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Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays.

Mak AC, Lai YY, Lam ET, Kwok TP, Leung AK, Poon A, Mostovoy Y, Hastie AR, Stedman W, Anantharaman T, Andrews W, Zhou X, Pang AW, Dai H, Chu C, Lin C, Wu JJ, Li CM, Li JW, Yim AK, Chan S, Sibert J, Džakula Ž, Cao H, Yiu SM, Chan TF, Yip KY, Xiao M, Kwok PY.

Genetics. 2015 Oct 28. pii: genetics.115.183483. [Epub ahead of print]


Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data.

Wu Y, Shi B, Ding X, Liu T, Hu X, Yip KY, Yang ZR, Mathews DH, Lu ZJ.

Nucleic Acids Res. 2015 Sep 3;43(15):7247-59. doi: 10.1093/nar/gkv706. Epub 2015 Jul 13.


Are special read alignment strategies necessary and cost-effective when handling sequencing reads from patient-derived tumor xenografts?

Tso KY, Lee SD, Lo KW, Yip KY.

BMC Genomics. 2014 Dec 23;15:1172. doi: 10.1186/1471-2164-15-1172.


A common set of distinct features that characterize noncoding RNAs across multiple species.

Hu L, Di C, Kai M, Yang YC, Li Y, Qiu Y, Hu X, Yip KY, Zhang MQ, Lu ZJ.

Nucleic Acids Res. 2015 Jan;43(1):104-14. doi: 10.1093/nar/gku1316. Epub 2014 Dec 12.


The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module.

Yim AK, Yu AC, Li JW, Wong AI, Loo JF, Chan KM, Kong SK, Yip KY, Chan TF.

Front Bioeng Biotechnol. 2014 Nov 6;2:49. doi: 10.3389/fbioe.2014.00049. eCollection 2014. Review.


VAS: a convenient web portal for efficient integration of genomic features with millions of genetic variants.

Ho ED, Cao Q, Lee SD, Yip KY.

BMC Genomics. 2014 Oct 11;15:886. doi: 10.1186/1471-2164-15-886.


FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer.

Fu Y, Liu Z, Lou S, Bedford J, Mu XJ, Yip KY, Khurana E, Gerstein M.

Genome Biol. 2014;15(10):480.


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, Kl Lam V, So WY, Wang Y, Lok S, Wang J, Ma RC, Tsui SK, Chan JC, Chan TF, Yip KY.

Genome Biol. 2014 Jul 30;15(7):408. doi: 10.1186/s13059-014-0408-0.


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.


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]


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.


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.


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.


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. Review.


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.


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.


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.


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.


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.

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