Publications
Google Scholar . Publons . Scopus . PubMed . ORCID . DBLP . BibTeX . F1000 Faculty Profile

Papers ordered by date of acceptance. *: Co-first authorship, $: Co-corresponding/co-senior authorship

Journal papers:
  • Enhancer Reprogramming by Selective HDAC8 Inhibition Potentiates T Cell Infiltration and Durable Antitumor Efficacy of PD-L1 Blockade W Yang*, Y Feng*, J Zhou*, OK Cheung, JQ Cao, J Wang, WS Tang, YL Tu, LL Xu, F Wu, Z Tan, H Sun, Y Tian, J Wong, PB Lai, SL Chan, AW Chan, P Tan, Z Chen, JJ Sung, KYL Yip, KF To and ASL Cheng,
    Enhancer Reprogramming by Selective HDAC8 Inhibition Potentiates T Cell Infiltration and Durable Antitumor Efficacy of PD-L1 Blockade,
    Science Translational Medicine, (in press)
  • A Proof-of-Concept Study for the Pathogenetic Role of Enhancer Hypomethylation of MYBPHL in Multiple Myeloma Kwan Yeung Wong, Gareth J. Morgan, Eileen M. Boyle, Alfred Sze Lok Cheng, Kevin Yuk-Lap Yip and Chor Sang Chim,
    A Proof-of-Concept Study for the Pathogenetic Role of Enhancer Hypomethylation of MYBPHL in Multiple Myeloma,
    Scientific Reports, vol. 11, article 7009, (2021)
    Full Text
  • Horseshoe Crab Genomes Reveal the Evolutionary Fates of Genes and MicroRNAs after Three Rounds (3R) of Whole Genome Duplication Wenyan Nong*, Zhe Qu*, Yiqian Li*, Tom Barton-Owen*, Annette Y.P. Wong*, Ho Yin Yip, Hoi Ting Lee, Satya Narayana, Tobias Baril, Thomas Swale, Jianquan Cao, Ting Fung Chan, Hoi Shan Kwan, Sai Ming Ngai, Gianni Panagiotou, Pei-Yuan Qian, Jian-Wen Qiu, Kevin Y. Yip, Noraznawati Ismail, Siddhartha Pati, Akbar John, Stephen S. Tobe, William G. Bendena, Siu Gin Cheung, Alexander Hayward and Jerome H.L. Hui,
    Horseshoe Crab Genomes Reveal the Evolutionary Fates of Genes and MicroRNAs after Three Rounds (3R) of Whole Genome Duplication,
    Communications Biology, vol. 4, article 83, (2021)
    Full Text
  • G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing and Chromatin Looping Qinghong Jiang*, Julie Y. J. Ang*, Ah Young Lee, Qin Cao, Kelly Y. Li, Kevin Y. Yip and Danny C. Y. Leung,
    G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing and Chromatin Looping,
    Cell Reports, vol. 33, issue 4, article 108315, (2020)
    Full Text
  • Whole-Genome Analysis of Noncoding Genetic Variations Identifies Multi-Scale Regulatory Element Perturbations Associated with Hirschsprung Disease Alexander Xi Fu*, Kathy Nga-Chu Lui*, Clara Sze-Man Tang, Ray Kit Ng, Frank Pui-Ling Lai, Sin-Ting Lau, Zhixin Li, Maria-Mercè Garcia-Barcelo, Pak-Chung Sham, Paul Kwong-Hang Tam$, Elly Sau-Wai Ngan$ and Kevin Y. Yip$,
    Whole-Genome Analysis of Noncoding Genetic Variations Identifies Multi-Scale Regulatory Element Perturbations Associated with Hirschsprung Disease,
    Genome Research, vol. 30, issue 11, pp. 1618-1632, (2020).
    Full Text


  • A General Near-Exact K-mer Counting Method with Low Memory Consumption Enables De Novo Assembly of 106x Human Sequence Data in 2.7 Hours Christina Huan Shi and Kevin Y. Yip,
    A General Near-Exact K-mer Counting Method with Low Memory Consumption Enables De Novo Assembly of 106x Human Sequence Data in 2.7 Hours,
    Bioinformatics, vol. 36, issue S2, pp. i625-i633, (2020). (Also in ECCB 2020)
    Preprint - Full Text - Web Sites: CQF-deNoise, SH-assembly
  • A Unified Framework for Integrative Study of Heterogeneous Gene Regulatory Mechanisms Qin Cao*, Zhenghao Zhang*, Alexander Xi Fu, Qiong Wu, Tin-Lap Lee, Eric Lo, Alfred S. L. Cheng, Chao Cheng, Danny Leung and Kevin Y. Yip,
    A Unified Framework for Integrative Study of Heterogeneous Gene Regulatory Mechanisms,
    Nature Machine Intelligence, vol. 2, issue 8, pp. 447-456, (2020).
    Full Text - Web Site
  • Supervised Enhancer Predition with Epigenetic Pattern Recognition and Targeted Validation Anurag Sethi*, Mengting Gu*, Emrah Gumusgoz, Landon Chan, Koon-Kiu Yan, Joel Rozowsky, Iros Barozzi, Veena Afzal, Jennifer Akiyama, Ingrid Plajzer-Frick, Chengfei Yan, Catherine Pickle, Momoe Kato, Tyler Garvin, Quan Pham, Anne Harrington, Brandon Mannion, Elizabeth Lee, Yoko Fukuda-Yuzawa, Axel Visel, Diane E. Dickel, Kevin Yip, Richard Sutton, Len A. Pennacchio and Mark Gerstein,
    Supervised Enhancer Prediction with Epigenetic Pattern Recognition and Targeted Validation,
    Nature Methods, vol. 17, no. 7, pp. 807-814, (2020).
    Full Text
  • Jellyfish Genomes Reveal Distinct Homeobox Gene Clusters and Conservation of Small RNA Processing Wenyan Nong*, Jianquan Cao*, Yiqian Li*, Zhe Qu*, Thomas C.N. Leung, Jin Sun, Thomas Swale, Ho Yin Yip, Pei Yuan Qian, Jian-Wen Qiu, Hoi Shan Kwan, William Bendena, Stephen Tobe, Ting Fung Chan, Kevin Y. Yip, Ka Hou Chu, Sai Ming Ngai, Karl YK Tsim, Peter W.H. Holland$ and Jerome H.L. Hui$,
    Jellyfish Genomes Reveal Distinct Homeobox Gene Clusters and Conservation of Small RNA Processing,
    Nature Communications, vol. 11, article 3051, (2020).
    Full Text
  • An integrative ENCODE Resource for Cancer Genomics Jing Zhang*, Donghoon Lee*, Vineet Dhiman*, Peng Jiang*, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Grace Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Flynn Chen, Yucheng Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessika Adrian, James Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert Klein, Michael Snyder, David Gilbert, Kevin Yip, Chao Cheng, Feng Yue, Xiaole Liu, Kevin White, and Mark Gerstein,
    An integrative ENCODE Resource for Cancer Genomics,
    Nature Communications, vol. 11, article 3696, (2020).
    Full Text
  • Flexible K-mers with Variable-Length Indels for Identifying Binding Sequences of Protein Dimers Chenyang Hong and Kevin Y. Yip,
    Flexible K-mers with Variable-Length Indels for Identifying Binding Sequences of Protein Dimers,
    Briefings in Bioinformatics, vol. 21, issue 5, pp. 1787-1797, (2020).
    Preprint - Full Text - Web Site
  • OMMA Enables Population-scale Analysis of Complex Genomic Features and Phylogenomic Relationships from Nanochannel-based Optical Maps Alden King-Yung Leung, Melissa Chun-Jiao Liu, Le Li, Yvonne Yuk-Yin Lai, Catherine Chu, Pui-Yan Kwok, Pak-Leung Ho, Kevin Y Yip$ and Ting-Fung Chan$,
    OMMA Enables Population-scale Analysis of Complex Genomic Features and Phylogenomic Relationships from Nanochannel-based Optical Maps,
    Giga Science, vol. 8, issue 7, article giz079, (2019).
    Full Text - Web Site

