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Results: 1 to 20 of 60

1.

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.

PMID:
24496725
[PubMed - in process]
Free PMC Article
2.

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.

PMID:
24496624
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
24156763
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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):1021-8. doi: 10.1038/ng.2713. Epub 2013 Jul 28.

PMID:
23892608
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

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.

PMID:
23874664
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
23650638
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
23620591
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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.

PMID:
23578135
[PubMed]
Free PMC Article
9.

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.

PMID:
23375746
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

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.

PMID:
23184988
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
22759862
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
22412381
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
22313678
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
22199387
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22174793
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

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.

PMID:
21628450
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
21602820
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

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.

PMID:
21278158
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

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.

PMID:
20806066
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

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.

PMID:
20431018
[PubMed - indexed for MEDLINE]
Free PMC Article

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