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Items: 1 to 50 of 72

1.

Stable enhancers are active in development, and fragile enhancers are associated with evolutionary adaptation.

Li S, Kvon EZ, Visel A, Pennacchio LA, Ovcharenko I.

Genome Biol. 2019 Jul 15;20(1):140. doi: 10.1186/s13059-019-1750-z.

2.

Identification of human silencers by correlating cross-tissue epigenetic profiles and gene expression.

Huang D, Petrykowska HM, Miller BF, Elnitski L, Ovcharenko I.

Genome Res. 2019 Apr;29(4):657-667. doi: 10.1101/gr.247007.118. Epub 2019 Mar 18.

3.

Dichotomy in redundant enhancers points to presence of initiators of gene regulation.

Song W, Ovcharenko I.

BMC Genomics. 2018 Dec 18;19(1):947. doi: 10.1186/s12864-018-5335-0.

4.

Enhancer reprogramming in mammalian genomes.

Flores MA, Ovcharenko I.

BMC Bioinformatics. 2018 Sep 10;19(1):316. doi: 10.1186/s12859-018-2343-7.

5.

The hypothesis of ultraconserved enhancer dispensability overturned.

Elnitski L, Ovcharenko I.

Genome Biol. 2018 May 8;19(1):57. doi: 10.1186/s13059-018-1433-1.

6.

SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome.

Vera Alvarez R, Li S, Landsman D, Ovcharenko I.

Bioinformatics. 2017 Sep 14. doi: 10.1093/bioinformatics/btx583. [Epub ahead of print]

7.

Epigenetic and genetic alterations and their influence on gene regulation in chronic lymphocytic leukemia.

Huang D, Ovcharenko I.

BMC Genomics. 2017 Mar 16;18(1):236. doi: 10.1186/s12864-017-3617-6.

8.

Quantifying deleterious effects of regulatory variants.

Li S, Alvarez RV, Sharan R, Landsman D, Ovcharenko I.

Nucleic Acids Res. 2017 Mar 17;45(5):2307-2317. doi: 10.1093/nar/gkw1263.

9.

Human Enhancers Are Fragile and Prone to Deactivating Mutations.

Li S, Ovcharenko I.

Mol Biol Evol. 2015 Aug;32(8):2161-80. doi: 10.1093/molbev/msv118. Epub 2015 May 14.

10.

Enhancer modeling uncovers transcriptional signatures of individual cardiac cell states in Drosophila.

Busser BW, Haimovich J, Huang D, Ovcharenko I, Michelson AM.

Nucleic Acids Res. 2015 Feb 18;43(3):1726-39. doi: 10.1093/nar/gkv011. Epub 2015 Jan 21.

11.

Identification and computational analysis of gene regulatory elements.

Taher L, Narlikar L, Ovcharenko I.

Cold Spring Harb Protoc. 2015 Jan 5;2015(1):pdb.top083642. doi: 10.1101/pdb.top083642. Review.

12.

Identifying causal regulatory SNPs in ChIP-seq enhancers.

Huang D, Ovcharenko I.

Nucleic Acids Res. 2015 Jan;43(1):225-36. doi: 10.1093/nar/gku1318. Epub 2014 Dec 17.

13.

Genome-wide analysis of functional and evolutionary features of tele-enhancers.

Huang D, Ovcharenko I.

G3 (Bethesda). 2014 Apr 16;4(4):579-93. doi: 10.1534/g3.114.010447.

14.

Machine learning classification of cell-specific cardiac enhancers uncovers developmental subnetworks regulating progenitor cell division and cell fate specification.

Ahmad SM, Busser BW, Huang D, Cozart EJ, Michaud S, Zhu X, Jeffries N, Aboukhalil A, Bulyk ML, Ovcharenko I, Michelson AM.

Development. 2014 Feb;141(4):878-88. doi: 10.1242/dev.101709.

15.

Sequence signatures extracted from proximal promoters can be used to predict distal enhancers.

Taher L, Smith RP, Kim MJ, Ahituv N, Ovcharenko I.

Genome Biol. 2013;14(10):R117.

16.

Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model.

Smith RP, Taher L, Patwardhan RP, Kim MJ, Inoue F, Shendure J, Ovcharenko I, Ahituv N.

Nat Genet. 2013 Sep;45(9):1021-1028. doi: 10.1038/ng.2713. Epub 2013 Jul 28.

17.

Interrogating transcriptional regulatory sequences in Tol2-mediated Xenopus transgenics.

Loots GG, Bergmann A, Hum NR, Oldenburg CE, Wills AE, Hu N, Ovcharenko I, Harland RM.

PLoS One. 2013 Jul 16;8(7):e68548. doi: 10.1371/journal.pone.0068548. Print 2013.

18.

Effects of gene regulatory reprogramming on gene expression in human and mouse developing hearts.

Hsu CH, Ovcharenko I.

Philos Trans R Soc Lond B Biol Sci. 2013 May 6;368(1620):20120366. doi: 10.1098/rstb.2012.0366. Print 2013.

19.

