Ivan Ovcharenko Research Group at NCBI

	Computational Biology Branch

	Ivan Ovcharenko Research Group


Research Projects	Publications	Collaborations	Resources	Group Members	Principal Investigator	Visiting us

Investigator
Computational Biology Branch
National Center for Biotechnology Information (NCBI)
National Library of Medicine (NLM)
National Institutes of Health (NIH)
Building 38A, Room 6S602
8600 Rockville Pike
Bethesda, Maryland 20894, USA
Phone: (301) 435-8944
Fax: (301) 480-2290
Email: ovcharei@ncbi.nlm.nih.gov

Ph.D., Physics and Mathematics, 1999
Novosibirsk State University, Novosibirsk, Russia
M.S. with honors, Physics, 1996
Novosibirsk State University, Novosibirsk, Russia

June 2007 - present	Investigator, NCBI/NLM, National Institutes of Health (NIH), Bethesda, MD
June 2003 - June 2007	Tenure-track Scientist, Lawrence Livermore National Laboratory (LLNL), Livermore, CA
January 2003 - June 2007	Visiting Scientist, Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA
January 2001 - June 2003	Staff Scientist, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA
October 1999 - December 2000	Postdoctoral Fellow, UC Berkeley, Berkeley, CA

Current research is funded by the NIH Intramural Research Program.

Previous funding
DOE/OBER, $305k/18month (FY'04-05)
  Development of computational methods for decoding the transcriptional machinery language of genomes to model novel biological systems. Role: PI.
LLNL LDRD, $750k/3years (FY'04-06)
  De novo identification of regulatory regions in intergenic spaces of prokaryotic genomes. Role: Co-PI.
LLNL LDRD, $1,050k/3years (FY'03-05)
  A coupled computational and experimental approach to determine functions of deeply conserved anonymous human genes. Role: Co-PI.
DOE/OBER, $1,260k/3years (FY'05-07)
  Identification and Validation of Low-Dose Irradiation Responsive Transcription Factor sites. Role: Co-PI.
LLNL LDRD, $250k/year (FY06)
  Development of Computational Techniques For Decoding The Language of Genomes. Role: PI.
NIH R01 (5R01HG003963-02), $450k/year
  Deciphering Principles of Regulatory Genomics; Role: PI
  PI-ship transferred to Co-PI, Gabriela Loots, after the move to the NIH Intramural Research Program.
NIH R21 grant proposal
  Computational tools for decoding vertebrate genome regulation; Role: PI
  withdrawn upon the move to the NIH Intramural Research Program.

Member of the Editorial Board of Bioinformatics, 2009-2012
Associate Editor of BMC Bioinformatics, 2009-2012
Ad-hoc Associate Editor of PLoS Genetics

Special Session organizer at the ISMB/ECCB 2009 Conference; "Regulatory Genome Architecture and Noncoding Mutations in Human Disease"
Committee member of the ISMB/ECCB 2009 program on "Sequence Analysis and Alignment"
Program Committee member of the ISMB/ECCB 2009 Travel Fellowship

Judge for the NIH Fellows Award for Research Excellence (FARE), 2008 and 2009.
Judge for the NIH National Graduate Student Research Festival, 2008

Reviewer for Genome Research, PLoS Genetics, Nature Genetics, Human Molecular Genetics, Nucleic Acids Research, Developmental Biology, BMC Bioinformatics, Briefings in Bioinformatics, and other journals Ad hoc referee for the National Science Foundation and the Biology and Biological Sciences Research Council, UK

2007 Excellence in publication award, Lawrence Livermore National Laboratory
2005 Nominated for the PECASE (Presidential Early Career Awards in Science and Engineering) award
2004 Certificate of Appreciation award, Lawrence Livermore National Laboratory
2001 Outstanding Performance award, Lawrence Berkeley National Laboratory
1999 Achievement in Chemical Physics award, Siberian Branch of Russian Academy of Sciences, Russia
1996 Best research award at the International Scientific Conference "Student and Scientific Progress", Novosibirsk, Russia
1995 Best student award, Department of Chemical Physics, Novosibirsk State University, Russia

2008  NIH Genome-wide Chromatin Structure and Function symposium, Bethesda, MD
2008  Program in Integrative Information, Computer and Application Sciences, Princeton University
2007  Penn State University
2007  "Deciphering the regulatory genome: development, evolution and disease" workshop, Baeza, Spain
2007  University of Maryland
2007  Stanford University
2007  Experimental Biology Annual Meeting, Washington, DC
2007  UC San Francisco
2006  UC San Diego School of Medicine
2006  National Human Genome Research Institute
2006  Department of Genetics, Harvard Medical School
2005  Department of Molecular and Cell Biology, UC Berkeley
2005  The Institute for Genome Research (TIGR)
2004  BioQUEST Workshop on Systems Biology Education for Undergraduate Faculty, Beloit College, Beloit, WI
2003  CSHL course on Computational Genomics, "Algorithms for Genome Comparisons", Cold Spring Harbor Laboratory
2003   Medical College of Wisconsin, Milwaukee, WI