  • Shaping the Nebulous Enhancer in the Era of High-Throughput Assays and Genome Editing Edwin Yu-Kiu Ho*, Qin Cao*, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu, Mark Gerstein and Kevin Y. Yip,
    Shaping the Nebulous Enhancer in the Era of High-Throughput Assays and Genome Editing,
    Briefings in Bioinformatics, vol. 21, issue 3, pp. 836-850, (2020).
    Preprint - Full Text
  • Genome Maps Across 26 Human Populations Reveal Population-specific Patterns of Structural Variation Michal Levy-Sakin*, Steven Pastor*, Yulia Mostovoy*, Le Li*, Alden KY Leung*, Jennifer McCaffrey*, Eleanor Young, Ernest T Lam, Alex R Hastie, Karen HY Wong, Claire YL Chung, Walfred Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene YC Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan$, Kevin Y Yip$, Ming Xiao$ and Pui-Yan Kwok$,
    Genome Maps Across 26 Human Populations Reveal Population-specific Patterns of Structural Variation,
    Nature Communications, vol. 10, article 1025, (2019).
    Full Text
  • New Guidelines for DNA Methylome Studies Regarding 5-hydroxymethylcytosine for Understanding Transcriptional Regulation Le Li*, Yuwei Gao*, Qiong Wu, Alfred S. L. Cheng$ and Kevin Y. Yip$,
    New Guidelines for DNA Methylome Studies Regarding 5-hydroxymethylcytosine for Understanding Transcriptional Regulation,
    Genome Research, vol. 29, issue 4, pp. 543-553, (2019).
    Preprint - Full Text


  • Aberrant Enhancer Hypomethylation Contributes to Hepatic Carcinogenesis through Global Transcriptional Reprogramming Lei Xiong, Feng Wu, Qiong Wu, Liangliang Xu, Otto K. Cheung, Wei Kang, Myth T. Mok, Lemuel L. Szeto, Cheuk-Yin Lun, Raymond W. Lung, Jinglin Zhang, Ken H. Yu, Sau-Dan Lee, Guangcun Huang, Chiou-Miin Wang, Joseph Liu, Zhuo Yu, Dae-Yeul Yu, Bo Feng, Jian-Liang Chou, Wan-Hong Huang, Yue-Sun Cheung, Paul B. Lai, Patrick Tan, Nathalie Wong, Michael W. Chan, Tim H. Huang, Kevin Y. Yip$, Alfred S. Cheng$ and Ka-Fai To$,
    Aberrant Enhancer Hypomethylation Contributes to Hepatic Carcinogenesis through Global Transcriptional Reprogramming,
    Nature Communications, vol. 10, article 335, (2019).
    Full Text
  • Comparative Analysis of Single-Cell Parallel Sequencing Approaches in Oocyte Application Yan Qian, Jinyue Liao, Ashley Hoi Ching Suen, Annie Wing Tung Lee, Hoi Sze Chung, Nelson Leung Sang Tang, King Lau Chow, Qin Cao, Yuk Lap Yip, Tak Yeung Leung, Wai-Yee Chan, David Yiu Leung Chan, Tin Chiu Li and Tin-Lap Lee,
    Comparative Analysis of Single-Cell Parallel Sequencing Approaches in Oocyte Application,
    The International Journal of Biochemistry and Cell Biology, vol. 107, pp. 1-5, (2019).
    Full Text
  • Identification of Genes Associated with Hirschsprung Disease, based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development Clara Sze-man Tang*, Peng Li*, Frank Pui-Ling Lai, Alexander Xi Fu, Sin-Ting Lau, Man Ting So, Kathy Nga-Chu Lui, Zhixin Li, Xuehan Zhuang, Michelle Yu, Xuelai Liu, Ngoc D Ngo, Xiaoping Miao, Xi Zhang, Bin Yi, Shaotao Tang, Xiaobing Sun, Furen Zhang, Hong Liu, Qiji Liu, Ruizhong Zhang, Hualong Wang, Liuming Huang, Xiao Dong, Jinfa Tou, Kathy SE Cheah, Wanling Yang, Zhenwei Yuan, Kevin Yuk-lap Yip, Pak-Chung Sham, Paul Kwang-Hang Tam, Maria-Mercè Garcia-Barcelo$ and Elly Sau-Wai Ngan$
    Identification of Genes Associated with Hirschsprung Disease, based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development,
    Gastroenterology, vol. 155, issue 6, pp. 1908-1922.e5, (2018).
    Full Text
  • Establishment and Characterization of New Tumor Xenografts and Cancer Cell Lines from EBV-Positive Nasopharyngeal Carcinoma Weitao Lin*, Yim Ling Yip*, Lin Jia*, Wen Deng, Hong Zheng, Wei Dai, Josephine Mun Yee Ko, Kwok Wai Lo, Grace Tin Yun Chung, Kevin Y. Yip, Sau-Dan Lee, Johnny Sheung-Him Kwan, Jun Zhang, Tengfei Liu, Jimmy Yu-Wai Chan, Dora Lai-Wan Kwong, Victor Ho-Fun Lee, John Malcolm Nicholls, Pierre Busson, Xuefeng Liu, Alan Kwok Shing Chiang, Kwai Fung Hui, Hin Kwok, Siu Tim Cheung, Yuk Chun Cheung, Chi Keung Chan, Bin Li, Annie Lai-Man Cheung, Pok Man Hau, Yuan Zhou, Chi Man Tsang, Jaap Middeldorp, Honglin Chen, Maria Li Lung and Sai Wah Tsao,
    Establishment and Characterization of New Tumor Xenografts and Cancer Cell Lines from EBV-Positive Nasopharyngeal Carcinoma,
    Nature Communications, vol. 9, article 4663, (2018).
    Full Text
  • Loss of Tumor Suppressor IGFBP4 Drives Epigenetic Reprogramming in Hepatic Carcinogenesis Ying-Ying Lee*, Myth Mok*, Wei Kang, Weiqin Yang, Wenshu Tang, Feng Wu, Liangliang Xu, Mingfei Yan, Zhou Yu, Sau Dan Lee, Joanna Tong, Yue-Sun Cheung, Paul Lai, Dae-Yeul Yu, Qianben Wang, Grace Wong, Andrew Chan, Kevin Yuk-Lap Yip, Ka-Fai To and Alfred SL Cheng,
    Loss of Tumor Suppressor IGFBP4 Drives Epigenetic Reprogramming in Hepatic Carcinogenesis,
    Nucleic Acids Research, vol. 46, issue 17, pp. 8832-8847, (2018).
    Full Text
  • A Comprehensive Web Tool for Toehold Switch Design Andrew Ching-Yuet To*, David Ho-Ting Chu*, Angela Ruoning Wang*, Frances Cheuk-Yau Li*, Alan Wai-On Chiu, Daisy Yuwei Gao, Chung Hang Jonathan Choi, Siu-Kai Kong, Ting-Fung Chan, King-Ming Chan and Kevin Y. Yip,
    A Comprehensive Web Tool for Toehold Switch Design,
    Bioinformatics, vol. 34, issue 16, pp. 2862-2864, (2018).
    Preprint - Full Text - Web Site
  • A Network Approach to Exploring the Functional Basis of Gene-Gene Epistatic Interactions in Disease Susceptibility Danny Kit-Sang Yip*, Landon L. Chan*, Iris K. Pang, Wei Jiang, Nelson L. S. Tang, Weichuan Yu and Kevin Y. Yip,
    A Network Approach to Exploring the Functional Basis of Gene-Gene Epistatic Interactions in Disease Susceptibility,
    Bioinformatics, vol. 34, issue 10, pp. 1741-1749, (2018).
    Preprint - Full Text