High mobility group N proteins modulate the fidelity of the cellular transcriptional profile in a tissue- and variant-specific manner.

Kugler JE, Horsch M, Huang D, Furusawa T, Rochman M, Garrett L, Becker L, Bohla A, Hölter SM, Prehn C, Rathkolb B, Racz I, Aguilar-Pimentel JA, Adler T, Adamski J, Beckers J, Busch DH, Eickelberg O, Klopstock T, Ollert M, Stöger T, Wolf E, Wurst W, Yildirim AÖ, Zimmer A, Gailus-Durner V, Fuchs H, Hrabě de Angelis M, Garfinkel B, Orly J, Ovcharenko I, Bustin M.

J Biol Chem. 2013 Jun 7;288(23):16690-703. doi: 10.1074/jbc.M113.463315. Epub 2013 Apr 24.

20.

Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.

Hosseini P, Ovcharenko I, Matthews BF.

Plant Methods. 2013 Apr 11;9(1):12. doi: 10.1186/1746-4811-9-12.

21.

A high-resolution enhancer atlas of the developing telencephalon.

Visel A, Taher L, Girgis H, May D, Golonzhka O, Hoch RV, McKinsey GL, Pattabiraman K, Silberberg SN, Blow MJ, Hansen DV, Nord AS, Akiyama JA, Holt A, Hosseini R, Phouanenavong S, Plajzer-Frick I, Shoukry M, Afzal V, Kaplan T, Kriegstein AR, Rubin EM, Ovcharenko I, Pennacchio LA, Rubenstein JL.

Cell. 2013 Feb 14;152(4):895-908. doi: 10.1016/j.cell.2012.12.041. Epub 2013 Jan 31.

22.

Integrative analysis of the zinc finger transcription factor Lame duck in the Drosophila myogenic gene regulatory network.

Busser BW, Huang D, Rogacki KR, Lane EA, Shokri L, Ni T, Gamble CE, Gisselbrecht SS, Zhu J, Bulyk ML, Ovcharenko I, Michelson AM.

Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20768-73. doi: 10.1073/pnas.1210415109. Epub 2012 Nov 26.

23.

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control.

Burzynski GM, Reed X, Taher L, Stine ZE, Matsui T, Ovcharenko I, McCallion AS.

Genome Res. 2012 Nov;22(11):2278-89. doi: 10.1101/gr.139717.112. Epub 2012 Jul 3.

24.

A machine learning approach for identifying novel cell type-specific transcriptional regulators of myogenesis.

Busser BW, Taher L, Kim Y, Tansey T, Bloom MJ, Ovcharenko I, Michelson AM.

PLoS Genet. 2012;8(3):e1002531. doi: 10.1371/journal.pgen.1002531. Epub 2012 Mar 8.

25.

Predicting tissue specific cis-regulatory modules in the human genome using pairs of co-occurring motifs.

Girgis HZ, Ovcharenko I.

BMC Bioinformatics. 2012 Feb 7;13:25. doi: 10.1186/1471-2105-13-25.

26.

CLARE: Cracking the LAnguage of Regulatory Elements.

Taher L, Narlikar L, Ovcharenko I.

Bioinformatics. 2012 Feb 15;28(4):581-3. doi: 10.1093/bioinformatics/btr704. Epub 2011 Dec 22.

27.

Global gene expression analysis of murine limb development.

Taher L, Collette NM, Murugesh D, Maxwell E, Ovcharenko I, Loots GG.

PLoS One. 2011;6(12):e28358. doi: 10.1371/journal.pone.0028358. Epub 2011 Dec 9.

28.

Genome-wide identification of conserved regulatory function in diverged sequences.

Taher L, McGaughey DM, Maragh S, Aneas I, Bessling SL, Miller W, Nobrega MA, McCallion AS, Ovcharenko I.

Genome Res. 2011 Jul;21(7):1139-49. doi: 10.1101/gr.119016.110. Epub 2011 May 31.

29.

Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

Martin D, Pantoja C, Fernández Miñán A, Valdes-Quezada C, Moltó E, Matesanz F, Bogdanović O, de la Calle-Mustienes E, Domínguez O, Taher L, Furlan-Magaril M, Alcina A, Cañón S, Fedetz M, Blasco MA, Pereira PS, Ovcharenko I, Recillas-Targa F, Montoliu L, Manzanares M, Guigó R, Serrano M, Casares F, Gómez-Skarmeta JL.

Nat Struct Mol Biol. 2011 Jun;18(6):708-14. doi: 10.1038/nsmb.2059. Epub 2011 May 22. Erratum in: Nat Struct Mol Biol. 2011 Sep;18(9):1084.

30.

Effects of HMGN variants on the cellular transcription profile.

Rochman M, Taher L, Kurahashi T, Cherukuri S, Uversky VN, Landsman D, Ovcharenko I, Bustin M.

Nucleic Acids Res. 2011 May;39(10):4076-87. doi: 10.1093/nar/gkq1343. Epub 2011 Jan 28.

31.

