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  Research Group of Ivan Ovcharenko

Selected Publications

W. Song, R.Sharan and I. Ovcharenko
The first enhancer in an enhancer chain safeguards subsequent enhancer-promoter contacts from a distance.
Genome Biology, 20(1):197-207 (2019) PDF

S. Li, E. Kvon, A. Visel, L. Pennacchio and I. Ovcharenko
Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation.
Genome Biology, 20(1):140-149 (2019) PDF

D. Huang, H. Petrykowska, B. Miller, L. Elnitski and I. Ovcharenko
Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression.
Genome Research, 29(4):657-667 (2019) PDF

Busser BW *, Huang D *, Rogacki KR *, ... Bulyk ML, Ovcharenko I #, Michelson AM #
Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network
PNAS, 109(50):20768-73 (2013) (* - co-first, # - co-corresponding authors) PDF

G. Burzynski *, X. Reed *, L. Taher *, Z.E. Stine, T. Matsui, I. Ovcharenko #, A.S. McCallion #
Systematic elucidation and in vivo validation of the sequence basis of hindbrain transcriptional control
Genome Research, 22(11):2278-89 (2012) (* - co-first, # - co-corresponding authors) PDF

Visel A, Taher L, ... Ovcharenko I, Pennacchio LA, Rubenstein JL (25 authors)
A High-Resolution Enhancer Atlas of the Developing Telencephalon
Cell, (2013) PDF

B.W. Busser *, L. Taher *, Y. Kim, T. Tansey, M.J. Bloom, I. Ovcharenko #, A.M. Michelson #
A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis
PLoS Genetics, 8(3):e1002531 (2012) PDF
(* co-first, # co-corresponding authors)

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), 1139-1149 (2011) PDF

U. Hellsten, et al. ... (48 authors)
The Genome of the Western Clawed Frog Xenopus tropicalis
Science, 328:633-636 (2010) PDF

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, 2010 PDF

G.G. Loots and I. Ovcharenko
Human Variation in Short Regions Predisposed to Deep Evolutionary Conservation
Molecular Biology and Evolution, 2010 PDF

L.A. Pennacchio, G.G. Loots, M.A. Nobrega, and I. Ovcharenko
Predicting tissue-specific enhancers in the human genome
Genome Research, 17(2), 201-11 (2007) PDF

G.G. Loots and I. Ovcharenko anthology of comparative genomic tools
Nucleic Acids Research, 33, W56-64, (2005) PDF

I. Ovcharenko, G.G. Loots, M.A. Nobrega, R.C. Hardison, W. Miller, and L. Stubbs
Evolution and functional classification of vertebrate gene deserts
Genome Research, 15, 137-145 (2005) PDF

M. Nobrega*, I. Ovcharenko*, V. Afzal, E. Rubin
Scanning Human Gene Deserts for Long-Range Enhancers
Science 302(5644), 413 (2003) PDF

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) PDF

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