  • EBV-Encoded miRNAs Target ATM-Mediated Response in Nasopharyngeal Carcinoma Raymond W-M Lung*, Pok-Man Hau*, Ken H-O Yu, Kevin Y. Yip, Joanna H-M Tong, W-P Chak, Anthony W-H Chan, Edith K-Y Tin, Jesse C-S Pang, Ka-Hei Lam, Johnny S-H Kwan, Angela K-F Lo, Shuk-Ling Chau, Pierre Busson, Lawrence S. Young, Lee-Fah Yap, Sai-Wah Tsao, Ka-Fai To$ and Kwok-Wai Lo$,
    EBV-Encoded miRNAs Target ATM-Mediated Response in Nasopharyngeal Carcinoma,
    The Journal of Pathology, vol. 244, issue 4, pp. 394-407, (2018).
    Full Text
  • OMSV Enables Accurate and Comprehensive Identification of Large Structural Variations from Nanochannel-based Single-Molecule Optical Maps Le Li*, Alden King-Yung Leung*, Tsz-Piu Kwok*, Yvonne Y. Y. Lai, Iris K. Pang, Grace Tin-Yun Chung, Angel C. Y. Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J. K. Wu, Ernest T. Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu, Ming Xiao, Kwok-Wai Lo, Pui-Yan Kwok, Ting-Fung Chan$ and Kevin Y Yip$,
    OMSV Enables Accurate and Comprehensive Identification of Large Structural Variations from Nanochannel-based Single-Molecule Optical Maps,
    Genome Biology, vol. 18, article 230, (2017).
    Preprint - Full Text - Web Site
  • START: A System for Flexible Analysis of Hundreds of Genomic Signal Tracks in Few Lines of SQL-like Queries Xinjie Zhu*, Qiang Zhang*, Eric Dun Ho, Ken Hung-On Yu, Chris Liu, Tim H. Huang, Alfred Sze-Lok Cheng, Ben Kao$, Eric Lo$ and Kevin Y. Yip$,
    START: A System for Flexible Analysis of Hundreds of Genomic Signal Tracks in Few Lines of SQL-like Queries,
    BMC Genomics, vol. 18, no. 749, (2017).
    Preprint - Full Text - Web Site
  • Reconstruction of Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines Qin Cao, Christine Anyansi, Xihao Hu, Liangliang Xu, Lei Xiong, Wenshu Tang, Myth T S Mok, Chao Cheng, Xiaodan Fan, Mark Gerstein, Alfred S L Cheng and Kevin Y Yip,
    Reconstruction of Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines,
    Nature Genetics, vol. 49, no. 10, pp. 1428-1436, (2017).
    Full Text - Web Site
  • OMTools: A Software Package for Visualizing and Processing Optical Mapping Data Alden King-Yung Leung, Nana Jin, Kevin Y. Yip$ and Ting-Fung Chan$,
    OMTools: A Software Package for Visualizing and Processing Optical Mapping Data,
    Bioinformatics, vol. 33, issue 18, pp. 2933-2935, (2017).
    Full Text

  • Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms Le Li and Kevin Y. Yip,
    Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms,
    Scientific Reports, vol. 6, article 39237, (2016).
    Preprint - Full Text - Web Site
  • Hendrik G. Stunnenberg, The International Human Epigenome Consortium and Martin Hirst,
    The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery,
    Cell, vol. 167, issue 5, pp. 1145-1149, (2016).
    Full Text
  • Exome and Genome Sequencing of Nasopharynx Cancer Identifies NF-kB Pathway Activating Mutations Yvonne Y Li*, Grace Tin-Yun Chung*, Vivian W.Y. Lui*, Ka-Fai To, Brigette Buig-Yue Ma, Chit Chow, John Kong-Sang Woo, Kevin Y. Yip, Jeongsun Seo, Edwin Pun Hui, Michael Ko-Fung Mak, Maria Rusan, Nicole G. Chau, Yvonne Yan-Yan Or, Marcus Hung-Nam Law, Peggy Pui-Ying Law, Zoey Wing-Yee Liu, Hoi Lam Ngan, Krista R. Verhoeft, Peony H.Y. Poon, Seong-Keun Yoo, Jong-Yeon Shin, Sau-Dan Lee, Samantha Wei-Man Lun, Anthony Wing-Hung Chan, Jason Ying-Kuen Chan, Paul Bo-San Lai, Choi-Yi Fung, Suet-Ting Hung, Lin Wang Lin, Ann Margaret V. Chang, Simion I. Chiosea, Matthew Louis Hedberg, Sai-Wah Tsao, Charles Andrew van Hasselt, Anthony Tak-Cheung Chan, Jennifer R. Grandis, Peter S. Hammerman$ and Kwok-Wai Lo$,
    Exome and Genome Sequencing of Nasopharynx Cancer Identifies NF-kB Pathway Activating Mutations,
    Nature Communications, vol. 8, article 14121, (2017).
    Full Text
  • Interactome-Transcriptome Analysis Discovers Signatures Complementary to GWAS Loci of Type 2 Diabetes Jing-Woei Li, Heung Man Lee, Ying Wang, Amy Hin Yan Tong, Kevin Y. Yip, Stephen Kwok-Wing Tsui, Si Lok, Risa Ozaki, Andrea Luk, Alice Kong, Wingyee So, Ronald Ma, Juliana Chan and Ting Fung Chan,
    Interactome-Transcriptome Analysis Discovers Signatures Complementary to GWAS Loci of Type 2 Diabetes,
    Scientific Reports, vol. 6, article 35228, (2016).
    Full Text

  • OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok, Kevin Y. Yip$ and Ting-Fung Chan$,
    OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach,
    Bioinformatics, vol. 33, issue 3, pp. 311-319, (2017).
    Full Text

  • A Novel Method for Discovering Local Spatial Clusters of Genomic Regions with Functional Relationships from DNA Contact Maps Xihao Hu, Christina Huan Shi and Kevin Y. Yip,
    A Novel Method for Discovering Local Spatial Clusters of Genomic Regions with Functional Relationships from DNA Contact Maps,
    Bioinformatics, vol. 32, issue 12, pp. i111-i120, (2016). (Also in ISMB 2016)
    Preprint - Full Text - Web Site
  • Yin Yang 1-Mediated Epigenetic Silencing of Tumor-Suppressive MicroRNAs Activates Nuclear Factor-kB in Hepatocellular Carcinoma Daisy P.F. Tsang*, William K.K. Wu*, Wei Kang*, Ying-Ying Lee, Feng Wu, Zhuo Yu, Leu Xiong, Anthony W. Chan, Joanna H. Tong, Weiqin Yang, May S.M. Li, Suki S. Lau, Xiangchun Li, Sau-Dan Lee, Yihua Yang, Paul B.S. Lai, Dae-Yeul Yu, Gang Xu, Kwok-Wai Lo, Matthew T.V. Chan, Huating Wang, Tin L. Lee, Jun Yu, Nathalie Wong, Kevin Y. Yip, Ka-Fai To and Alfred S.L. Cheng,
    Yin Yang 1-Mediated Epigenetic Silencing of Tumor-Suppressive MicroRNAs Activates Nuclear Factor-kB in Hepatocellular Carcinoma,
    The Journal of Pathology, vol. 238, issue 5, pp. 651-664, (2016).
    Full Text
  • Analysis of Sequencing Data for Probing RNA Secondary Structures and Protein-RNA Binding in Studying Post-Transcriptional Regulations Xihao Hu*, Yang Wu*, Zhi John Lu and Kevin Y. Yip,
    Analysis of Sequencing Data for Probing RNA Secondary Structures and Protein-RNA Binding in Studying Post-Transcriptional Regulations,
    Briefings in Bioinformatics vol. 17, issue 6, pp. 1032-1043, (2016).
    Preprint - Full Text
  • Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays Angel C. Y. Mak, Yvonne Y. Y. Lai, Ernest T. Lam, Tsz-Piu Kwok, Alden K. Y. Leung, Annie Poon, Yulia Mostovoy, Alex R. Hastie, William Stedman, Thomas Anantharaman, Warren Andrews, Xiang Zhou, Andy W. C. Pang, Heng Dai, Catherine Chu, Chin Lin, Jacob J. K. Wu, Catherine M. L. Li, Jing-Woei Li, Aldrin K. Y. Yim, Saki Chan, Justin Sibert, Zeljko Dzakula, Han Cao, Siu-Ming Yiu, Ting-Fung Chan, Kevin Y. Yip, Ming Xiao and Pui-Yan Kwok,
    Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays,
    Genetics, vol. 202, no. 1, pp. 351-362, (2016).
    Full Text
  • Improved Prediction of RNA Secondary Structure by Integrating the Free Energy Model with Restraints Derived from Experimental Probing Data Yang Wu, Binbin Shi, Xinqiang Ding, Tong Liu, Xihao Hu, Kevin Y. Yip, Zheng Rong Yang, David H. Mathews and Zhi John Lu,
    Improved Prediction of RNA Secondary Structure by Integrating the Free Energy Model with Restraints Derived from Experimental Probing Data,
    Nucleic Acids Research, vol. 43, issue 15, pp. 7247-7259, (2015).
    Full Text
  • Are Special Read Alignment Strategies Necessary and Cost-Effective when Handling Sequencing Reads from Patient-Derived Tumor Xenografts? Kai-Yuen Tso, Sau Dan Lee, Kwok-Wai Lo and Kevin Y Yip,
    Are Special Read Alignment Strategies Necessary and Cost-Effective when Handling Sequencing Reads from Patient-Derived Tumor Xenografts?,
    BMC Genomics, vol. 15, no. 1172, (2014).
    Preprint - Full Text
  • Systematic Exploration of Autonomous Modules in Noisy MicroRNA-Target Networks for Testing the Generality of the ceRNA Hypothesis Danny Kit-Sang Yip, Iris K Pang and Kevin Y Yip,
    Systematic Exploration of Autonomous Modules in Noisy MicroRNA-Target Networks for Testing the Generality of the ceRNA Hypothesis,
    BMC Genomics, vol. 15, no. 1178, (2014).
    (Preliminary version: RECOMB/ISCB RSG 2013)
    Preprint - Full Text
  • A Common Set of Distinct Features that Characterize Noncoding RNAs across Multiple Species Long Hu, Chao Di, Mingxuan Kai, Yu-Cheng T. Yang, Yang Li, Yunjiang Qiu, Xihao Hu, Kevin Y. Yip, Michael Q. Zhang and Zhi John Lu,
    A Common Set of Distinct Features that Characterize Noncoding RNAs across Multiple Species,
    Nucleic Acids Research, vol. 43, issue 1, pp. 104-114, (2015).
    Full Text
  • The Essential Component in DNA-based Information Storage System: Robust Error-Tolerating Module Aldrin Kay-Yuen Yim, Chi-Shing Yu, Jing-Woei Li, Ada In-Chun Wong, Jacky F. C. Loo, King Ming Chan, S. K. Kong, Kevin Y. Yip and Tingfung Chan,
    The Essential Component in DNA-based Information Storage System: Robust Error-Tolerating Module,
    Frontiers in Bioengineering and Biotechnology, vol. 2, no. 49, (2014).
    Full Text
  • VAS: A Convenient Web Portal for Efficient Integration of Genomic Features with Millions of Genetic Variants Eric Dun Ho, Qin Cao, Sau Dan Lee and Kevin Y Yip,
    VAS: A Convenient Web Portal for Efficient Integration of Genomic Features with Millions of Genetic Variants,
    BMC Genomics, vol. 15, no. 886, (2014).
    Preprint - Full Text - Web Site
  • FunSeq2: A Framework for Prioritizing Noncoding Regulatory Variants in Cancer Yao Fu, Zhu Liu, Shaoke Lou, Jason Bedford, Xinmeng J Mu, Kevin Y Yip, Ekta Khurana and Mark Gerstein,
    FunSeq2: A Framework for Prioritizing Noncoding Regulatory Variants in Cancer,
    Genome Biology, vol. 15, issue 10, no. 480, (2014).
    Full Text - Web Site


  • Whole-Genome Bisulfite Sequencing of Multiple Individuals Reveals Complementary Roles of Promoter and Gene Body Methylation in Transcriptional Regulation Shaoke Lou*, Heung-Man Lee*, Hao Qin, Jing-Woei Li, Zhibo Gao, Xin Liu, Landon L. Chan, Vincent K. L. Lam, Wing-Yee So, Ying Wang, Si Lok, Jun Wang, Ronald C. W. Ma, Stephen Kwok-Wing Tsui, Juliana C. N. Chan$, Ting-Fung Chan$ and Kevin Y. Yip$,
    Whole-Genome Bisulfite Sequencing of Multiple Individuals Reveals Complementary Roles of Promoter and Gene Body Methylation in Transcriptional Regulation,
    Genome Biology, vol. 15, issue 7, no. 408, (2014).
    Preprint - Full Text - Web Site
  • Comparative Analysis of the Transcriptome across Distant Species Mark B. Gerstein$, Joel Rozowsky, Koon-Kiu Yan, Daifeng Wang, Chao Cheng, James B. Brown, Carrie A. Davis, LaDeana Hillier, Cristina Sisu, Jingyi Jessica Li, Baikang Pei, Arif O. Harmanci, Michael O. Duff, Sarah Djebali, Roger P. Alexander, Burak H. Alver, Raymond Auerbach, Kimberly Bell, Peter J. Bickel, Max E. Boeck, Nathan P. Boley, Benjamin W. Booth, Lucy Cherbas, Peter Cherbas, Chao Di, Alex Dobin, Jorg Drenkow, Brent Ewing, Gang Fang, Megan Fastuca, Elise A. Feingold, Adam Frankish, Guanjun Gao, Peter J. Good, Roderic Guigó, Ann Hammonds, Jen Harrow, Roger A. Hoskins, Cedric Howald, Long Hu, Haiyan Huang, Tim J. P. Hubbard, Chau Huynh, Sonali Jha, Dionna Kasper, Masaomi Kato, Thomas C. Kaufman, Robert R. Kitchen, Erik Ladewig, Julien Lagarde, Eric Lai, Jing Leng, Zhi Lu, Michael MacCoss, Gemma May, Rebecca McWhirter$, Gennifer Merrihew, David M. Miller, Ali Mortazavi, Rabi Murad, Brian Oliver, Sara Olson, Peter J. Park, Michael J. Pazin, Norbert Perrimon, Dmitri Pervouchine, Valerie Reinke, Alexandre Reymond, Garrett Robinson, Anastasia Samsonova, Gary I. Saunders, Felix Schlesinger, Anurag Sethi, Frank J. Slack, William C. Spencer, Marcus H. Stoiber, Pnina Strasbourger, Andrea Tanzer, Owen A. Thompson, Kenneth H. Wan, Guilin Wang, Huaien Wang, Kathie L. Watkins, Jiayu Wen, Kejia Wen, Chenghai Xue, Li Yang, Kevin Yip, Chris Zaleski, Yan Zhang, Henry Zheng, Steven E. Brenner$, Brenton R. Graveley$, Susan E. Celniker$, Thomas R. Gingeras$ and Robert Waterston$,
    Comparative Analysis of the Transcriptome across Distant Species,
    Nature, vol. 512, no. 7515, pp. 445-448, (2014).
    Full Text
  • ECplot: An Online Tool for Making Standardized Plots from Large Datasets for Bioinformatics Publications Alex Chun-Hong Fok*, Sunny Siu-Nam Mok*, Sau Dan Lee and Kevin Y. Yip,
    ECplot: An Online Tool for Making Standardized Plots from Large Datasets for Bioinformatics Publications,
    Bioinformatics, vol. 30, no. 10, pp. 1467-1468, (2014).
    Preprint - Full Text - Web Site
  • Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity Catherine Chen, Byung Hak Ha, Anastasia F. Thévenin, Hua Jane Lou, Rong Zhang, Kevin Y. Yip, Jeffrey R. Peterson, Mark Gerstein, Philip M. Kim, Panagis Filippakopoulos, Stefan Knapp, Titus J. Boggon, Benjamin E. Turk,
    Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity,
    Molecular Cell, vol. 53, issue 1, pp. 140-147, (2014).
    Full Text
  • Computational Identification of Protein Binding Sites on RNAs using High-Throughput RNA Structure-Probing Data Xihao Hu, Thomas K. F. Wong, Zhi John Lu, Ting Fung Chan, Terrence Chi Kong Lau, Siu Ming Yiu and Kevin Y. Yip,
    Computational Identification of Protein Binding Sites on RNAs using High-Throughput RNA Structure-Probing Data,
    Bioinformatics, vol. 30, no. 8, pp. 1049-1055, (2014).
    Preprint - Full Text - Web Site
  • Identification of a Recurrent Transforming UBR5-ZNF423 Fusion Gene in EBV-Associated Nasopharyngeal Carcinoma Grace Tin-Yun Chung, Raymond Wai-Ming Lung, Angela Bik-Yu Hui, Kevin Yuk-Lap Yip, John Kong-Sang Woo, Chit Chow, Carol Yuen-Kwan Tong, Sau-Dan Lee, Jessie Wai-Fong Yuen, Samantha Wei-Man Lun, Ken Kai-Yuen Tso, Nathalie Wong, Sai-Wah Tsao, Timothy Tak-Chun Yip, Pierre Busson, Hyungtae Kim, Jeong-Sun Seo, Brian O'Sullivan, Fei-Fei Liu, Ka-Fai To and Kwok-Wai Lo,
    Identification of a Recurrent Transforming UBR5-ZNF423 Fusion Gene in EBV-Associated Nasopharyngeal Carcinoma,
    The Journal of Pathology, vol. 231, issue 2, pp. 158-167, (2013).
    Full Text
  • Complete Genomic Sequence of Epstein-Barr Virus in Nasopharyngeal Carcinoma Cell Line C666-1 Ken Kai-Yuen Tso*, Kevin Y. Yip*, Cathy Mak, Grace Tin-Yun Chung, Sau-Dan Lee, Siu-Tim Cheung, Ka-Fai To and Kwok-Wai Lo,
    Complete Genomic Sequence of Epstein-Barr Virus in Nasopharyngeal Carcinoma Cell Line C666-1,
    Infectious Agents and Cancer, vol. 8, issue 1, no. 29, (2013).
    Full Text



  • Machine Learning and Genome Annotation: A Match Meant to be? Kevin Y. Yip, Chao Cheng and Mark Gerstein,
    Machine Learning and Genome Annotation: A Match Meant to be?,
    Genome Biology, vol. 14, issue 5, no. 205, (2013).
    Preprint - Full Text


  • An Integrated Encyclopedia of DNA Elements in the Human Genome The ENCODE Project Consortium,
    An Integrated Encyclopedia of DNA Elements in the Human Genome,
    Nature, vol. 489, no. 7414, pp. 57-74, (2012).
    Full Text - Web Site


  • Classification of Human Genomic Regions based on Experimentally-determined Binding Sites of More Than 100 Transcription-related Factors Kevin Y. Yip, Chao Cheng, Nitin Bhardwaj, James B. Brown, Jing Leng, Anshul Kundaje, Joel Rozowsky, Ewan Birney, Peter Bickel, Michael Snyder and Mark Gerstein,
    Classification of Human Genomic Regions based on Experimentally-determined Binding Sites of More Than 100 Transcription-related Factors,
    Genome Biology, vol. 13, issue 9, no. R48, (2012).
    Preprint - Full Text - Web Site


