2004 - present. Junior researcher, Research and Training Center “Bioinformatics”, IITP RAS
Ph.D. (bioinformatics), 2008

Research interests:

• short reads
• ncRNA
• alternative splicing
• regulation of transcription
• molecular evolution
• programming

Education:

2003-2006. Post-graduate student, Department of Bioengineering and Bioinformatics, Moscow State University
Diploma, Mathematics, 2003, magna cum laude, Department of Mathematics and Mechanics, Moscow State University

Reviewing activity:

Trends in Genetics, Gene


Publications:

Leyn S.A., Kazanov M.D., Sernova N.V., Ermakova E.O., Novichkov P.S., Rodionov D.A. Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis. J Bacteriol 2013 195(11): 2463-2473. PubMed  PDF

Medvedeva YA, Fridman MV, Oparina NJ, Malko DB, Ermakova EO, Kulakovskiy IV, Heinzel A, Makeev VJ. Intergenic, gene terminal, and intragenic CpG islands in the human genome. BMC Genomics. 2010, 11(1):48 PubMed  PDF

Ermakova EO, Nurtdinov RN, Gelfand MS. Overlapping alternative donor splice sites in the human genome JBCB. 2007, 5(5):991-1004. PubMed  PDF

Nurtdinov RN, Neverov AD, Mal'ko DB, Kosmodem'ianskii IA, Ermakova EO, Ramenskii VE, Mironov AA, Gel'fand MS. EDAS, database of alternatively spliced human genes. Biofizika. 2006, 51(4):589-92 PubMed  PDF

Ermakova EO, Mal'ko DB, Gel'fand MS. Different patterns of evolution in alternative and constitutive coding regions of Drosophila alternatively spliced genes Biofizika. 2006, 51(4):581-8 PubMed  PDF

Ermakova EO, Nurtdinov RN, Gelfand MS. Fast rate of evolution in alternatively spliced coding regions of mammalian genes. BMC Genomics. 2006, 7(1):84 PubMed  PDF


Conferences:

The 5th International Moscow Conference on Computational Molecular Biology, MCCMB-2011. Moscow. Russia, 21-14.07.2011
• E.Ermakova, M.Gelfand, D.Rodionov. CodY regulon in Bacillaceae (poster)
Berlin Summer Meeting. Berlin, Germany, 23-25.06.2011
• E.Ermakova. CodY regulon in Bacillaceae (poster)

ISBRA 2011. Changsha, China, 27-29.05.2011
• E.Ermakova. CodY regulon in Bacillaceae (poster)

4th Int. Moscow Conference on Computational Molecular Biology MCCMB’09 (Moscow, Russia, July 2009)
• D.B. Malko, E.O. Ermakova, and M.S. Gelfand. Evolution of structure and sequence in alternatively spliced Drosophila genes (poster)

17th Annu. Int. Conf. On Intelligent Systems for Molecular Biology and 8th European Conf. On Computational Biology ISMB/ECCB’09 (Stockholm, Sweden, June - July 2009)
• E.O. Ermakova, D.B. Malko, and M.S. Gelfand. Evolution of structure and sequence in alternatively spliced Drosophila genes (poster)

6th Special Interest Group meeting on Alternative Splicing AS-SIG 2009 (Stockholm, Sweden, June 2009)
• E.O. Ermakova, D.B. Malko, and M.S. Gelfand. Evolution of structure and sequence in alternatively spliced Drosophila genes (poster)

4th EMBO Conference: From Functional Genomics to Systems Biology (Heidelberg, Germany, November 2008)
• E.O. Ermakova, D.B. Malko, and M.S. Gelfand. Evolution of alternatively spliced coding regions in 11 Drosophila genomes (poster)

3rd Int. Moscow Conference on Computational Molecular Biology MCCMB’07 (Moscow, Russia, July 2007)
• D.B. Malko, E.O. Ermakova. Evolution of splicing in insects (poster)

15th Annu. Int. Conf. On Intelligent Systems for Molecular Biology and 6th European Conf. On Computational Biology ISMB/ECCB’07 (Vienna, Austria, July 2007)
• E.O. Ermakova, R.N. Nurtdinov, and M.S. Gelfand. Ovelapping alternative donor splicing sites in the human genome (poster)

4th Special Interest Group meeting on Alternative Splicing AS-SIG 2007 (Vienna, Austria, July 2007)
• E.O. Ermakova, D.B. Malko, and M.S. Gelfand. Patterns of selection and evolution of the exon-intron structure in alternatively spliced genes of nine Droshophila species and the malarial mosquito (oral presentation)

Human Genome Meeting HGM2006 (Helsinki, Finland, May 31 - June 3 2006)
• EO. Ermakova. Evolutionary patterns of alternatively spliced coding regions of mammalian and Drosophila genes (poster)

2nd Int. Moscow Conference on Computational Molecular Biology MCCMB’05 (Moscow, Russia, July 2005)
• Ekaterina O. Ermakova. Alternatively spliced regions evolve faster. (poster)