42. L. Taher and I.Ovcharenko, Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements, Bioinformatics, 25:578-84 (2009).
41. I. Ovcharenko, Widespread ultraconservation divergence in primates, Molecular Biology and Evolution, 25(8), 1668-1676 (2008).
40. V.Gotea and I. Ovcharenko, DiRE: identifying distant regulatory elements of co-expressed genes, Nucleic Acids Research, 36, 133-139 (2008).
39. G.G. Loots and I. Ovcharenko, Mulan: multiple-sequence alignment to predict functional elements in genomic sequences, Methods Mol Biol., 395:237-254 (2007).
38. L. Gordon, S. Yang, M. Tran-Gyamfi, D. Baggott, M. Christensen, A. Hamilton, R. Crooijmans, M. Groenen, S. Lucas, I. Ovcharenko, and L. Stubbs, Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions, Genome Research, 17(11), 1603-1613 (2007).
37. L.A. Pennacchio, G.G. Loots, M.A. Nobrega, and I. Ovcharenko, Predicting Tissue-Specific Enhancers in the Human Genome, Genome Research, 17, 201-211, (2007) (featured on the cover of the journal)
36. J. Aerts, H.J. Megens, T. Veenendaal, I. Ovcharenko, R. Crooijmans, L. Gordon, L. Stubbs, M. Groenen, Extent of linkage disequilibrium in chicken, Cytogenet Genome Research, 117(1-4):338-45 (2007).
35. G.G. Loots and I. Ovcharenko, ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes., Bioinformatics, 23(1), 122-124 (2007).
34. G.G. Loots, P.S.G. Chain, S. Mabery, A. Rasley, E. Garcia, and I. Ovcharenko, Array2BIO: from microarray expression data to functional annotation of co-regulated genes, BMC Bioinformatics, 7, 307-311 (2006),
33. J.D. Kim, A.K. Hinz, A. Bergmann, J.M. Huang, I. Ovcharenko, L. Stubbs, J. Kim, Identification of clustered YY1 binding sites in imprinting control regions, Genome Research, 16(7), 901-911 (2006)
32. G.G. Loots and I. Ovcharenko, DCODE.ORG Anthology of Comparative Genomic Tools, Nucleic Acids Research, 33, W56-64 (2005)
31. I. Ovcharenko and M.A. Nobrega, Identifying Synonymous Regulatory Elements in Vertebrate Genomes, Nucleic Acids Research, 33, W403-7, (2005)
30. I. Ovcharenko, G. Loots, M. Nobrega, R. Hardison, W. Miller, and L. Stubbs, Evolution and Functional Classification of Vertebrate Gene Deserts, Genome Research, 15(1), 137-145 (2005). (featured on the cover of the journal.)
29. L.W. Hillier, … I. Ovcharenko, … R.K. Wilson (117 authors total), Generation and annotation of the DNA sequences of human chromosomes 2 and 4, Nature, 434, 724-731 (2005).
28. I. Ovcharenko, G. Loots, B. Giardine, M. Hou, J. Ma, R. Hardison, L. Stubbs, and W. Miller, Mulan: Multiple-Sequence Local Alignment and Visualization for Studying Function and Evolution, Genome Research, 15(1), 184-194 (2005)
27. J.T. Shin, J.R. Priest, I. Ovcharenko, A. Ronco, R.K. Moore, C.G. Burns, C.A. MacRae, Human-zebrafish non-coding conserved elements act in vivo to regulate transcription, Nucleic Acids Research, 33(17), 5437-5445 (2005)
26. L.W. Hillier, … I. Ovcharenko, … R.K. Wilson (175 authors total), Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution, Nature, 432, 695-716 (2004).
25. G.K. Wong, … I. Ovcharenko, …H. Yang (114 authors total) , A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms, Nature, 432, 717-722 (2004)
24. I. Ovcharenko, L. Stubbs, and G.G. Loots, Interpreting Mammalian Evolution using Fugu Genome Comparisons, Genomics, 84(5), 890-895 (2004)
23. I. Ovcharenko, M.A. Nobrega, G.G. Loots, and L. Stubbs, ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes, Nucleic Acids Research, 32, W280-W286 (2004)
22. R. Sharan, A. Ben-Hur, G.G. Loots, I. Ovcharenko, CREME: Cis-Regulatory Module Explorer for the human genome, Nucleic Acids Research, 32, W253-256 (2004).
21. I. Ovcharenko, D. Boffelli, G. Loots, eShadow: A Tool for Comparing Closely Related Sequences, Genome Research, 14(6), 1191-1198 (2004)
20. G.G. Loots and I. Ovcharenko, rVISTA 2.0: evolutionary analysis of transcription factor binding sites, Nucleic Acids Research, 32, W217-W221 (2004)
