Yuk-Lap (Kevin) Yip, Ph.D.
Lab Website
Yuk-Lap (Kevin) Yip's Research Focus
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, New Haven
2009: Ph.D., Computer Science, Yale University, New Haven
2003: M.Phil., Computer Science, The University of Hong Kong, Hong Kong
1999: B.Eng., Computer Engineering, The University of Hong Kong, Hong Kong
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
Author Correction: Whole-genome profiling of nasopharyngeal carcinoma reveals viral-host co-operation in inflammatory NF-κB activation and immune escape.
Bruce JP, To KF, Lui VWY, Chung GTY, Chan YY, Tsang CM, Yip KY, Ma BBY, Woo JKS, Hui EP, Mak MKF, Lee SD, Chow C, Velapasamy S, Or YYY, Siu PK, El Ghamrasni S, Prokopec S, Wu M, Kwan JSH, Liu Y, Chan JYK, van Hasselt CA, Young LS, Dawson CW, Paterson IC, Yap LF, Tsao SW, Liu FF, Chan ATC, Pugh TJ, Lo KW
Nat Commun 2022 Jul 27 ;13(1):4353
Accurate reconstruction of viral genomes in human cells from short reads using iterative refinement.
Lee SD, Wu M, Lo KW, Yip KY
BMC Genomics 2022 Jun 6 ;23(1):422
Deep learning identifies and quantifies recombination hotspot determinants.
Li Y, Chen S, Rapakoulia T, Kuwahara H, Yip KY, Gao X
Bioinformatics 2022 May 13 ;38(10):2683-2691
Deep learning identifies and quantifies recombination hotspot determinants.
Li Y, Chen S, Rapakoulia T, Kuwahara H, Yip KY, Gao X
Bioinformatics 2022 Apr 12 ;
Sirtuin 7 super-enhancer drives epigenomic reprogramming in hepatocarcinogenesis.
Wu F, Xu L, Tu Y, Cheung OK, Szeto LL, Mok MT, Yang W, Kang W, Cao Q, Lai PB, Chan SL, Tan P, Sung JJ, Yip KY, Cheng AS, To KF
Cancer Lett 2022 Jan 28 ;525:115-130
Quantifying full-length circular RNAs in cancer.
Yu KH, Shi CH, Wang B, Chow SH, Chung GT, Lung RW, Tan KE, Lim YY, Tsang AC, Lo KW, Yip KY
Genome Res 2021 Oct 18 ;