  • Architecture of the Human Regulatory Network Derived from ENCODE Data Mark B. Gerstein*$, Anshul Kundaje*, Manoj Hariharan*, Stephen G. Landt*, Koon-Kiu Yan*, Chao Cheng*, Xinmeng Jasmine Mu*, Ekta Khurana*, Joel Rozowsky*, Roger Alexander*, Renqiang Min*, Pedro Alves*, Alexej Abyzov, Nick Addleman, Nitin Bhardwaj, Alan P. Boyle, Philip Cayting, Alexandra Charos, David Z. Chen, Yong Cheng, Declan Clarke, Catharine Eastman, Ghia Euskirchen, Seth Frietze, Yao Fu, Jason Gertz, Fabian Grubert, Arif Harmanci, Preti Jain, Maya Kasowski, Phil Lacroute, Jing (Jane) Leng, Jin Lian, Hannah Monahan, Henriette O'Geen, Zhengqing Ouyang, E. Christopher Partridge, Dorrelyn Patacsil, Florencia Pauli, Debasish Raha, Lucia Ramirez, Timothy E. Reddy, Brian Reed, Minyi Shi, Teri Slifer, Jing Wang, Linfeng Wu, Xinqiong Yang, Kevin Y. Yip, Gili Zilberman-Schapira, Serafim Batzoglou, Arend Sidow, Peggy J. Farnham, Richard M. Myers, Sherman M. Weissman and Michael Snyder$,
    Architecture of the Human Regulatory Network Derived from ENCODE Data,
    Nature, vol. 489, no. 7414, pp. 91-100, (2012).
    Full Text - Web Site
  • Understanding Transcriptional Regulation by Integrative Analysis of Transcription Factor Binding Data Chao Cheng, Roger Alexander, Renqiang Min, Jing Leng, Kevin Y. Yip, Joel Rozowsky, Koon-kiu Yan, Xianjun Dong, Sarah Djebali, Yijun Ruan, Carrie A Davis, Piero Carninci, Timo Lassman, Thomas R. Gingeras, Roderic Guigó Serra, Ewan Birney, Zhiping Weng, Michael Snyder and Mark Gerstein,
    Understanding Transcriptional Regulation by Integrative Analysis of Transcription Factor Binding Data,
    Genome Research, vol. 22, no. 9, pp. 1658-1667, (2012).
    Preprint - Full Text
  • Sustained Antidiabetic Effects of a Berberine-containing Chinese Herbal Medicine through Regulation of Hepatic Gene Expression Hai-Lu Zhao*$, Yi Sui*, Chun-Feng Qiao, Kevin Y. Yip, Ross K.K. Leung, Stephen K.W. Tsui, Harriet K.T. Wong, Xun Zhu, Jennifer J. Siu, Lan He, Jing Guan, Li-Zhong Liu, Heung-Man Lee, Hong-Xi Xu, Peter C.Y. Tong and Juliana C.N. Chan$,
    Sustained Antidiabetic Effects of a Berberine-containing Chinese Herbal Medicine through Regulation of Hepatic Gene Expression,
    Diabetes, vol. 61, no. 4, pp. 933-943, (2012).
    Preprint - Full Text
  • Genome-wide Analysis of Chromatin Features Identifies Chromatin-Sensitive and Chromatin-Insensitive Classes of Yeast Transcription Factors Chao Cheng*, Chong Shou*, Kevin Y. Yip, Koon-Kiu Yan and Mark B. Gerstein,
    Genome-wide Analysis of Chromatin Features Identifies Chromatin-Sensitive and Chromatin-Insensitive Classes of Yeast Transcription Factors,
    Genome Biology, vol. 12, issue 11, no. R111, (2011).
    Preprint - Full Text



  • Identification of Specificity Determining Residues in Peptide Recognition Domains using an Information Theoretic Approach Applied to Large-Scale Binding Maps Kevin Y. Yip*, Lukas Utz*, Simon Sitwell, Xihao Hu, Sachdev S. Sidhu, Benjamin E. Turk, Mark Gerstein$ and Philip M. Kim$,
    Identification of Specificity Determining Residues in Peptide Recognition Domains using an Information Theoretic Approach Applied to Large-Scale Binding Maps,
    BMC Biology, vol. 9, no. 53, (2011).
    Preprint - Full Text
  • Mining Order-Preserving Submatrices from Data with Repeated Measurements Kevin Y. Yip, Ben Kao, Xinjie Zhu, Chun Kit Chui, Sau Dan Lee and David W. Cheung,
    Mining Order-Preserving Submatrices from Data with Repeated Measurements,
    IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 25, issue 7, pp. 1587-1600, (2013).
    (Preliminary version: ICDM 2008)
    Preprint - Full Text
  • A User's Guide to the Encyclopedia of DNA Elements (ENCODE) The ENCODE Project Consortium,
    A User's Guide to the Encyclopedia of DNA Elements (ENCODE),
    PLoS Biology, vol. 9, issue 4, e1001046, (2011).
    Preprint - Full Text
  • A Statistical Framework for Modeling Gene Expression using Chromatin Features with Application to modENCODE Datasets Chao Cheng, Koon-Kiu Yan, Kevin Y. Yip, Joel Rozowsky, Roger Alexander, Chong Shou and Mark Gerstein,
    A Statistical Framework for Modeling Gene Expression using Chromatin Features with Application to modENCODE Datasets,
    Genome Biology, vol. 12, issue 2, no. R15, (2011).
    Preprint - Full Text - Web Site



  • Prediction and Characterization of Non-coding RNAs in C. elegans by Integrating Conservation, Secondary Structure and High Throughput Sequencing and Array Data Zhi John Lu*, Kevin Y. Yip*, Guilin Wang, Chong Shou, LaDeana W. Hillier, Ekta Khurana, Ashish Agarwal, Raymond Auerbach, Joel Rozowsky, Chao Cheng, Masaomi Kato, David M. Miller, Frank Slack, Michael Snyder, Robert H. Waterston, Valerie Reinke and Mark Gerstein,
    Prediction and Characterization of Non-coding RNAs in C. elegans by Integrating Conservation, Secondary Structure and High Throughput Sequencing and Array Data,
    Genome Research, vol. 21, no. 2, pp. 276-285, (2011).
    Preprint - Full Text - Web Site
  • ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks Justin Jee*, Joel Rozowsky*, Kevin Y. Yip*, Lucas Lochovsky, Robert Bjornson, Guoneng Zhong, Zhengdong Zhang, Yutao Fu, Jie Wang, Zhiping Weng and Mark Gerstein,
    ACT: Aggregation and Correlation Toolbox for Analyses of Genome Tracks,
    Bioinformatics, vol. 27, no 8, pp. 1152-1154, (2011).
    Preprint - Full Text - Web Site



  • Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project Mark B. Gerstein*$, Zhi John Lu*, Eric L. Van Nostrand*, Chao Cheng*, Bradley I. Arshinoff*, Tao Liu*, Kevin Y. Yip*, Rebecca Robilotto*, Andreas Rechtsteiner*, Kohta Ikegami*, Pedro Alves*, Aurelien Chateigner*, Marc Perry*, Mitzi Morris*, Raymond K. Auerbach*, Xin Feng*, Jing Leng*, Anne Vielle*, Wei Niu*, Kahn Rhrissorrakrai*, Ashish Agarwal, Roger P. Alexander, Galt Barber, Cathleen M. Brdlik, Jennifer Brennan, Jeremy Jean Brouillet, Adrian Carr, Ming-Sin Cheung, Hiram Clawson, Sergio Contrino, Luke O. Dannenberg, Abby F. Dernburg, Arshad Desai, Lindsay Dick, Andrea C. Dose, Jiang Du, Thea Egelhofer, Sevinc Ercan, Ghia Euskirchen, Brent Ewing, Elise A. Feingold, Reto Gassman, Peter J. Good, Phil Green, Francois Gullier, Michelle Gutwein, Mark S. Guyer, Lukas Habegger, Ting Han, Jorja G. Henikoff, Stefan R. Henz, Angie Hinrichs, Heather Holster, Tony Hyman, A. Leo Iniguez, Judith Janette, Morten Jensen, Masaomi Kato, W. James Kent, Ellen Kephart, Vishal Khivansara, Ekta Khurana, John K. Kim, Paulina Kolasinska-Zwierz, Eric C. Lai, Isabel Latorre, Amber Leahey, Suzanna Lewis, Paul Lloyd, Lucas Lochovsky, Rebecca F. Lowdon, Yaniv Lubling, Rachel Lyne, Michael MacCoss, Sebastian D. Mackowiak, Marco Mangone, Sheldon McKay, Desirea Mecenas, Gennifer Merrihew, David M. Miller III, Andrew Muroyama, John I. Murray, Siew-Loon Ooi, Hoang Pham, Taryn Phippen, Elicia A. Preston, Nikolaus Rajewsky, Gunnar Ratsch, Heidi Rosenbaum, Joel Rozowsky, Kim Rutherford, Peter Ruzanov, Mihail Sarov, Rajkumar Sasidharan, Andrea Sboner, Paul Scheid, Eran Segal, Hyunjin Shin, Chong Shou, Frank J. Slack, Cindie Slightam, Richard Smith, William C. Spencer, E.O. Stinson, Scott Taing, Teruaki Takasaki, Dionne Vafeados, Ksenia Voronina, Guilin Wang, Nicole L. Washington, Christina Whittle, Beijing Wu, Koon-Kiu Yan, Georg Zeller, Zheng Zha, Mei Zhong, Xingliang Zhou, modENCODE Consortium, Julie Ahringer$, Susan Strome$, Kristin C. Gunsalus$, Gos Micklem$, X. Shirley Liu$, Valerie Reinke$, Stuart K. Kim$, LaDeana W. Hillier$, Steven Henikoff$, Fabio Piano$, Michael Snyder$, Lincoln Stein$, Jason D. Lieb$ and Robert H. Waterston$,
    Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project,
    Science, vol. 330, no. 6012, pp. 1775-1787, (2010).
    Full Text
  • Extensive in vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses Xiyan Li, Tara A. Gianoulis, Kevin Y. Yip, Mark Gerstein and Michael Snyder,
    Extensive in vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses,
    Cell, vol. 143, issue 4, pp. 639-650, (2010).
    Full Text
  • Metric and Trigonometric Pruning for Clustering of Uncertain Data in 2D Geometric Space Wang Kay Ngai, Ben Kao, Reynold Cheng, Michael Chau, Sau Dan Lee, David W. Cheung and Kevin Y. Yip,
    Metric and Trigonometric Pruning for Clustering of Uncertain Data in 2D Geometric Space,
    Information Systems, vol. 36, issue 2, pp. 476-497, (2011).
    Preprint - Full Text
  • Analysis of Membrane Proteins in Metagenomics: Networks of Correlated Environmental Features and Protein Families Prianka V. Patel*, Tara A. Gianoulis*, Robert D. Bjornson, Kevin Y. Yip, Donald M. Engelman and Mark B. Gerstein,
    Analysis of Membrane Proteins in Metagenomics: Networks of Correlated Environmental Features and Protein Families,
    (Chosen as volume cover)
    Genome Research, vol. 20, no. 7, pp. 960-971, (2010).
    Full Text - Web Site
  • Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data Kevin Y. Yip, Roger P. Alexander, Koon-Kiu Yan and Mark Gerstein,
    Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data,
    (DREAM3 in silico challenge best performer paper),
    PLoS ONE, vol. 5, issue 1, no. e8121, (2010).
    Preprint - Full Text
  • Multi-level Learning: Improving the Prediction of Protein, Domain and Residue Interactions by Allowing Information Flow between Levels Kevin Y. Yip, Philip M. Kim, Drew McDermott and Mark Gerstein,
    Multi-level Learning: Improving the Prediction of Protein, Domain and Residue Interactions by Allowing Information Flow between Levels,
    BMC Bioinformatics, vol. 10, no. 241, (2009).
    Preprint - Full Text - Web Site
  • Decision Trees for Uncertain Data Smith Tsang, Ben Kao, Kevin Y. Yip, Wai-Shing Ho and Sau Dan Lee,
    Decision Trees for Uncertain Data,
    IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 23, no. 1, pp. 64-78, (2011).
    (Preliminary version: ICDE 2009)
    Preprint - Full Text
  • Training Set Expansion: An Approach to Improving the Reconstruction of Biological Networks from Limited and Uneven Reliable Interactions Kevin Y. Yip and Mark Gerstein,
    Training Set Expansion: An Approach to Improving the Reconstruction of Biological Networks from Limited and Uneven Reliable Interactions,
    Bioinformatics, vol. 25, no. 2, pp. 243-250, (2009).
    Preprint - Full Text - Web Site
  • Development of Grid-like Applications for Public Health using Web 2.0 Mashup Techniques Matthew Scotch, Kevin Y. Yip and Kei-Hoi Cheung,
    Development of Grid-like Applications for Public Health using Web 2.0 Mashup Techniques,
    Journal of the American Medical Informatics Association (JAMIA), vol. 15, no. 6, pp. 783-786, (2008).
    Preprint - Full Text
  • HCLS 2.0/3.0: Health Care and Life Sciences Data Mashup using Web 2.0/3.0 Kei-Hoi Cheung, Kevin Y. Yip, Jeffrey P. Townsend and Matthew Scotch,
    HCLS 2.0/3.0: Health Care and Life Sciences Data Mashup using Web 2.0/3.0,
    Journal of Biomedical Informatics (JBI), vol. 41, issue 5, pp. 694-705, (2008).
    Preprint - Full Text
  • A Semi-supervised Approach to Projected Clustering with Applications to Microarray Data Kevin Y. Yip, Lin Cheung, David W. Cheung, Liping Jing and Michael K. Ng,
    A Semi-supervised Approach to Projected Clustering with Applications to Microarray Data,