19. I. Ovcharenko and G. Loots, Comparative Genomics Tools for Exploring the Human Genome. CSHL Symposia on Quantitative Biology; The genome of Homo Sapiens, 68, 283-291, (2004)
18. International Human Genome Sequencing Consortium, Finishing the euchromatic sequence of the human genome, Nature 431(7011), 931-945 (2004).
17. J. Grimwood, … I. Ovcharenko, … S.M. Lucas (98 authors total), The sequence and biology of human chromosome 19, Nature, 428, 529-535 (2004)
16. I. Ovcharenko, G. Loots, R.C. Hardison, W. Miller, Lisa Stubbs, zPicture: Dynamic alignment and visualization tool for analyzing conservation profiles, Genome Research, 14(3), 472-477 (2004)
15. M. Nobrega*, I. Ovcharenko*, V. Afzal, E. Rubin, Scanning Human Gene Deserts for Long-Range Enhancers, Science, 302(5644), 413 (2003) (co-first author)
14. R. Sharan, A. Ben-Hur, G.G. Loots, and I. Ovcharenko, CREME: Cis-Regulatory Module Explorer for the human genome, Nucleic Acids Research, 32, W253-W256 (2004)
13. D. Boffelli, J. MacAuliffe, D. Ovcharenko, K. Lewis, I. Ovcharenko, L. Pachter, E. Rubin, Phylogenetic analysis of primate sequences reveals functional regions of the human genome, Science, 299(5611), 1391-4, (2003)
12. I. Ovcharenko and G. Loots, Finding the Needle in the Haystack: Computational Strategies for Discovering Regulatory Sequences in Genomes, Current Genomics, 4, 557-568, (2003).
11. G. Loots, I. Ovcharenko, L. Pachter, I. Dubchak, E. Rubin, rVista for comparative sequence-based discovery of functional transcription factor binding sites, Genome Research, 12(5):832-9, (2002)
10. I. Ovcharenko, W.A. Lester, C. Xiao, and F. Hagelberg, Quantum Monte Carlo characterization of small Cu-doped silicon clusters: CuSi 4 and CuSi6, J. Chem. Phys., 114 (20) , 9028-9032 (2001)
9. I. Ovcharenko, A. Aspuru-Guzik, W.A. Lester, Soft pseudopotentials for efficient quantum Monte carlo calculations: From Be to Ne and Al to Ar, J. Chem. Phys., 114 (18), 7790-7794 (2001)
8. C. Xiao, F. Hagelberg, I. Ovcharenko, and W.A. Lester, Geometric structures and stabilities of CuSin clusters (n=8,10,12), J. Mol. Struct. (THEOCHEM), 549, 181-192 (2001)
7. M.B. Taraban, A.I. Kruppa, O.S. Volkova, I. Ovcharenko, R.N. Musin, T.V. Leshina, E.C. Korolenko, and K. Kitahara, Origin of Magnetic Field Effect in the Photolysis of 7-Silanorbornadiene Derivatives in Solution, J. Phys. Chem. A, 104(9), 1811-1816, (2000).
6. I. Ovcharenko, Y.G. Shvedenkov, R.N. Musin, and V.N. Ikorskii, Determination of exchange interaction parameters in heterospin exchange clusters , J. Structural Chem., 40(1), 36-43 (1999).
5. V.A. Reznikov, I. Ovcharenko, N.V. Pervukhina, V.N. Ikorskii, A. Grand, and V.I. Ovcharenko, Persistent vinylnitroxides, Chem. Commun., 539-540 (1999).
4. A.B. Burdukov, V.I. Ovcharenko, N.V. Pervukhina, V.N. Ikorskii, I.A. Grigoriev, I.A. Kirillyuk, I. Ovcharenko, and R.N. Musin, Synthesis, Structure, and Magnetic Properties of Mixed-Ligand Complexes of Nickel and Cobalt Hexafluoroacetylacetonates with the Nytroxyl Radical 4-Carbamoyl-2,2-dimethyl-5,5-dimethoxy-3-imidazolin-1-yloxy, Russian J. of Inorganic Chem., 44 (7), 1131-1138 (1999).
3. V.I. Ovcharenko, G.V. Romanenko, I.V. Korobkov, V.N. Ikorskii, I. Ovcharenko, R.N. Musin, K.E. Vostrikova, A.V. Podoplelov, O.V. Shishkin, and Y.T. Struchkov, Crystal structure and magnetic properties of octahedral Ni(II) complexes with 3-imidazoline nitroxides, J. Structural Chem., 39 (5) , 734-746 (1998).
2. R.N. Musin, I. Ovcharenko, L. Orstrem, and P. Rey, Magnetic properties of Cu(II) bischelate complexes with 3-imidazoline nitroxides. I. An ab initio analysis of spin density delocalization channels, J. Structural Chem., 38 (5) , 703-710 (1997).
1. R.N. Musin, I. Ovcharenko, L. Orstrem, and P. Rey, Magnetic properties of Cu(II) bischelate complexes with 3-imidazoline nitroxides. II. An ab initio analysis of exchange interaction mechanisms, J. Structural Chem., 38 (5), 711-715 (1997).

Disclaimer Privacy statement
Last modified: April 22, 2009