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Journal papers:
Papers ordered by date of acceptance. *: Co-first authorship; $: Co-corresponding/co-senior authorship
  1. Chromosomal-Level Genome Assembly and Single-Nucleotide Polymorphism Sites of Black-Faced Spoonbill Platalea minor Hong Kong Biodiversity Genomics Consortium,
    Chromosomal-Level Genome Assembly and Single-Nucleotide Polymorphism Sites of Black-Faced Spoonbill Platalea minor,
    GigaByte, vol. 2024, article 130, (2024).
    Full Text

  2. Genome Assembly of the Rare and Endangered Grantham’s Camellia, Camellia granthamiana Hong Kong Biodiversity Genomics Consortium,
    Genome Assembly of the Rare and Endangered Grantham’s Camellia, Camellia granthamiana,
    GigaByte, vol. 2024, article 124, (2024).
    Full Text

  3. Commonly used Software Tools Produce Conflicting and Overly-Optimistic AUPRC Values Wenyu Chen*, Chen Miao*, Zhenghao Zhang, Cathy Sin-Hang Fung, Ran Wang, Yizhen Chen, Yan Qian, Lixin Cheng, Kevin Y. Yip$, Stephen Kwok-Wing Tsui$ and Qin Cao$,
    Commonly used Software Tools Produce Conflicting and Overly-Optimistic AUPRC Values,
    Genome Biology, vol. 25, article 118, (2024).
    Full Text
  4. Chromosome-level Genome Assembly of the Common Chiton, Liolophura japonica (Lischke, 1873) Hong Kong Biodiversity Genomics Consortium,
    Chromosome-level Genome Assembly of the Common Chiton, Liolophura japonica (Lischke, 1873),
    GigaByte, vol. 2024, article 123, (2024).
    Full Text


  5. Chromosomal-level Genome Assembly of Golden Birdwing Troides aeacus (Felder & Felder, 1860) Hong Kong Biodiversity Genomics Consortium,
    Chromosomal-level Genome Assembly of Golden Birdwing Troides aeacus (Felder & Felder, 1860),
    GigaByte, vol. 2024, article 122, (2024).
    Full Text
  6. Chromosomal-level Genome Assembly of the Long-Spined Sea Urchin Diadema setosum (Leske, 1778) Hong Kong Biodiversity Genomics Consortium,
    Chromosomal-level Genome Assembly of the Long-Spined Sea Urchin Diadema setosum (Leske, 1778),
    GigaByte, vol. 2024, article 121, (2024).
    Full Text


  7. Genome Assembly of the Edible Jelly Fungus Dacryopinax spathularia (Dacrymycetaceae) Hong Kong Biodiversity Genomics Consortium,
    Genome Assembly of the Edible Jelly Fungus Dacryopinax spathularia (Dacrymycetaceae),
    GigaByte, vol. 2024, article 120, (2024).
    Full Text
  8. Genome Assembly of the Milky Mangrove Excoecaria agallocha Hong Kong Biodiversity Genomics Consortium,
    Genome Assembly of the Milky Mangrove Excoecaria agallocha,
    GigaByte, vol. 2024, article 119, (2024).
    Full Text

  9. A Long-Read Sequencing Strategy with Overlapping Linkers on Adjacent Fragments (OLAF-Seq) for Targeted Resequencing and Enrichment Lahari Uppuluri*, Christina Huan Shi*, Dharma Varapula, Eleanor Young, Rachel L. Ehrlich, Yilin Wang, Danielle Piazza, Joshua Chang Mell, Kevin Y. Yip and Ming Xiao,
    A Long-Read Sequencing Strategy with Overlapping Linkers on Adjacent Fragments (OLAF-Seq) for Targeted Resequencing and Enrichment,
    Scientific Reports, vol. 14, article 5583, (2024).
    Full Text
  10. Accurate Identification of Structural Variations from Cancer Samples Le Li*, Chenyang Hong*, Jie Xu*, Claire Yik-Lok Chung, Alden King-Yung Leung, Delbert Almerick T. Boncan, Lixin Cheng, Kwok-Wai Lo, Paul B. S. Lai, John Wong, Jingying Zhou, Alfred Sze-Lok Cheng, Ting-Fung Chan, Feng Yue$ and Kevin Y. Yip$,
    Accurate Identification of Structural Variations from Cancer Samples,
    Briefings in Bioinformatics, vol. 25, issue 1, article bbad520, (2024).
    Preprint - Full Text
  11. PRNF185 Control of COL3A1 Expression Limits Prostate Cancer Migration and Metastatic Potential Benjamin Van Espen, Htoo Zarni Oo, Colin Collins, Ladan Fazil, Alfredo Molinolo, Kevin Yip, Rabi Murad, Martin Gleave and Ze'ev Ronai,
    PRNF185 Control of COL3A1 Expression Limits Prostate Cancer Migration and Metastatic Potential,
    Molecular Cancer Research, vol. 22, issue 1, pp. 41-54, (2024).
    Full Text
  12. PSGL-1 Attenuates Early TCR Signaling to Suppress CD8+ T Cell Progenitor Differentiation and Elicit Terminal CD8+ T Cell Exhaustion Jennifer L. Hope, Dennis C. Otero, Eun-Ah Bae, Christopher J. Stairiker, Ashley B. Palete, Hannah A. Faso, Michelle Lin, Monique L. Henriquez, Sreeja Roy, Hyungseok Seo, Xue Lei, Eric S. Wang, Savio Chow, Roberto Tinoco, Gregory A. Daniels, Kevin Yip, Alexandre Rosa Campos, Jun Yin, Peter D. Adams, Anjana Rao and Linda M. Bradley,
    PSGL-1 Attenuates Early TCR Signaling to Suppress CD8+ T Cell Progenitor Differentiation and Elicit Terminal CD8+ T Cell Exhaustion,
    Cell Reports, vol. 42, issue 5, article 112436, (2023).
    Full Text
  13. DNA Methylation Markers for Kidney Function and Progression of Diabetic Kidney Disease Kelly Yichen Li, Claudia Ha Ting Tam, Hongbo Liu, Samantha Day, Cadmon King Poo Lim, Wing Yee So, Chuiguo Huang, Guozhi Jiang, Mai Shi, Heung Man Lee, TRANSCEND Consortium, Hui-yao Lan, Cheuk-Chun Szeto, Robert L. Hanson, Robert G. Nelson, Katalin Susztak, Juliana C. N. Chan, Kevin Y. Yip$ and Ronald C.W. Ma$,
    DNA Methylation Markers for Kidney Function and Progression of Diabetic Kidney Disease,
    Nature Communications, vol. 14, article 2543, (2023).
    Full Text
  14. Identification of a Common Variant for Coronary Heart Disease at PDE1A Contributes to Individualized Treatment Goals for Cardiovascular Complications in Chinese Patients with Type 2 Diabetes Claudia H.T. Tam, Cadmon K.P. Lim, Andrea O.Y. Luk, Mai Shi, Hoi Man Cheung, Alex C.W. Ng, Heung-man Lee, Eric S.H. Lau, Baoqi Fan, Guozhi Jiang, Alice P.S. Kong, Risa Ozaki, Elaine Y.K. Chow, Ka Fai Lee, Shing Chung Siu, Grace Hui, Chiu Chi Tsang, Kam Piu Lau, Jenny Y.Y. Leung, Elaine Y.N. Cheung, Man Wo Tsang, Grace Kam, Ip Tim Lau, June K.Y. Li, Vincent T.F. Yeung, Emmy Lau, Stanley Lo, Samuel Fung, Yuk Lun Cheng, Chun Chung Chow, The Hong Kong Diabetes Biobank Study Group, FIELD Study Investigators, Xiaodan Fan, Ting Fung Chan, Kevin Y.L. Yip, Si Lok, Weichuan Yu, Stephen K.W. Tsui, Hui-yao Lan, Cheuk Chun Szeto, Nelson L.S. Tang, Brian Tomlinson, Yu Huang, Alicia J Jenkins, Anthony Keech, Wing-yee So, Juliana C.N. Chan and Ronald C.W. Ma, for the TRANSCEND Consortium,
    Identification of a Common Variant for Coronary Heart Disease at PDE1A Contributes to Individualized Treatment Goals for Cardiovascular Complications in Chinese Patients with Type 2 Diabetes,
    Diabetes Care, vol. 46, issue 6, pp. 1271-1281, (2023).
