Publications
DBLP PubMed BibTeX

*: Co-first authorship, $: Co-corresponding authorship

Journal papers:
  • 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, (in press).
    Preprint

  • 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


  • 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


  • 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
  • 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 (subscription required)
  • 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), (in press).
    (Preliminary version: ICDM 2008)
    Preprint Full Text (subscription required)
  • 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



  • 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
  • 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



  • 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$, Jason D. Lieb$, 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, no. 4, pp. 639-650, (2010).
    Preprint Full Text (subscription required)
  • 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 (subscription required)
  • 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).
    Preprint Full Text (subscription required)
  • 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
  • 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 (subscription required)
  • 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
  • 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 (subscription required)
  • 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 (subscription required)
  • 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
  • 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 (subscription required)
  • 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 PDF (subscription required)
  • LinkHub: A Semantic Web System for Efficiently Handling Complex Graphs of Proteomics Identifier Relationships that Facilitates Cross-database Queries and Information Retrieval Andrew K. Smith, Kei-Hoi Cheung, Kevin Y. Yip, Martin Schultz and Mark B. Gerstein,
    LinkHub: A Semantic Web System for Efficiently Handling Complex Graphs of Proteomics Identifier Relationships that Facilitates Cross-database Queries and Information Retrieval,
    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 (subscription required)
  • 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
  • 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 (subscription required)
  • 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 PDF
  • 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 (subscription required)
  • 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 (subscription required)
  • 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:
  • Pui Yan Kwok, Yvonne Yuk Lai, Angel Chi Mak, Ernest T. Lam, Justin Silbert, Tsz Piu Kwok, Jing Woei Li, Alden K. Leung, Jacob J. Wu, Aldrin K. Yim, Annie Poon, Catherine Chu, Chin Lin, Michael Requa, Alex Hastie, Thomas Anantharaman, Harper VanSteenhouse, Heng Dai, Fedor Trintchouk, Michael Saghbini, Michael Austin, Kirt Haden, Han Cao, Siu Ming Yiu, Kevin Y. Yip, Ting Fung Chan and Ming Xiao,
    Mapping of Two Human Genomes with a Single Molecule Nanochannel Array Platform for Genome-wide Structural Variation Analysis and de novo Sequence Assembly,
    European Conference of Human Genetics (ESHG), (2013).
Book chapters:
Theses:
Technical reports: