Yuk-Lap (Kevin) Yip, Ph.D.

Kevin Yip profile photo

Yuk-Lap (Kevin) Yip, Ph.D.

Director
Associate Director, Training and Education


Lab Website

Yuk-Lap (Kevin) Yip's Research Focus

Cancer, Diabetes - General, Liver Cancer, Type 2 Diabetes, Biliary Atresia, Hirschsprung Disease, Nasopharyngeal Carcinoma
Cancer Epigenetics, Gene Regulation, Oncogenes, Posttranslational Modification, Transcriptional Regulation, Tumor Microenvironment
Endocrine System, General Cell Biology, Immune System and Inflammation, Liver
Computational Modeling, Computational Modeling
Bioinformatics, Comparative Genomics, Genomics, Machine Learning, Protein-Protein Interactions, Systems Biology

We study gene regulatory mechanisms by means of computational modeling. To facilitate our data-centric approach, we develop novel methods for analyzing large amounts of biological data, including those produced by cutting-edge high-throughput experiments. Our computational models provide a systematic way to investigate the functional effects of different types of perturbations to regulatory mechanisms, which creates testable hypotheses for studying human diseases and facilitates translational research.

Yuk-Lap (Kevin) Yip's Bio

Education and training

2010: Postdoctoral associate, Molecular Biophysics and Biochemistry, Yale University
2009: Ph.D., Computer Science, Yale University
2003: M.Phil., Computer Science, The University of Hong Kong
1999: B.Eng., Computer Engineering, The University of Hong Kong


scientist at work

Publications

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium

Nature 2012 Sep 6 ;489(7414):57-74

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

Reconstruction of enhancer-target networks in 935 samples of human primary cells, tissues and cell lines.

Cao Q, Anyansi C, Hu X, Xu L, Xiong L, Tang W, Mok MTS, Cheng C, Fan X, Gerstein M, Cheng ASL, Yip KY

Nat Genet 2017 Oct ;49(10):1428-1436

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A long-read sequencing strategy with overlapping linkers on adjacent fragments (OLAF-Seq) for targeted resequencing and enrichment.

Uppuluri L, Shi CH, Varapula D, Young E, Ehrlich RL, Wang Y, Piazza D, Mell JC, Yip KY, Xiao M

Sci Rep 2024 Mar 7 ;14(1):5583

Commonly used software tools produce conflicting and overly-optimistic AUPRC values.

Chen W, Miao C, Zhang Z, Fung CS, Wang R, Chen Y, Qian Y, Cheng L, Yip KY, Tsui SK, Cao Q

bioRxiv 2024 Feb 7 ;

Accurate identification of structural variations from cancer samples.

Li L, Hong C, Xu J, Chung CY, Leung AK, Boncan DAT, Cheng L, Lo KW, Lai PBS, Wong J, Zhou J, Cheng AS, Chan TF, Yue F, Yip KY

Brief Bioinform 2023 Nov 22 ;25(1)

DNA methylation markers for kidney function and progression of diabetic kidney disease.

Li KY, Tam CHT, Liu H, Day S, Lim CKP, So WY, Huang C, Jiang G, Shi M, Lee HM, TRANSCEND Consortium, Lan HY, Szeto CC, Hanson RL, Nelson RG, Susztak K, Chan JCN, Yip KY, Ma RCW

Nat Commun 2023 May 15 ;14(1):2543

Targeting PPAR-gamma counteracts tumour adaptation to immune-checkpoint blockade in hepatocellular carcinoma.

Xiong Z, Chan SL, Zhou J, Vong JSL, Kwong TT, Zeng X, Wu H, Cao J, Tu Y, Feng Y, Yang W, Wong PP, Si-Tou WW, Liu X, Wang J, Tang W, Liang Z, Lu J, Li KM, Low JT, Chan MW, Leung HHW, Chan AWH, To KF, Yip KY, Lo YMD, Sung JJ, Cheng AS

Gut 2023 Sep ;72(9):1758-1773

ICI efficacy information portal: a knowledgebase for responder prediction to immune checkpoint inhibitors.

Chen J, Rebibo D, Cao J, Mok SY, Patel N, Tseng PC, Zhang Z, Yip KY

NAR Cancer 2023 Mar ;5(1):zcad012

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