    Full Text
  15. The ENCODE Imputation Challenge: A Critical Assessment of Methods for Cross-Cell Type Imputation of Epigenomic Profiles Jacob Schreiber*, Carles Boix*, Jin wook Lee, Hongyang Li, Yuanfang Guan, Chun-Chieh Chang, Jen-Chien Chang, Alex Hawkins-Hooker, Bernhard Schoelkopf, Gabriele Schweikert, Mateo Rojas Carulla, Arif Canakoglu, Francesco Guzzo, Luca Nanni, Marco Masseroli, Mark James Carman, Pietro Pinoli, Chenyang Hong, Kevin Y Yip, Jeffrey P Spence, Sanjit Singh Batra, Yun S Song, Shaun Mahony, Zheng Zhang, Wuwei Tan, Yang Shen, Yuanfei Sun, Minyi Shi, Jessika Adrian, Richard S Sandstrom, Nina Farrell, Jessica M Halow, Kristen Lee, Lixia Jiang, Xinqiong Yang, Charles B Epstein, J. Seth Strattan, Bradley Bernstein, Michael P Snyder, Manolis Kellis, William S Noble and Anshul B Kundaje,
    The ENCODE Imputation Challenge: A Critical Assessment of Methods for Cross-Cell Type Imputation of Epigenomic Profiles,
    Genome Biology, vol. 24, article 79, (2023).
    Full Text
  16. Targeting PPAR-gamma Counteracts Tumor Adaptation to Immune-Checkpoint Blockade in Hepatocellular Carcinoma Zhewen Xiong*, Stephen Lam Chan*, Jingying Zhou*, Joaquim S.L. Vong, Tsz Tung Kwong, Xuezhen Zeng, Haoran Wu, Jianquan Cao, Yalin Tu, Yu Feng, Weiqin Yang, Patrick Pak-Chun Wong, Willis Wai-Yiu Si-Tou, Xiaoyu Liu, Jing Wang, Wenshu Tang, Zhixian Liang, Jiahuan Lu, Ka Man Li, Jie Ting Low, Michael Wing-Yan Chan, Howard H.W. Leung, Anthony W.H. Chan, Ka-fai To, Kevin Yuk-Lap Yip, Yuk Ming Dennis Lo, Joseph Jao-Yiu Sung$ and Alfred Sze-Lok Cheng$,
    Targeting PPAR-gamma Counteracts Tumor Adaptation to Immune-Checkpoint Blockade in Hepatocellular Carcinoma,
    Gut, vol. 72, issue 9, pp. 1758-1773, (2023).
    Full Text
  17. ICI Efficacy Information Portal: A Knowledgebase for Responder Prediction to Immune Checkpoint Inhibitors Jiamin Chen, Daniel Rebibo, Jianquan Cao, Simon Yat-Man Mok, Neel Patel, Po-Cheng Tseng, Zhenghao Zhang and Kevin Y. Yip,
    ICI Efficacy Information Portal: A Knowledgebase for Responder Prediction to Immune Checkpoint Inhibitors,
    NAR Cancer, vol. 5, issue 1, article zcad012, (2023).
    Full Text
  18. Whole Genome Sequencing Reveals Epistasis Effects within RET for Hirschsprung Disease Yanbing Wang, Timothy Shin Heng Mak, Saloni Dattani, Maria-Merce Garcia-Barcelo, Alexander Xi Fu, Kevin Y. Yip, Elly Sau-Wai Ngan, Paul Kwang-Hang Tam, Clara Sze-Man Tang$ and Pak Chung Sham$,
    Whole Genome Sequencing Reveals Epistasis Effects within RET for Hirschsprung Disease,
    Scientific Reports, vol. 12, article 20423, (2022).