Tissue-specific and ubiquitous expression patterns from alternative promoters of human genes.

Jacox E, Gotea V, Ovcharenko I, Elnitski L.

PLoS One. 2010 Aug 18;5(8):e12274. doi: 10.1371/journal.pone.0012274.

32.

The genome of the Western clawed frog Xenopus tropicalis.

Hellsten U, Harland RM, Gilchrist MJ, Hendrix D, Jurka J, Kapitonov V, Ovcharenko I, Putnam NH, Shu S, Taher L, Blitz IL, Blumberg B, Dichmann DS, Dubchak I, Amaya E, Detter JC, Fletcher R, Gerhard DS, Goodstein D, Graves T, Grigoriev IV, Grimwood J, Kawashima T, Lindquist E, Lucas SM, Mead PE, Mitros T, Ogino H, Ohta Y, Poliakov AV, Pollet N, Robert J, Salamov A, Sater AK, Schmutz J, Terry A, Vize PD, Warren WC, Wells D, Wills A, Wilson RK, Zimmerman LB, Zorn AM, Grainger R, Grammer T, Khokha MK, Richardson PM, Rokhsar DS.

Science. 2010 Apr 30;328(5978):633-6. doi: 10.1126/science.1183670.

33.

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers.

Gotea V, Visel A, Westlund JM, Nobrega MA, Pennacchio LA, Ovcharenko I.

Genome Res. 2010 May;20(5):565-77. doi: 10.1101/gr.104471.109. Epub 2010 Apr 2.

34.

Human variation in short regions predisposed to deep evolutionary conservation.

Loots GG, Ovcharenko I.

Mol Biol Evol. 2010 Jun;27(6):1279-88. doi: 10.1093/molbev/msq011. Epub 2010 Jan 21.

35.

Genome-wide discovery of human heart enhancers.

Narlikar L, Sakabe NJ, Blanski AA, Arimura FE, Westlund JM, Nobrega MA, Ovcharenko I.

Genome Res. 2010 Mar;20(3):381-92. doi: 10.1101/gr.098657.109. Epub 2010 Jan 14.

36.

Identifying regulatory elements in eukaryotic genomes.

Narlikar L, Ovcharenko I.

Brief Funct Genomic Proteomic. 2009 Jul;8(4):215-30. doi: 10.1093/bfgp/elp014. Epub 2009 Jun 4. Review.

37.

Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements.

Taher L, Ovcharenko I.

Bioinformatics. 2009 Mar 1;25(5):578-84. doi: 10.1093/bioinformatics/btp043. Epub 2009 Jan 25.

38.

Widespread ultraconservation divergence in primates.

Ovcharenko I.

Mol Biol Evol. 2008 Aug;25(8):1668-76. doi: 10.1093/molbev/msn116. Epub 2008 May 19.

39.

DiRE: identifying distant regulatory elements of co-expressed genes.

Gotea V, Ovcharenko I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W133-9. doi: 10.1093/nar/gkn300. Epub 2008 May 17.

40.
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42.

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions.

Gordon L, Yang S, Tran-Gyamfi M, Baggott D, Christensen M, Hamilton A, Crooijmans R, Groenen M, Lucas S, Ovcharenko I, Stubbs L.

Genome Res. 2007 Nov;17(11):1603-13. Epub 2007 Oct 5.

43.

Extent of linkage disequilibrium in chicken.

Aerts J, Megens HJ, Veenendaal T, Ovcharenko I, Crooijmans R, Gordon L, Stubbs L, Groenen M.

Cytogenet Genome Res. 2007;117(1-4):338-45.

PMID:
17675876
44.

Predicting tissue-specific enhancers in the human genome.

Pennacchio LA, Loots GG, Nobrega MA, Ovcharenko I.

Genome Res. 2007 Feb;17(2):201-11. Epub 2007 Jan 8.

45.

ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes.

Loots G, Ovcharenko I.

Bioinformatics. 2007 Jan 1;23(1):122-4. Epub 2006 Nov 7.

PMID:
17090579
46.

Array2BIO: from microarray expression data to functional annotation of co-regulated genes.

Loots GG, Chain PS, Mabery S, Rasley A, Garcia E, Ovcharenko I.

BMC Bioinformatics. 2006 Jun 16;7:307.

47.

Identification of clustered YY1 binding sites in imprinting control regions.

Kim JD, Hinz AK, Bergmann A, Huang JM, Ovcharenko I, Stubbs L, Kim J.

Genome Res. 2006 Jul;16(7):901-11. Epub 2006 Jun 7.

48.

Human-zebrafish non-coding conserved elements act in vivo to regulate transcription.

Shin JT, Priest JR, Ovcharenko I, Ronco A, Moore RK, Burns CG, MacRae CA.

Nucleic Acids Res. 2005 Sep 22;33(17):5437-45. Print 2005.

49.

Dcode.org anthology of comparative genomic tools.

Loots GG, Ovcharenko I.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

50.

Identifying synonymous regulatory elements in vertebrate genomes.

Ovcharenko I, Nobrega MA.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W403-7.

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