russian). PHD thesis. Moscow State University. 2010. PDF
2007Shaytan AK. Study of hydration and adsorption of amino acid side chains via MD simulations (in Russian). Master thesis. Moscow State University. 2007. PDF
PATENTS/
SOFTWARE
REGISTRATION
• (RU0002580006) METHOD FOR SCREENING OF POTENTIAL ANTICANCER PREPARATIONS - FACT INHIBITORS
• Software suite for reconstruction of spatial structures of proteins and complex based on low-resolution electron density maps (in Russian)
REFERENCES
Prof. Alexei R. Khokhlov (PHD advisor)
Member of Russian Academy of Sciences
Chief, Chair of Polymer and Crystal Physics
Moscow State University, Russia
Dr. Anna R. Panchenko (Post-doctoral advisor)
Lead Scientist
National Center for Biotechnology
Information, NIH, USA
Dr. David Landsman
Chief, Computational Biology Branch
National Center for Biotechnology
Information, NIH, USA
Prof. Carl Wu
Member of National Academy of Sciences
Department of Biology, Johns Hopkins University, USA
Prof. Pavel G. Khalatur
Institute of Advanced Energy Related
Nanomaterials, University of Ulm, Germany
PROFESSIONAL
ACTIVITIES
Reviewer
  • PLOS Computational Biology
  • Journal of Molecular Biology
  • Journal of Physical Chemistry
  • Nucleic Acids Research
  • Biophysical Journal
  • Journal of Biomolecular Structure and Dynamics
  • Molecular Simulation/Journal of Experimental Nanoscience
  • Scientific Reports
Member
  • Biophysical Society