    Full Text
  19. Hypomorphic and Dominant Negative Impact of Truncated SOX9 Dysregulates Hedgehog-Wnt Signalling, Causing Campomelia Tiffany Y.K. Au*, Raymond K.H. Yip*, Sarah L. Wynn, Tiong Y. Tan, Alex Fu, Yu Hong Geng, Irene Y.Y. Szeto, Ben Niu, Kevin Y. Yip, Martin C.H. Cheung, Robin Lovell-Badge and Kathryn S.E. Cheah,
    Hypomorphic and Dominant Negative Impact of Truncated SOX9 Dysregulates Hedgehog-Wnt Signalling, Causing Campomelia,
    Proceedings of the National Academy of Sciences (PNAS) of the United States of America, vol. 120, issue 1, article e2208623119, (2022).
    Full Text
  20. Accurate Reconstruction of Viral Genomes in Human Cells from Short Reads using Iterative Refinement Sau-Dan Lee, Man Wu, Kwok-Wai Lo$ and Kevin Y. Yip$,
    Accurate Reconstruction of Viral Genomes in Human Cells from Short Reads using Iterative Refinement,
    BMC Genomics, vol. 23, article 422, (2022).
    Preprint - Full Text - Web Site
  21. Deep Learning Identifies and Quantifies Recombination Hotspot Determinants Yu Li*$, Siyuan Chen*, Trisevgeni Rapakoulia, Hiroyuki Kuwahara, Fowzan S. Alkuraya, Kevin Y. Yip and Xin Gao$,
    Deep Learning Identifies and Quantifies Recombination Hotspot Determinants,
    Bioinformatics, vol. 38, issue 10, pp. 2683-2691, (2022).
    Full Text
  22. Reusability Report: Capturing Properties of Biological Objects and Their Relationships using Graph Neural Networks Chenyang Hong*, Qin Cao*$, Zhenghao Zhang, Stephen Kwok-Wing Tsui and Kevin Y. Yip$,
    Reusability Report: Capturing Properties of Biological Objects and Their Relationships using Graph Neural Networks,
    Nature Machine Intelligence, vol. 4, issue 3, pp. 222-226, (2022).
    Full Text - Web Site
  23. Sirtuin 7 Super-Enhancer Drives Epigenomic Reprogramming in Hepatocarcinogenesis Feng Wu*, Liangliang Xu*, Yalin Tu*, Otto KW Cheung, Lemuel LM Szeto, Myth TS Mok, Weiqin Yang, Wei Kang, Qin Cao, Paul BS Lai, Stephen L Chan, Patrick Tan, Joseph JY Sung, Kevin Y Yip$, Alfred SL Cheng$ and Ka F To$,
    Sirtuin 7 Super-Enhancer Drives Epigenomic Reprogramming in Hepatocarcinogenesis,
    Cancer Letters, vol. 525, pp. 115-130, (2022).
    Full Text
  24. Quantifying Full-Length Circular RNAs in Cancer Ken Hung-On Yu*, Christina Huan Shi*, Bo Wang, Savio Ho-Chit Chow, Grace Tin-Yun Chung, Raymond Wai-Ming Lung, Ke-En Tan, Yat-Yuen Lim, Anna Chi-Man Tsang, Kwok-Wai Lo$ and Kevin Y. Yip$,
    Quantifying Full-Length Circular RNAs in Cancer,
    Genome Research, vol. 31, issue 12, pp. 2340-2353, (2021).
    Full Text

  25. Identification and Characterization of a Novel Epstein-Barr Virus-Encoded Circular RNA from LMP-2 Gene Ke-En Tan, Wei Lun Ng, Georgi K Marinov, Ken Hung-On Yu, Lu Ping Tan, Ee Shan Liau, Sook Yan Goh, Kok Siong Yeo, Kevin Y. Yip, Kwok-Wai Lo, Alan Soo-Beng Khoo, Lee-Fah Yap, Chee-Kwee Ea and Yat-Yuen Lim,
    Identification and Characterization of a Novel Epstein-Barr Virus-Encoded Circular RNA from LMP-2 Gene,
    Scientific Reports, vol. 11, article 14392, (2021).