    International Journal of Data Mining and Bioinformatics (IJDMB), vol. 3, no. 3, pp. 229-259, (2009).
    (Preliminary version: ICDE 2005)
    Preprint - Full Text
  • An Integrated System for Studying Residue Coevolution in Proteins Kevin Y. Yip*, Prianka Patel*, Philip M. Kim, Donald M. Engelman, Drew McDermott and Mark Gerstein,
    An Integrated System for Studying Residue Coevolution in Proteins,
    Bioinformatics, vol. 24, no. 2, pp. 290-292, (2008).
    Preprint - Full Text - Web Site
  • Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology Long J. Lu, Andrea Sboner, Yuanpeng J. Huang, Hao Xin Lu, Tara A. Gianoulis, Kevin Y. Yip, Philip M. Kim, Gaetano T. Montelione and Mark B. Gerstein,
    Comparing Classical Pathways and Modern Networks: Towards the Development of an Edge Ontology,
    Trends in Biochemical Sciences (TIBS), vol. 32, issue 7, pp. 320-331, (2007).
    Preprint - Full Text
  • Mining Periodic Patterns with Gap Requirement from Sequences Minghua Zhang, Ben Kao, David W. Cheung and Kevin Y. Yip,
    Mining Periodic Patterns with Gap Requirement from Sequences,
    ACM Transactions on Knowledge Discovery from Data (TKDD), vol. 1, issue 2, article 7, (2007).
    (Preliminary version: SIGMOD 2005)
    Preprint - Full Text
  • LinkHub: A Semantic Web System that Facilitates Cross-Database Queries and Information Retrieval in Proteomics Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Martin Schultz and Mark B. Gerstein,
    LinkHub: A Semantic Web System that Facilitates Cross-Database Queries and Information Retrieval in Proteomics,
    BMC Bioinformatics, vol. 8 (Suppl 3), no. S5, (2007).
    (Preliminary version: SeS 2006)
    Preprint - Full Text
  • On Mining Micro-array Data by Order-Preserving Submatrix Lin Cheung, Kevin Y. Yip, David W. Cheung, Ben Kao, and Michael K. Ng
    On Mining Micro-array Data by Order-Preserving Submatrix,
    International Journal of Bioinformatics Research and Applications (IJBRA), vol. 3, no. 1, pp. 42-64, (2007).
    (Preliminary version: BMDE 2006)
    Preprint - Full Text
  • The tYNA Platform for Comparative Interactomics: A Web Tool for Managing, Comparing and Mining Multiple Networks Kevin Y. Yip, Haiyuan Yu, Philip M. Kim, Martin Schultz and Mark Gerstein,
    The tYNA Platform for Comparative Interactomics: A Web Tool for Managing, Comparing and Mining Multiple Networks,
    (Featured in Journal of Proteome Research and Canadian Bioinformatics Help Desk Newsletter)
    Bioinformatics, vol. 22, no. 23, pp. 2968-2970, (2006).
    Preprint - Full Text - Web Site
  • Progressive Skylining over Web-Accessible Databases Eric Lo, Kevin Y. Yip, King-Ip Lin, and David W. Cheung,
    Progressive Skylining over Web-Accessible Databases,
    Data & Knowledge Engineering (DKE), vol. 57, issue 2, pp. 122-147, (2006).
    Preprint - Full Text
  • YeastHub: A Semantic Web Use Case for Integrating Data in the Life Sciences Domain Kei-Hoi Cheung, Kevin Y. Yip, Andrew Smith, Remko de Knikker, Andy Masiar and Mark Gerstein,
    YeastHub: A Semantic Web Use Case for Integrating Data in the Life Sciences Domain,
    Bioinformatics, vol. 21, supp 1, pp. i85-i96, (2005). (Also in ISMB 2005)
    Preprint - Full Text
  • CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs S. I. Ao, Kevin Yip, Michael Ng, David Cheung, Pui-Yee Fong, Ian Melhado and Pak C Sham,
    CLUSTAG: Hierarchical Clustering and Graph Methods for Selecting Tag SNPs,
    Bioinformatics, vol. 21, no. 8, pp. 1735-1736, (2005).
    Preprint - Full Text
  • Biosphere: the Interoperation of Web Services in Microarray Cluster Analysis Kei-Hoi Cheung, Remko de Knikker, Youjun Guo, Guoneng Zhong, Janet Hager, Kevin Y. Yip, Albert K. H. Kwan, Peter Li and David W. Cheung,
    Biosphere: the Interoperation of Web Services in Microarray Cluster Analysis,
    Applied Bioinformatics, vol. 3, no. 4, pp. 253-256, (2004).
    Preprint - Full Text
  • Identifying Projected Clusters from Gene Expression Profiles Kevin Y. Yip, David W. Cheung, Michael K. Ng and Kei-Hoi Cheung,
    Identifying Projected Clusters from Gene Expression Profiles,
    Journal of Biomedical Informatics (JBI), vol. 37, issue 5, pp. 345-357, (2004).
    (Preliminary version: BIBE 2004)
    Preprint - Full Text
  • HARP: A Practical Projected Clustering Algorithm Kevin Y. Yip, David W. Cheung and Michael K. Ng,
    HARP: A Practical Projected Clustering Algorithm,
    IEEE Transactions on Knowledge and Data Engineering (TKDE), vol. 16, no. 11, pp. 1387-1397, (2004).
    Preprint - Full Text
  • A Web Services Choreography Scenario for Interoperating Bioinformatics Applications Remko de Knikker, Youjun Guo, Jin-long Li, Albert K. H. Kwan, Kevin Y. Yip, David W. Cheung and Kei-Hoi Cheung,
    A Web Services Choreography Scenario for Interoperating Bioinformatics Applications,
    BMC Bioinformatics, vol. 5, no. 25, (2004).
    Preprint - Full Text
  • Kevin Y. Yip, Michael K. Ng and David W. Cheung,
    A Review on Projected Clustering Algorithms,
    International Journal of Applied Mathematics (IJAM), vol. 13, no. 1, pp. 35-47, (2003).
    Preprint
Conference/workshop proceedings:
Conference/workshop abstracts/posters:
Book chapters:
Theses:
Technical reports:
Others:
  • Qin Cao and Kevin Y. Yip,
    Reply to 'Inflated Performance Measures in Enhancer–Promoter Interaction-Prediction Methods',
    Nature Genetics, vol. 51, no. 8, pp. 1201-1202, (2019).
    Full Text
  • Jason Y. K. Chan, Peony Hiu Yan Poon, Yong Zhang, Cherrie W. K. Ng, Wen Ying Piao, Meng Ma, Kevin Y. Yip, Amy B. W. Chan and Vivian Wai Yan Lui,
    Exome Sequencing Reveals Recurrent Mutations and a Loss-of-Function POLDIP2 Mutation in a Rare Undifferentiated Tongue Sarcoma,
    F1000 Research, vol. 7, article 499, (2018).
    Full Text