Maria Poptsova |
Email: maria.poptsova@gmail.com |
Moscow State University Faculty of Physics Chair of Biophysics Bioinformatics Group Leader |
Academic
Background |
2011-present |
Research
Fellow, Chair of
Biophysics, Faculty of Physics, Lomonosov
Moscow State University, Russia |
2010-2011 |
Postdoc, Institute of Computational Biomedicine, Weill Cornell Medical College |
2005-2009 |
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 |
Research |
Comparative genomics:
developing
bioinformatics algorithms and
computer tools 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)
analysis
Visual
genomicsapplication
of method
of 2D DNA walk to various chromosomes from bacteria
to humans to study
functional and structural organizations of
chromosomes of different
organisms.
|
Software and
Algorithms |
DNA Punctuation | Program
that
searches for and visualizes short palindromes and
direct repeats http://www.dnapunctuation.org |
BranchClust | Algorithm
for
selecting gene families: http://www.bioinformatics.org/branchclust |
GPX | Genome
Phylogeny
Explorer http://www.bioinformatics.cs.uri.edu/gpx/ |
SOM maps | SOM
maps applied to
bipartition and quartet spectrum analysis: http://bioinformatics.cs.uri.edu/gene-vis/template/ |
Teaching |
System Biology. Computer Methods. Spring 2012. |
|
Bioinformatics. Spring 2013. |
Books and Book Chapters |
Maria
S. Poptsova, (Editor) Genome Analysis: Current Procedures and Applications. Caister Academic Press, Norfolk, UK (January 1, 2014) , ISBN: 978-1-908230-29-4 publisher link |
|
Poptsova
M.
Computational Techniques for Orthologous Gene
Prediction in
Prokaryotes. 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. publisher link |
|
Poptsova
M. Testing
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 publisher link |
|
Larionov,
S. A., A.
Loskutov, M. S. Poptsova, S. D. Rybalko and E. V.
Ryadchenko. Visual
Genomics. Chapter in 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 |
Some Publications |
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
analyzing
phylogenetic trees BMC
Bioinformatics.
2012 Jun 7;13:123. doi:10.1186/1471-2105-13-123
Link
|
Invited Lectures |
“Horizontal
Gene
Transfer and Microbial Evolution: Testing Methods of
Detection”,
Invited lecture at the University of Rhode Island,
February 2006 "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.
|
Presentations at
Meetings |
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. |