    Full Text
  26. Whole-Genome Profiling of Nasopharyngeal Carcinoma Reveals Viral-Host Co-operation in Inflammatory NF-kB Activation and Immune Escape Jeff P. Bruce*, Ka Fai To*, Vivian W.Y. Lui*, Grace Tin-Yun Chung*, Yuk-Yu Chan, Chi Man Tsang, Kevin Y. Yip, Brigette Ma, John Woo, Edwin Hui, Michael Mak, Sau-Dan Lee, Chit Chow, Sharmila Velapasamy, Yvonne Y.Y. Or, Pui Kei Siu, Samah El Ghamrasni, Stephenie Prokopec, Man Wu, Johnny Kwan, Yuchen Liu, Jason Ying-Kuen Chan, Andrew van Hasselt, Lawrence Young, Christopher W. Dawson, Ian Paterson, Lee-Fah Yap, Sai-Wah Tsao, Fei-Fei Liu, Anthony Chan, Trevor Pugh$ and Kwok-Wai Lo$,
    Whole-Genome Profiling of Nasopharyngeal Carcinoma Reveals Viral-Host Co-operation in Inflammatory NF-kB Activation and Immune Escape,
    Nature Communications, vol. 12, article 4193, (2021).
    Full Text
  27. A Selective HDAC8 Inhibitor Potentiates Antitumor Immunity and Efficacy of Immune Checkpoint Blockade in Hepatocellular Carcinoma Weiqin Yang*, Yu Feng*, Jingying Zhou*, Otto Ka-Wing Cheung, Jianquan Cao, Jing Wang, Wenshu Tang, Yalin Tu, Liangliang Xu, Feng Wu, Zhiwu Tan, Hanyong Sun, Yuan Tian, John Wong, Paul Bo-San Lai, Stephen Lam Chan, Anthony Wing-Hung Chan, Patrick Boon-Ooi Tan, Zhiwei Chen, Joseph Jao-Yiu Sung, Kevin Yuk-Lap Yip, Ka-Fai To and Alfred Sze-Lok Cheng,
    A Selective HDAC8 Inhibitor Potentiates Antitumor Immunity and Efficacy of Immune Checkpoint Blockade in Hepatocellular Carcinoma,
    Science Translational Medicine, vol. 13, issue 588, article eaaz6804, (2021).
    Full Text
  28. 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
  29. 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
  30. 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
  31. 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

  32. 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
  33. 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
  34. 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
  35. 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$,
    Jellyfish Genomes Reveal Distinct Homeobox Gene Clusters and Conservation of Small RNA Processing,
    Nature Communications, vol. 11, article 3051, (2020).
    Full Text
  36. An integrative ENCODE Resource for Cancer Genomics Jing Zhang*, Donghoon Lee*, Vineet Dhiman*, Peng Jiang*, Jie Xu, Patrick McGillivray, Hongbo Yang, Jason Liu, William Meyerson, Declan Clarke, Mengting Gu, Shantao Li, Shaoke Lou, Jinrui Xu, Lucas Lochovsky, Matthew Ung, Lijia Ma, Grace Yu, Qin Cao, Arif Harmanci, Koon-Kiu Yan, Anurag Sethi, Gamze Gürsoy, Michael Schoenberg, Joel Rozowsky, Jonathan Warrell, Prashant Emani, Flynn Chen, Yucheng Yang, Timur Galeev, Xiangmeng Kong, Shuang Liu, Xiaotong Li, Jayanth Krishnan, Yanlin Feng, Juan Carlos Rivera-Mulia, Jessika Adrian, James Broach, Michael Bolt, Jennifer Moran, Dominic Fitzgerald, Vishnu Dileep, Tingting Liu, Shenglin Mei, Takayo Sasaki, Claudia Trevilla-Garcia, Su Wang, Yanli Wang, Chongzhi Zang, Daifeng Wang, Robert Klein, Michael Snyder, David Gilbert, Kevin Yip, Chao Cheng, Feng Yue, Xiaole Liu, Kevin White, and Mark Gerstein,
    An integrative ENCODE Resource for Cancer Genomics,
    Nature Communications, vol. 11, article 3696, (2020).
    Full Text
  37. Flexible K-mers with Variable-Length Indels for Identifying Binding Sequences of Protein Dimers Chenyang Hong and Kevin Y. Yip,
    Flexible K-mers with Variable-Length Indels for Identifying Binding Sequences of Protein Dimers,
    Briefings in Bioinformatics, vol. 21, issue 5, pp. 1787-1797, (2020).
    Preprint - Full Text - Web Site
  38. OMMA Enables Population-scale Analysis of Complex Genomic Features and Phylogenomic Relationships from Nanochannel-based Optical Maps Alden King-Yung Leung, Melissa Chun-Jiao Liu, Le Li, Yvonne Yuk-Yin Lai, Catherine Chu, Pui-Yan Kwok, Pak-Leung Ho, Kevin Y Yip$ and Ting-Fung Chan$,
    OMMA Enables Population-scale Analysis of Complex Genomic Features and Phylogenomic Relationships from Nanochannel-based Optical Maps,
    Giga Science, vol. 8, issue 7, article giz079, (2019).
    Full Text - Web Site
  39. Shaping the Nebulous Enhancer in the Era of High-Throughput Assays and Genome Editing Edwin Yu-Kiu Ho*, Qin Cao*, Mengting Gu, Ricky Wai-Lun Chan, Qiong Wu, Mark Gerstein and Kevin Y. Yip,
    Shaping the Nebulous Enhancer in the Era of High-Throughput Assays and Genome Editing,
    Briefings in Bioinformatics, vol. 21, issue 3, pp. 836-850, (2020).
    Preprint - Full Text
  40. Genome Maps Across 26 Human Populations Reveal Population-specific Patterns of Structural Variation Michal Levy-Sakin*, Steven Pastor*, Yulia Mostovoy*, Le Li*, Alden KY Leung*, Jennifer McCaffrey*, Eleanor Young, Ernest T Lam, Alex R Hastie, Karen HY Wong, Claire YL Chung, Walfred Ma, Justin Sibert, Ramakrishnan Rajagopalan, Nana Jin, Eugene YC Chow, Catherine Chu, Annie Poon, Chin Lin, Ahmed Naguib, Wei-Ping Wang, Han Cao, Ting-Fung Chan$, Kevin Y Yip$, Ming Xiao$ and Pui-Yan Kwok$,
    Genome Maps Across 26 Human Populations Reveal Population-specific Patterns of Structural Variation,
    Nature Communications, vol. 10, article 1025, (2019).
    Full Text
  41. New Guidelines for DNA Methylome Studies Regarding 5-hydroxymethylcytosine for Understanding Transcriptional Regulation Le Li*, Yuwei Gao*, Qiong Wu, Alfred S. L. Cheng$ 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


  42. 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$,
    Aberrant Enhancer Hypomethylation Contributes to Hepatic Carcinogenesis through Global Transcriptional Reprogramming,
    Nature Communications, vol. 10, article 335, (2019).
    Full Text
  43. Comparative Analysis of Single-Cell Parallel Sequencing Approaches in Oocyte Application Yan Qian, Jinyue Liao, Ashley Hoi Ching Suen, Annie Wing Tung Lee, Hoi Sze Chung, Nelson Leung Sang Tang, King Lau Chow, Qin Cao, Yuk Lap Yip, Tak Yeung Leung, Wai-Yee Chan, David Yiu Leung Chan, Tin Chiu Li and Tin-Lap Lee,
    Comparative Analysis of Single-Cell Parallel Sequencing Approaches in Oocyte Application,
    The International Journal of Biochemistry and Cell Biology, vol. 107, pp. 1-5, (2019).
