Moscow State University
Faculty of Physics
Chair of Biophysics
Bioinformatics Group Leader
Fellow, Chair of
Biophysics, Faculty of Physics, Lomonosov
Moscow State University, Russia
||Postdoc, Institute of Computational Biomedicine, Weill Cornell Medical College|
|| Postdoc, Peter Gogarten Lab,
University of Connecticut, USA
|2004||Ph.D. in Biophysics (Nonlinear dynamics), Faculty of Physics, Moscow State University, Russia|
|1995||Diploma in Biophysics (Nonlinear dynamics), Faculty of Physics, Moscow State University, Russia|
|1993||Group Cell Biophysics, Institute of Neurobiology, Amsterdam University, Netherlands|
bioinformatics algorithms and
Cryptic Language of the DNA
software development (DNA Punctuation); detection, visulazation and comparative analysis of short palinddromes and direct repeats
Orthologous Gene Families
phylogenetic algorithm (BranchClust), genome annotation, evolution of large homologous superfamilies, domain migration in and accross genomes
Horizontal Gene Transfer
phylogentic methods to detect horizontal gene transfer, software tool (GPX) that applies machine learning algorithms such as self-organizing maps (SOM) to genome spectrum (bipartition and quartet) analysisVisual genomics
application of method of 2D DNA walk to various chromosomes from bacteria to humans to study functional and structural organizations of chromosomes of different organisms.
|DNA Punctuation|| Program
searches for and visualizes short palindromes and
selecting gene families:
maps applied to
bipartition and quartet spectrum analysis:
System Biology. Computer Methods. Spring 2012.
Bioinformatics. Spring 2013.
|Books and Book Chapters
S. Poptsova, (Editor)
Genome Analysis: Current Procedures and Applications. Caister Academic Press, Norfolk, UK (January 1, 2014) , ISBN: 978-1-908230-29-4
Computational Techniques for Orthologous Gene
Chapter 9 in
Ying Xu and J Peter Gogarten (eds.) (2008) Computational Methods for Understanding Bacterial and Archaeal Genomes. Imperial College Press, London, ISBN-13: 978-1-86094-982-1.
Phylogenetic Methods to Identify HGT,
Chapter 13 in
Maria B. Gogarten, Johann Peter Gogarten, Lorraine C. Olendzenski (eds.) (2009) Horizontal Gene Transfer: Genomes in Flux. Humana Press - Springer; 1 edition, ISBN-13: 978-1603278522
S. A., A.
Loskutov, M. S. Poptsova, S. D. Rybalko and E. V.
A. Rubin and B. Riznichenko (eds.) (2010) Dynamic models of the processes in the cell and subcellular nanostructures. RHD. (in Russian) ISBN 978-5-93972-783-9
Poptsova M, Banerjee S, Gokcumen O, Rubin MA, Demichelis F. (2013)Impact of constitutional copy number variants on biological pathway evolution. BMC Evol Biol. 2013 Jan 23;13:19. doi: 10.1186/1471-2148-13-19. Link
Mao F, Williams D, Zhaxybayeva O, Poptsova M, Lapierre P,
Gogarten JP, Xu Y.
(2012) Quartet decomposition server: a platform for
phylogenetic trees BMC
2012 Jun 7;13:123. doi:10.1186/1471-2105-13-123
Transfer and Microbial Evolution: Testing Methods of
Invited lecture at the University of Rhode Island,
"Automated Assembly of Gene Families and Detection of Horizontally Transferred Genes". Invited lecture at the workshop on Comparative Genome Analysis of Bacterial Genomes and Applications.Computational Systems Bioinformatics Conference (CSB2006), The Life Science Society, August 14-18, 2006. Stanford, CA
“BranchClust: a phylogenetic algorithm for selecting gene families”, Invited lecture at the XVII NEMEB Meeting (New England Molecular Evolutionary Biologists), November 4, 2006, University of Massachusetts Amherst, MA
“Computational Techniques for Orthologous Gene Prediction in Prokaryotes”, Invited lecture at the Physic Department, Moscow State University, Russia, October 29, 2008.
"Automated Assembly of Gene Families and Detection of Horizontally Transferred Genes". Invited lecture at the National Center for Biotechnology Information, Bethesda, MD, November 30, 2009.
"Automated Assembly of Gene Families and Detection of Horizontally Transferred Genes". Invited lecture at Weill Cornelll Medical College, New York, NY, October 19, 2009.
"Automated Assembly of Gene Families and Detection of Horizontally Transferred Genes". Invited lecture at University of California Berkeley, CA, December 21, 2010.
Larionov S., Rybalko, Poptsova M. and Loskutov A: Intermittency as a universal characteristics of the complete chromosome DNA sequences of eukaryotes: From protozoa to human genomes, XXXI Dynamics Days in Europe, Oldenburg, Germany, September 12-16, 2011.
Fenglou Mao, Maria Poptsova, David Williams, Olga Zhaxybayeva, Peter Gogarten and Ying Xu: Quartet Decomposition Server: A Platform For Analyzing Phylogenetic Trees, 6th International Symposium on Bioinformatics Research and Applications, Storrs, CT, May 23-26, 2010.
Olga Zhaxybayeva, J. Peter Gogarten, Maria Poptsova, R. Thane Papke and W. Ford Doolittle: Evolution of Prochlorococcus and marine Synechococcus: an update , CIFAR Integrated Microbial Biodiversity program meeting, Vancouver, BC, October 9-12, 2007
Larionov S.A., Loskutv A. Yu., Ryadchenko E.V., Poptsova M.S., Zakharov I.A: Visual genomics: Gigantic palindrome disintegration as a common event of genomes evolution: Moscow Conference on Computational Molecular Biology (MCCMB'07) Moscow, Russia, 27-30 July 2007
Larionov S.A., Loskutov A. Yu., Ryadchenko E.V., Poptsova M.S., Zakharov I.A: Visual Genomics and Distributed Context Correlation Analysis: Gigantic Palindrome Disintegration as a Common Event of Genomes Evolution, Possible Origin of Function Diversity and Co-functionality. 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) & 6th European Conference on Computational Biology (ECCB), Austria, Vienna, July 19-20, 2007
Larionov S.A., Loskutov A. Yu., Ryadchenko E.V., Poptsova M.S., Zakharov I.A: Visual genomics: Gigantic palindrome disintegration as a common event of genomes evolution, Physical and Chemical Foundations of Bioinformatics Methods International workshop, June 18 - 22, 2007, MPIPKS, Dresden, Germany
Maria Poptsova, Timothy J. Harlow and J. Peter Gogarten: The Power of Phylogenetic Approaches to Detect Horizontally transferred Genes, presented at the Phylogenomics Conference, Saint-Adèle, Québec, Canada, March 15-19 2006.
Maria Poptsova, Georgy Guria: Autowave Tunneling Through a Non-excitable Area of Active Media. Thesis on international conference Self-organization Criteria in Physical, Chemical and Biological Systems. Souzdal 1995.