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Results: 1 to 20 of 47

1.

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M.

Genome Res. 2012 Sep;22(9):1813-31. doi: 10.1101/gr.136184.111.

PMID:
22955991
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data.

Cheng C, Alexander R, Min R, Leng J, Yip KY, Rozowsky J, Yan KK, Dong X, Djebali S, Ruan Y, Davis CA, Carninci P, Lassman T, Gingeras TR, Guigó R, Birney E, Weng Z, Snyder M, Gerstein M.

Genome Res. 2012 Sep;22(9):1658-67. doi: 10.1101/gr.136838.111.

PMID:
22955978
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Landscape of transcription in human cells.

Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR.

Nature. 2012 Sep 6;489(7414):101-8. doi: 10.1038/nature11233.

PMID:
22955620
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Architecture of the human regulatory network derived from ENCODE data.

Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng J, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M.

Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245.

PMID:
22955619
[PubMed - indexed for MEDLINE]
5.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.

Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M.

Genome Biol. 2012 Sep 26;13(9):R48. doi: 10.1186/gb-2012-13-9-r48.

PMID:
22950945
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment.

Habegger L, Balasubramanian S, Chen DZ, Khurana E, Sboner A, Harmanci A, Rozowsky J, Clarke D, Snyder M, Gerstein M.

Bioinformatics. 2012 Sep 1;28(17):2267-9. Epub 2012 Jun 28.

PMID:
22743228
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.

Cheng C, Yan KK, Hwang W, Qian J, Bhardwaj N, Rozowsky J, Lu ZJ, Niu W, Alves P, Kato M, Snyder M, Gerstein M.

PLoS Comput Biol. 2011 Nov;7(11):e1002190. doi: 10.1371/journal.pcbi.1002190. Epub 2011 Nov 17.

PMID:
22125477
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

AlleleSeq: analysis of allele-specific expression and binding in a network framework.

Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M.

Mol Syst Biol. 2011 Aug 2;7:522. doi: 10.1038/msb.2011.54.

PMID:
21811232
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

The reality of pervasive transcription.

Clark MB, Amaral PP, Schlesinger FJ, Dinger ME, Taft RJ, Rinn JL, Ponting CP, Stadler PF, Morris KV, Morillon A, Rozowsky JS, Gerstein MB, Wahlestedt C, Hayashizaki Y, Carninci P, Gingeras TR, Mattick JS.

PLoS Biol. 2011 Jul;9(7):e1000625; discussion e1001102. doi: 10.1371/journal.pbio.1000625. Epub 2011 Jul 12. No abstract available.

PMID:
21765801
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Diverse roles and interactions of the SWI/SNF chromatin remodeling complex revealed using global approaches.

Euskirchen GM, Auerbach RK, Davidov E, Gianoulis TA, Zhong G, Rozowsky J, Bhardwaj N, Gerstein MB, Snyder M.

PLoS Genet. 2011 Mar;7(3):e1002008. doi: 10.1371/journal.pgen.1002008. Epub 2011 Mar 3.

PMID:
21408204
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

ACT: aggregation and correlation toolbox for analyses of genome tracks.

Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M.

Bioinformatics. 2011 Apr 15;27(8):1152-4. doi: 10.1093/bioinformatics/btr092. Epub 2011 Feb 23.

PMID:
21349863
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Tiling array data analysis: a multiscale approach using wavelets.

Karpikov A, Rozowsky J, Gerstein M.

BMC Bioinformatics. 2011 Feb 21;12:57. doi: 10.1186/1471-2105-12-57.

PMID:
21338513
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets.

Cheng C, Yan KK, Yip KY, Rozowsky J, Alexander R, Shou C, Gerstein M.

Genome Biol. 2011;12(2):R15. doi: 10.1186/gb-2011-12-2-r15. Epub 2011 Feb 16.

