DNA punctuation Logo

Maria Poptsova


Email: maria.poptsova@gmail.com

Moscow State University
Faculty of Physics
Chair of
Bioinformatics Group Leader

Academic Background

MSU Thumb Research Fellow, Chair of Biophysics,  Faculty of Physics, Lomonosov Moscow State University, Russia
 Cornell Logo Postdoc, Institute of Computational Biomedicine, Weill Cornell Medical College 
UconnLogo  Postdoc, Peter Gogarten Lab, University of Connecticut, USA
2004 MSU Thumb Ph.D. in Biophysics (Nonlinear dynamics), Faculty of Physics, Moscow State University, Russia
1995 MSU Thumb Diploma in Biophysics (Nonlinear dynamics), Faculty of Physics, Moscow State University, Russia
1993 UAmst Logo  Group Cell Biophysics, Institute of Neurobiology, Amsterdam University, Netherlands


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 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.

Software and Algorithms

DNA Punctuation  Program that searches for and visualizes short palindromes and direct repeats
BranchClust Algorithm for selecting gene families:
GPX Genome Phylogeny Explorer
SOM maps SOM maps applied to bipartition and quartet spectrum analysis:


System Biology. Computer Methods. Spring 2012.

Bioinformatics. Spring 2013.

Books and Book Chapters

Genome Analysis
Maria S. Poptsova, Genome Analysis: Current Procedures and Applications. Caister Academic Press, Norfolk, UK (January 1, 2014) , ISBN: 978-1-908230-29-4
publisher link

                Computational Methods

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
Genomes in
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

Rybalko S, Larionov S, Poptsova M, Loskutov A. (2011) Intermittency as a universal characteristic of the complete chromosome DNA sequences of eukaryotes: from protozoa to human genomes. Phys. Rev. E 84, 042902. DOI:10.1103/PhysRevE.84.042902. Link

Banerjee S, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F.A (2011) A computational framework discovers new copy number variants with functional importance. PLoS One. 2011 Mar 29;6(3):e17539. doi:10.1371/journal.pone.0017539 Link

Poptsova MS, Gogarten JP (2010) Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 156, 1909-1917; DOI 10.1099/mic.0.033811-0 Link

Poptsova MS, Larionov SA, Ryadchenko EV, Rybalko SD, Zakharov IA, et al. (2009) Hidden Chromosome Symmetry: In Silico Transformation Reveals Symmetry in 2D DNA Walk Trajectories of 671 Chromosomes. PLoS ONE 4(7): e6396.  doi:10.1371/journal.pone.0006396 Link

Poptsova M. Testing phylogenetic methods to identify horizontal gene transfer. Methods Mol Biol. (2009); 532:227-40 Link

Hamel L, Nahar N, Popstova MS, Zhaxybayeva O, Gogarten JP (2008) Unsupervised learning in detection of gene transfer. J. Biomed Biotech 2008, doi: 10.1155/2008/472719 Link

Hamel, L., Nahar, N., Poptsova, M.S., Zhaxybayeva, O. and Gogarten, J.P. (2007) Proceeding of the IEEE Conference Frontiers in the Convergence of Bioscience and Information Technologies (FBIT 2007), October 2007, pp317 - 321, IEEE Press, ISBN 0-7695-2999-2 pdf

Nahar, Neha, Poptsova, Maria S., Hamel, Lutz, and Gogarten, J. Peter (2007) GPX: A Tool for the Exploration and Visualization of Genome Evolution. Proceedings of the IEEE 7th International Symposium on Bioinformatics & Bioengineering (BIBE07) Boston, pp1338 - 1342, IEEE Press, ISBN 1-4244-1509-8. Link

Poptsova MS, Gogarten JP (2007) BranchClust: A phylogenetic algorithm for selecting gene families. BMC Bioinformatics 8:120 Link

Poptsova MS, Gogarten JP (2007) The power of phylogenetic approaches to detect horizontally transferred genes. BMC Evolutionary Biology 7:45 Link
Poptsova M.S., Guria G.T.: Autowave Tunneling Through a Non-excitable Area of Active Media. General Physiology and Biophysics 1997: 16: 241-261. Link

Siegenbeek van Heukelom J., H.G.J. van Mil, M.S. Poptsova, R.Dounaid: What is Controlling the Cell Membrane Potential? Modern Trends in BioThermoKinetics 1994, 3: 169-173 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.