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  Research Group of Ivan Ovcharenko




Ivan Ovcharenko, Ph.D.

Senior 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, MD 20894
Email: ovcharen _at_ nih _dot_ gov

and

Adjunct Professor
Bioinformatics Graduate Program at Boston University

Professional Experience

Sep'14 - present  Senior Investigator, NCBI/NLM, National Institutes of Health (NIH), Bethesda, MD
Jun'07 - Sep'14  Tenure-Track Investigator, NCBI/NLM, National Institutes of Health (NIH), Bethesda, MD
Jun'03 - Jun'07Tenure-track Scientist, Lawrence Livermore National Laboratory (LLNL), Livermore, CA
Jan'03 - Jun'07Visiting Scientist, Department of Energy Joint Genome Institute (JGI), Walnut Creek, CA
Jan'01 - Jun'03Staff Scientist, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA
Oct'99 - Dec'00Postdoctoral Fellow, UC Berkeley, Berkeley, CA
1999Ph.D., Physics and Mathematics, Novosibirsk State University, Novosibirsk, Russia
1996M.S. with honors, Physics, Novosibirsk State University, Novosibirsk, Russia

Funding

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

Scientific Community Service

Member of the Editorial Board of Bioinformatics, 2009-present
Associate Editor of BMC Bioinformatics, 2009-present
Ad-hoc Associate Editor of PLoS Genetics and PLoS Computational Biology

Session chair at the Keystone Symposium on Biomolecular Interaction Networks, 2010
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 "Sequence Analysis and Alignment"
Committee member of the ISMB 2010, ISMB 2011, ISMB 2012, and ISMB 2013 program "Sequence Analysis" and the ISMB 2012 program "Evolution and Comparative Genomics"
Committee member of the ISMB 2011 and ISMB 2012 Special Interest Group (SIG) review panel
Program committee member of the 2013 ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics
Technical Program Committee member of the 2012 Brazilian Symposium on Bioinformatics (BSB 2012)
Program Committee member of the ISMB/ECCB 2009 Travel Fellowship

Chair of the NCBI Seminar Series, 2009-present
Co-organizer of the 1st CBB/NCBI Scientific Retreat, 2013. Session chair at the 2nd CBB/ NCBI Scientific Retreat, 2014.

Serving on the NIH Grant Review panel of NHGRI reviewing applications submitted in response to the RFA-HG-11-025 "Computational Analysis of the Encyclopedia of DNA Elements (ENCODE) Data (U01)" (2012), RFA-HG-00-72-34 "The Genomic Resource Grants for Community Resource Projects (U41)" (2012), and RFA-HG-13-012 "Genomics of Gene Regulation (U01)" (2014).
Serving on the NIH Grant Review panel of NINDS reviewing applications submitted in response to the RFA-NS-11-001 call for developing a re-designed and enhanced Parkinson's Disease Data Organizing Center (PD-DOC), 2010
Serving on the grant review panel of Genome Canada for "2010 Large-Scale Applied Research Project Competition", 2011 and Genome Canada Bioinformatics and Computational Biology (2013).
Serving on graduate student thesis committees. Zachary Stine, Johns Hopkins University, 2009-2011. Parsa Hosseini, George Mason University, 2012-2013. Justin Malin, University of Maryland, College Park, 2013-2014.

Member of the NIH-Boston University Graduate Partnership Program search committee, 2010-present
Member of the Earl Stadtman NIH-wide tenure-track Investigator search Systems Biology committee, 2010.
Member of the NIH Tenure-Track committee, 2012-present

Judge for the NIH Fellows Award for Research Excellence (FARE, 2008, 2009, 2010, 2011, 2012, 2013, and 2014) and the NIH National Graduate Student Research Festival (2008)

Reviewer for Genome Research, PLOS Genetics, Nature Genetics, Nature Communications, Human Molecular Genetics, Nucleic Acids Research, Developmental Biology, BMC Bioinformatics, PLOS ONE, Briefings in Bioinformatics, and several other journals.

Ad hoc referee for the National Science Foundation and the Biology and Biological Sciences Research Council, UK

Recent Publications

67. D. Huang and I. Ovcharenko, Identifying causal regulatory SNPs in ChIP-seq enhancers, Nucleic Acids Research (2014, in press)
66. D. Huang and I. Ovcharenko, Genome-Wide Analysis of Functional and Evolutional Features of Tele-Enhancers, G3: Genes, Genomes, Genetics, 16(4):579-93 (2014)
65. S.M. Ahmad*, B.W. Busser*, D. Huang*, E.J. Cozart, S. Michaud, X. Zhu, N. Jeffries, A. Aboukhalil, M.L. Bulyk, I. Ovcharenko+, and A.M. Michelson+, Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification, Development, 141:878-888 (2014) (* co-first, + co-corresponding)
64. L. Taher, R.P. Smith, M.J. Kim, N. Ahituv+, I. Ovcharenko+, Sequence signatures extracted from proximal promoters can be used to predict distal enhancers, Genome Biology, 14(10):R117 (2013) (+ co-corresponding)
63. R.P. Smith*, L. Taher*, R.P. Patwardhan, M.J. Kim, F. Inoue, J. Shendure+, I. Ovcharenko+, N. Ahituv+, Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model, Nat Genet., 45(9):1021-8 (2013) (* co-first, + co-corresponding)
62. C.H. Hsu and I. Ovcharenko, Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts, Phil. Trans. R. Soc. B, 368:1620 (2013)
61. A. Visel, L. Taher, H. Girgis, D. May, O. Golonzhka, R. Hoch, G.L. McKinsey, K. Pattabiraman, S.N. Silberberg, M.J. Blow, D.V. Hansen, A.S. Nord, J.A. Akiyama, A. Holt, R. Hosseini, S. Phouanenavong, I. Plajzer-Frick, M. Shoukry, V. Afzal, T. Kaplan, A.R. Kriegstein, E.M. Rubin, I. Ovcharenko, L.A. Pennacchio, J.L.R. Rubenstein, A High-Resolution Enhancer Atlas of the Developing Telencephalon, Cell, 152(4):895-908 (2013)
60. J.E. Kugler, M. Horsch, D. Huang, ... I. Ovcharenko and M. Bustin (30 authors total), High Mobility Group N (HMGN) Proteins Modulate The Fidelity Of The Cellular Transcriptional Profile In A Tissue And Variant Specific Manner, JBC, 288(23):16690-703 (2013)
59. P. Hosseini, I. Ovcharenko and B.F. Matthews, Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites, Plant Methods, 9(1):12 (2013) 58. G.G. Loots, A. Bergmann, N.R. Hum, C.E. Oldenburg, A.E. Wills, N. Hu, I. Ovcharenko, R.M. Harland, Interrogating transcriptional regulatory sequences in tol2-mediated Xenopus transgenics, PLoS One, 8(7):e68548 (2013)
57. B.W. Busser*, D. Huang*, K.R. Rogacki*, E.A. Lane, L. Shokri, T. Ni, S.S. Gisselbrecht, J. Zhu, M.L. Bulyk, I. Ovcharenko+, A.M. Michelson+, Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network, PNAS, 109(50):20768-73 (2012) (* co-first, + co-corresponding)
56. G. Burzynski, X. Reed, L. Taher, ZE. Stine, T. Matsui, I. Ovcharenko*, AS. McCallion*, Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control, Genome Research, 22(11), 2278-89 (2012) (* co-corresponding)
55. BW. Busser*, L. Taher*, Y. Kim, T. Tansey, MJ. Bloom, I. Ovcharenko+, AM. Michelson+, A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis, PLoS Genetics, 8(3):e1002531 (2012) (* co-first, + co-corresponding)
54. H. Girgis and I. Ovcharenko, Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs, BMC Bioinformatics, 13(1):25 (2012)
53. L. Taher, L. Narlikar, I. Ovcharenko, CLARE: Cracking the LAnguage of Regulatory Elements, Bioinformatics, 28(4):581-3 (2012)
52. L. Taher, D.M. McGaughey, S. Maragh, I. Aneas, S.L. Bessling, W. Miller, M.A. Nobrega, A.S. McCallion, I. Ovcharenko, Genome-wide identification of conserved regulatory function in diverged sequences, Genome Research, 21(7):1139-49 (2011)
51. L. Taher, N.M. Collette, D. Murugesh, E. Maxwell, I. Ovcharenko, G.G. Loots, Global gene expression analysis of murine limb development, PLoS ONE, 6(12):e28358 (2011)
50. D. Martin, … (24 authors), Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes, Nature Structural Molecular Biology, 18(6):708-14 (2011).
49. M. Rochman, L. Taher, T. Kurahashi, S. Cherukuri, V.N. Uversky, D. Landsman, I. Ovcharenko, M. Bustin, Effects of HMGN variants on the cellular transcription profile, Nucleic Acids Research, 39(10):4076-4087 (2011).
48. Hellsten U, ... (48 authors), The Genome of the Western Clawed Frog Xenopus tropicalis, Science, 328:633-636 (2010)
47. Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I., Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers, Genome Research, 20(5):565-77 (2010)
46. L. Narlikal, N.J. Sakabe, A.A. Blanski, F.E. Arimura, J.M. Westlund, M.A. Nobrega, I. Ovcharenko, Genome-wide discovery of human heart enhancers, Genome Research, 20(3):381-92 (2010).
45. G.G. Loots and I. Ovcharenko, Human Variation in Short Regions Predisposed to Deep Evolutionary Conservation, Molecular Biology and Evolution, 2010 (in press).
44. L. Narlikal and I. Ovcharenko, Identifying regulatory elements in eukaryotic genomes, Brief Funct Genomic Proteomic, 8(4), 215-230 (2009).
43. 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).
42. I. Ovcharenko, Widespread ultraconservation divergence in primates, Molecular Biology and Evolution, 25(8), 1668-1676 (2008).
41. V.Gotea and I. Ovcharenko, DiRE: identifying distant regulatory elements of co-expressed genes, Nucleic Acids Research, 36, 133-139 (2008).
40. 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)






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