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| 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 |
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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. In 2018 Dr. Shaytan was awarded Moscow City Government Award for Young Scientists. In 2021 Dr. Shaytan received habilitation and now holds the position of professor at Lomonosov Moscow State University. In 2022 Prof. Shaytan was elected as a corresponding member of the Russian Academy of Sciences.
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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.
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WORK
EXPERIENCE |
| 2021- | Full Professor | Department of Bioengineering, Faculty of Biology, Moscow State University |
| 2021- | Associate Professor | Department of Bioengineering, Faculty of Biology, Moscow State University |
| 2017- | Group Leader | Integrative Biology Group, Department of Bioengineering, Faculty of Biology, Moscow State University |
| 2013--2017 | Postdoctoral Visiting Fellow | National Center for Biotechnology Information, National Institutes of Health, USA; Advisor: Dr. Anna R. Panchenko |
| 2012- | Leading researcher | Moscow State University, Faculty of Biology, Department of Bioengineering |
| 2010 | Scientific Coordinator | Russian Technology Platform “Supercomputers and high performance computing” |
| 2010--2012 | Research fellow | Moscow State University, Faculty of Biology, Department of Bioengineering; focus on computer simulations of bio and nano structures |
| 2009--2011 | Research fellow | University of Ulm, Institute of Polymer Science, Ulm, Germany; Advisors: Prof. A.R. Khokhlov, Prof. P.G. Khalatur |
| 2008--2010 | Leading engineer | Moscow State University, Faculty of Biology, Department of Bioengineering; focus on IT infrastructure for computer simulations |
| 2006--2008 | School teacher | School N1326/Lyceum 1586, subjects: computer modeling (10-11 grades), computer methods in biology and physics (7-9 grades) |
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EDUCATION/
DEGREES |
| 2021 | Doctor of Science (computational biology and bioinformatics) | Moscow State University, Russia; Thesis title “Integrative modeling of structure and dynamics of biomacromolecular complexes”; Advisor Prof. M.P. Kirpichnikov |
| 2016 | Certificate | Advanced Studies in Technology Transfer, FAES Graduate School at National Institues of Health, USA (15 credits, GPA 4.0, max 4.0) |
| 2014--2016 | | Advanced Studies in Technology Transfer, FAES Graduate School at National Institues of Health, USA |
| 2011 | Dr. 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 |
| 2010 | PHD 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--2010 | PHD student | Moscow State University, Faculty of Physics, Chair of Physics of Polymers and Crystals |
| 2007--2008 | | “Innovation Studio” Entrepreneurship Study Program at Moscow State University |
| 2007 | Master of Science degree | Moscow 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--2007 | Student | Moscow State M.V. Lomonosov University, Faculty of Physics |
| 2002--2005 | | Russian-German Institute of Science and Culture at MSU |
| 1991--2001 | School student | Moscow Comprehensive School No. 1260 with advanced studies of English language. School-leaving certificate with gold medal (GPA 5.0, max 5.0) |
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AWARDS
SCHOLARSHIPS |
| 2018 | | Moscow City Government Award for Young Scientists |
| 2013 | | Scholarship of US-Russia Collaboration in the Biomedical Sciences NIH Visiting Fellows Program |
| 2013 | | Finalist of the 37-th competition of scientific works by young scientists of Lomonosov Moscow state University |
| 2012 | | Finalist of the contest of works by talented students, graduates and young scientists of Lomonosov Moscow State University established by O.V. Deripaska |
| 2008 | | BioCamp 2008, Novartis International Biotechnology Leadership Camp, Hong Kong: leader of the best Best Performing Team, 2nd Runner Up Best Performing Student |
| 2008 | | Russian Innovation Contest, participant of the 2nd round |
| 2005 | | Scholarship of Vladimir Potanin Foundation |
| 2005 | | Scholarship “Grant of Moscow” |
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| PUBLICATIONS |
| GoogleScholar Pubmed Complete list of publications with PDFs |
| Selected papers |
| 2019 | Hada A., Hota S.K., Luo J., Lin Y., Kale S., Shaytan AK, Bhardwaj S.K., Persinger J., Ranish J., Panchenko A.R., Bartholomew B. Histone Octamer Structure Is Altered Early in ISW2 ATP-Dependent Nucleosome Remodeling Cell Reports 2019; doi:10.1016/j.celrep.2019.05.106 |
| 2019 | Armeev GA, Gribkova AK, Pospelova I, Komarova GA, Shaytan AK*. Linking chromatin composition and structural dynamics at the nucleosome level Curr Opin Struct Biol 2018; doi:10.1016/j.sbi.2018.11.006*-corresponding author |
| 2018 | Shaytan AK*, Xiao H, Armeev G, et al. Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID Nature Protocols 2018; doi:10.1038/s41596-018-0048-z; *-corresponding author |
| 2017 | Xiao 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 |
| 2017 | Shaytan 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 |
| 2017 | El 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 |
| 2016 | Draizen 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 |
| 2016 | Shaytan 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 |
| 2016 | Valieva 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 |
| 2015 | Shaytan 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 |
| 2014 | Nishi H, Shaytan A, Panchenko AR. Physicochemical mechanisms of protein regulation by phosphorylation. Front Genet. 2014;5: 270. doi:10.3389/fgene.2014.00270 |
| 2013 | Yolamanova 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 |
| 2011 | Shaytan 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 |
| 2010 | Shaytan 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 |
| 2009 | Shaytan 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 |
| 2011 | Shaytan AK. Computer simulations of self-assembling nanofibers from thiophene-peptide oligomers. PHD thesis. Universität Ulm. 2012. doi:10.18725/OPARU-1936 |
| 2010 | Shaytan AK. Computer simulations and statistical analysis of self-organizing molecular structures based on peptides (in Russian). PHD thesis. Moscow State University. 2010. PDF |
| 2007 | Shaytan AK. Study of hydration and adsorption of amino acid side chains via MD simulations (in Russian). Master thesis. Moscow State University. 2007. PDF |
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PATENTS/
SOFTWARE
REGISTRATION |
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| 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 |
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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
- Current Opinion in Structural Biology
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Member
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