    Full Text
  44. Identification of Genes Associated with Hirschsprung Disease, based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development Clara Sze-man Tang*, Peng Li*, Frank Pui-Ling Lai, Alexander Xi Fu, Sin-Ting Lau, Man Ting So, Kathy Nga-Chu Lui, Zhixin Li, Xuehan Zhuang, Michelle Yu, Xuelai Liu, Ngoc D Ngo, Xiaoping Miao, Xi Zhang, Bin Yi, Shaotao Tang, Xiaobing Sun, Furen Zhang, Hong Liu, Qiji Liu, Ruizhong Zhang, Hualong Wang, Liuming Huang, Xiao Dong, Jinfa Tou, Kathy SE Cheah, Wanling Yang, Zhenwei Yuan, Kevin Yuk-lap Yip, Pak-Chung Sham, Paul Kwang-Hang Tam, Maria-Mercè Garcia-Barcelo$ 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
  45. 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
  46. 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
  47. 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
  48. 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,
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  49. 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$,
    EBV-Encoded miRNAs Target ATM-Mediated Response in Nasopharyngeal Carcinoma,
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  50. OMSV Enables Accurate and Comprehensive Identification of Large Structural Variations from Nanochannel-based Single-Molecule Optical Maps Le Li*, Alden King-Yung Leung*, Tsz-Piu Kwok*, Yvonne Y. Y. Lai, Iris K. Pang, Grace Tin-Yun Chung, Angel C. Y. Mak, Annie Poon, Catherine Chu, Menglu Li, Jacob J. K. Wu, Ernest T. Lam, Han Cao, Chin Lin, Justin Sibert, Siu-Ming Yiu, Ming Xiao, Kwok-Wai Lo, Pui-Yan Kwok, Ting-Fung Chan$ and Kevin Y Yip$,
    OMSV Enables Accurate and Comprehensive Identification of Large Structural Variations from Nanochannel-based Single-Molecule Optical Maps,
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  51. START: A System for Flexible Analysis of Hundreds of Genomic Signal Tracks in Few Lines of SQL-like Queries Xinjie Zhu*, Qiang Zhang*, Eric Dun Ho, Ken Hung-On Yu, Chris Liu, Tim H. Huang, Alfred Sze-Lok Cheng, Ben Kao$, Eric Lo$ and Kevin Y. Yip$,
    START: A System for Flexible Analysis of Hundreds of Genomic Signal Tracks in Few Lines of SQL-like Queries,
    BMC Genomics, vol. 18, no. 749, (2017).
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  52. Reconstruction of Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines Qin Cao, Christine Anyansi, Xihao Hu, Liangliang Xu, Lei Xiong, Wenshu Tang, Myth T S Mok, Chao Cheng, Xiaodan Fan, Mark Gerstein, Alfred S L Cheng and Kevin Y Yip,
    Reconstruction of Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines,
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  53. OMTools: A Software Package for Visualizing and Processing Optical Mapping Data Alden King-Yung Leung, Nana Jin, Kevin Y. Yip$ and Ting-Fung Chan$,
    OMTools: A Software Package for Visualizing and Processing Optical Mapping Data,
    Bioinformatics, vol. 33, issue 18, pp. 2933-2935, (2017).
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  54. Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms Le Li and Kevin Y. Yip,
    Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms,
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  55. Hendrik G. Stunnenberg, The International Human Epigenome Consortium and Martin Hirst,
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  56. Exome and Genome Sequencing of Nasopharynx Cancer Identifies NF-kB Pathway Activating Mutations Yvonne Y Li*, Grace Tin-Yun Chung*, Vivian W.Y. Lui*, Ka-Fai To, Brigette Buig-Yue Ma, Chit Chow, John Kong-Sang Woo, Kevin Y. Yip, Jeongsun Seo, Edwin Pun Hui, Michael Ko-Fung Mak, Maria Rusan, Nicole G. Chau, Yvonne Yan-Yan Or, Marcus Hung-Nam Law, Peggy Pui-Ying Law, Zoey Wing-Yee Liu, Hoi Lam Ngan, Krista R. Verhoeft, Peony H.Y. Poon, Seong-Keun Yoo, Jong-Yeon Shin, Sau-Dan Lee, Samantha Wei-Man Lun, Anthony Wing-Hung Chan, Jason Ying-Kuen Chan, Paul Bo-San Lai, Choi-Yi Fung, Suet-Ting Hung, Lin Wang Lin, Ann Margaret V. Chang, Simion I. Chiosea, Matthew Louis Hedberg, Sai-Wah Tsao, Charles Andrew van Hasselt, Anthony Tak-Cheung Chan, Jennifer R. Grandis, Peter S. Hammerman$ and Kwok-Wai Lo$,
    Exome and Genome Sequencing of Nasopharynx Cancer Identifies NF-kB Pathway Activating Mutations,
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  57. Interactome-Transcriptome Analysis Discovers Signatures Complementary to GWAS Loci of Type 2 Diabetes Jing-Woei Li, Heung Man Lee, Ying Wang, Amy Hin Yan Tong, Kevin Y. Yip, Stephen Kwok-Wing Tsui, Si Lok, Risa Ozaki, Andrea Luk, Alice Kong, Wingyee So, Ronald Ma, Juliana Chan and Ting Fung Chan,
    Interactome-Transcriptome Analysis Discovers Signatures Complementary to GWAS Loci of Type 2 Diabetes,
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  58. OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach Alden King-Yung Leung, Tsz-Piu Kwok, Raymond Wan, Ming Xiao, Pui-Yan Kwok, Kevin Y. Yip$ and Ting-Fung Chan$,
    OMBlast: Alignment Tool for Optical Mapping using a Seed-and-Extend Approach,
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  59. 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)
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  60. 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,
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  61. 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,
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    Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays,
    Genetics, vol. 202, no. 1, pp. 351-362, (2016).
