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  Research Group of Ivan Ovcharenko

Selected Publications

De novo human brain enhancers created by single-nucleotide mutations.
Li S, Hannenhalli S, Ovcharenko I.
Science Advances, 9(7) 2023 PDF

Enhancer-silencer transitions in the human genome.
Huang D, Ovcharenko I.
Genome Research, 32(3):437-448 (2022) PDF

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants.
Kvon EZ, Zhu Y, ... Hudaiberdiev S, Ovcharenko I, ... Pennacchio LA.
Cell, 180(6):1262-1271 (2020) PDF

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

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

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

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

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

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

Genome-wide identification of conserved regulatory function in diverged sequences
L. Taher, D.M. McGaughey, S. Maragh, I. Aneas, S.L. Bessling, W. Miller, M.A. Nobrega, A.S. McCallion, I. Ovcharenko
Genome Research, 21(7), 1139-1149 (2011) PDF

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

Genome-wide discovery of human heart enhancers
L. Narlikal, N.J. Sakabe, A.A. Blanski, F.E. Arimura, J.M. Westlund, M.A. Nobrega, I. Ovcharenko
Genome Research, 2010 PDF

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

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

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

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