PMID:
21324173
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Gerstein MB, Lu ZJ, Van Nostrand EL, Cheng C, Arshinoff BI, Liu T, Yip KY, Robilotto R, Rechtsteiner A, Ikegami K, Alves P, Chateigner A, Perry M, Morris M, Auerbach RK, Feng X, Leng J, Vielle A, Niu W, Rhrissorrakrai K, Agarwal A, Alexander RP, Barber G, Brdlik CM, Brennan J, Brouillet JJ, Carr A, Cheung MS, Clawson H, Contrino S, Dannenberg LO, Dernburg AF, Desai A, Dick L, Dosé AC, Du J, Egelhofer T, Ercan S, Euskirchen G, Ewing B, Feingold EA, Gassmann R, Good PJ, Green P, Gullier F, Gutwein M, Guyer MS, Habegger L, Han T, Henikoff JG, Henz SR, Hinrichs A, Holster H, Hyman T, Iniguez AL, Janette J, Jensen M, Kato M, Kent WJ, Kephart E, Khivansara V, Khurana E, Kim JK, Kolasinska-Zwierz P, Lai EC, Latorre I, Leahey A, Lewis S, Lloyd P, Lochovsky L, Lowdon RF, Lubling Y, Lyne R, MacCoss M, Mackowiak SD, Mangone M, McKay S, Mecenas D, Merrihew G, Miller DM 3rd, Muroyama A, Murray JI, Ooi SL, Pham H, Phippen T, Preston EA, Rajewsky N, Rätsch G, Rosenbaum H, Rozowsky J, Rutherford K, Ruzanov P, Sarov M, Sasidharan R, Sboner A, Scheid P, Segal E, Shin H, Shou C, Slack FJ, Slightam C, Smith R, Spencer WC, Stinson EO, Taing S, Takasaki T, Vafeados D, Voronina K, Wang G, Washington NL, Whittle CM, Wu B, Yan KK, Zeller G, Zha Z, Zhong M, Zhou X; modENCODE Consortium, Ahringer J, Strome S, Gunsalus KC, Micklem G, Liu XS, Reinke V, Kim SK, Hillier LW, Henikoff S, Piano F, Snyder M, Stein L, Lieb JD, Waterston RH.

Science. 2010 Dec 24;330(6012):1775-87. doi: 10.1126/science.1196914. Epub 2010 Dec 22. Erratum in: Science. 2011 Jan 7;331(6013):30.

PMID:
21177976
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Lu ZJ, Yip KY, Wang G, Shou C, Hillier LW, Khurana E, Agarwal A, Auerbach R, Rozowsky J, Cheng C, Kato M, Miller DM, Slack F, Snyder M, Waterston RH, Reinke V, Gerstein MB.

Genome Res. 2011 Feb;21(2):276-85. doi: 10.1101/gr.110189.110. Epub 2010 Dec 22. Erratum in: Genome Res. 2011 May;21(5):811.

PMID:
21177971
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

RSEQtools: a modular framework to analyze RNA-Seq data using compact, anonymized data summaries.

Habegger L, Sboner A, Gianoulis TA, Rozowsky J, Agarwal A, Snyder M, Gerstein M.

Bioinformatics. 2011 Jan 15;27(2):281-3. doi: 10.1093/bioinformatics/btq643. Epub 2010 Dec 5.

PMID:
21134889
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.

Sboner A, Habegger L, Pflueger D, Terry S, Chen DZ, Rozowsky JS, Tewari AK, Kitabayashi N, Moss BJ, Chee MS, Demichelis F, Rubin MA, Gerstein MB.

Genome Biol. 2010;11(10):R104. doi: 10.1186/gb-2010-11-10-r104. Epub 2010 Oct 21.

PMID:
20964841
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Annotating non-coding regions of the genome.

Alexander RP, Fang G, Rozowsky J, Snyder M, Gerstein MB.

Nat Rev Genet. 2010 Aug;11(8):559-71. doi: 10.1038/nrg2814. Epub 2010 Jul 13. Review.

PMID:
20628352
[PubMed - indexed for MEDLINE]
19.

Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays.

Agarwal A, Koppstein D, Rozowsky J, Sboner A, Habegger L, Hillier LW, Sasidharan R, Reinke V, Waterston RH, Gerstein M.

BMC Genomics. 2010 Jun 17;11:383. doi: 10.1186/1471-2164-11-383.

PMID:
20565764
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Variation in transcription factor binding among humans.

Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, Waszak SM, Habegger L, Rozowsky J, Shi M, Urban AE, Hong MY, Karczewski KJ, Huber W, Weissman SM, Gerstein MB, Korbel JO, Snyder M.

Science. 2010 Apr 9;328(5975):232-5. doi: 10.1126/science.1183621. Epub 2010 Mar 18.

PMID:
20299548
[PubMed - indexed for MEDLINE]
Free PMC Article

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