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Results: 1 to 20 of 37

1.

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation.

Lou S, Lee HM, Qin H, Li JW, Gao Z, Liu X, Chan LL, Lam V, So WY, Wang Y, Lok S, Wang J, Ma R, Tsui S, Chan J, Chan TF, Yip KY.

Genome Biol. 2014 Jul 30;15(7):408. [Epub ahead of print]

PMID:
25074712
[PubMed - as supplied by publisher]
2.

ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications.

Fok AC, Mok SS, Lee SD, Yip KY.

Bioinformatics. 2014 May 15;30(10):1467-8. doi: 10.1093/bioinformatics/btu038. Epub 2014 Jan 24.

PMID:
24463182
[PubMed - indexed for MEDLINE]
3.

Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data.

Hu X, Wong TK, Lu ZJ, Chan TF, Lau TC, Yiu SM, Yip KY.

Bioinformatics. 2014 Jan 21. [Epub ahead of print]

PMID:
24376038
[PubMed - as supplied by publisher]
4.

Identification of a major determinant for serine-threonine kinase phosphoacceptor specificity.

Chen C, Ha BH, Thévenin AF, Lou HJ, Zhang R, Yip KY, Peterson JR, Gerstein M, Kim PM, Filippakopoulos P, Knapp S, Boggon TJ, Turk BE.

Mol Cell. 2014 Jan 9;53(1):140-7. doi: 10.1016/j.molcel.2013.11.013. Epub 2013 Dec 26.

PMID:
24374310
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1.

Tso KK, Yip KY, Mak CK, Chung GT, Lee SD, Cheung ST, To KF, Lo KW.

Infect Agent Cancer. 2013 Aug 2;8(1):29. doi: 10.1186/1750-9378-8-29.

PMID:
23915735
[PubMed]
Free PMC Article
6.

Identification of a recurrent transforming UBR5-ZNF423 fusion gene in EBV-associated nasopharyngeal carcinoma.

Chung GT, Lung RW, Hui AB, Yip KY, Woo JK, Chow C, Tong CY, Lee SD, Yuen JW, Lun SW, Tso KK, Wong N, Tsao SW, Yip TT, Busson P, Kim H, Seo JS, O'Sullivan B, Liu FF, To KF, Lo KW.

J Pathol. 2013 Oct;231(2):158-67. doi: 10.1002/path.4240.

PMID:
23878065
[PubMed - indexed for MEDLINE]
7.

Machine learning and genome annotation: a match meant to be?

Yip KY, Cheng C, Gerstein M.

Genome Biol. 2013 May 29;14(5):205. doi: 10.1186/gb-2013-14-5-205.

PMID:
23731483
[PubMed - in process]
Free PMC Article
8.

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
9.

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]
Free PMC Article
10.

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
11.

Sustained antidiabetic effects of a berberine-containing Chinese herbal medicine through regulation of hepatic gene expression.

Zhao HL, Sui Y, Qiao CF, Yip KY, Leung RK, Tsui SK, Lee HM, Wong HK, Zhu X, Siu JJ, He L, Guan J, Liu LZ, Xu HX, Tong PC, Chan JC.

Diabetes. 2012 Apr;61(4):933-43. doi: 10.2337/db11-1164. Epub 2012 Mar 6.

PMID:
22396199
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors.

Cheng C, Shou C, Yip KY, Gerstein MB.

Genome Biol. 2011 Nov 7;12(11):R111. doi: 10.1186/gb-2011-12-11-r111.

PMID:
22060676
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps.

Yip KY, Utz L, Sitwell S, Hu X, Sidhu SS, Turk BE, Gerstein M, Kim PM.

BMC Biol. 2011 Aug 11;9:53. doi: 10.1186/1741-7007-9-53.

PMID:
21835011
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

Subcellular localization of SUN2 is regulated by lamin A and Rab5.

Liang Y, Chiu PH, Yip KY, Chan SY.

PLoS One. 2011;6(5):e20507. doi: 10.1371/journal.pone.0020507. Epub 2011 May 31.

PMID:
21655223
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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
16.

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
17.

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
18.

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
19.

Extensive in vivo metabolite-protein interactions revealed by large-scale systematic analyses.

Li X, Gianoulis TA, Yip KY, Gerstein M, Snyder M.

Cell. 2010 Nov 12;143(4):639-50. doi: 10.1016/j.cell.2010.09.048. Epub 2010 Oct 28.

PMID:
21035178
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families.

Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM, Gerstein MB.

Genome Res. 2010 Jul;20(7):960-71. doi: 10.1101/gr.102814.109. Epub 2010 Apr 29.

PMID:
20430783
[PubMed - indexed for MEDLINE]
Free PMC Article

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