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  63. 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,
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  64. 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,
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  65. 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,
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  66. 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,
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    Nucleic Acids Research, vol. 43, issue 1, pp. 104-114, (2015).
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  67. 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).
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  68. 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,
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    Preprint - Full Text - Web Site
  69. 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


  70. 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).
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    Comparative Analysis of the Transcriptome across Distant Species,
    Nature, vol. 512, no. 7515, pp. 445-448, (2014).
    Full Text
  72. 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
  73. 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,
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  74. 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
  75. 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
  76. 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



  77. 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


  78. 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).
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  79. 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).
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  80. 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
  81. 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
  82. 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
  83. 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



  84. 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
  85. 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).
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  86. 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),
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  87. 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).
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  88. 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).
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  89. 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,
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  90. 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
  91. 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).
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  92. 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).
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  93. 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
  94. 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).
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  95. 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
  96. 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
  97. 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
  98. 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
  99. 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
  100. 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
  101. 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
  102. 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
  103. 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
  104. 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
  105. 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
  106. 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
  107. 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
  108. 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
  109. 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
  110. 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
  111. 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
  112. 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
  113. 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
  114. 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:
  1. 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,
    in European Conference on Computational Biology (ECCB), (2020).
    Preprint - Full Text - Web Sites: CQF-deNoise, SH-assembly
  2. 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,
    in International Conference on Intelligent Systems for Molecular Biology (ISMB), (2016).
    Preprint - Full Text - Web Site
  3. Menglu Li, Angel C.Y. Mak, Ernest T. Lam, Pui-Yan Kwok, Kevin Y. Yip, Ting Fung Chan and Siu Ming Yiu,
    Towards A More Accurate Error Model for BioNano Optical Maps,
    in The 12th International Symposium on Bioinformatics Research and Applications (ISBRA), (2016).
    Full Text
  4. Danny Kit-Sang Yip and Kevin Y. Yip,
    Systematic Exploration of Autonomous Modules in Noisy MicroRNA-Target Networks for Testing the Generality of the ceRNA Hypothesis,
    in Sixth Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges, (2013).
  5. Kevin Y. Yip, Roger P. Alexander, Koon-Kiu Yan and Mark Gerstein,
    Combining Multiple Models in Reconstructing in silico Regulatory Networks,
    in The 5th Annual RECOMB Satellite on Regulatory Genomics, the 4th Annual RECOMB Satellite on Systems Biology, and the 3rd Annual DREAM Reverse Engineering Challenges, (2008).
    (Invited abstract for best performer)
    Preprint
  6. Smith Tsang, Ben Kao, Kevin Y. Yip, Wai-Shing Ho and Sau Dan Lee,
    Decision Trees for Uncertain Data,
    in IEEE International Conference on Data Engineering (ICDE), (2009).
    Preprint - Full Text
  7. Chun Kit Chui, Ben Kao, Kevin Y. Yip and Sau Dan Lee,
    Mining Order-Preserving Submatrices from Data with Repeated Measurements,
    in IEEE International Conference on Data Mining (ICDM), (2008).
    Preprint - Full Text
  8. Songhua Xu, Suchao Chen, Kevin Y. Yip, Francis C. M. Lau and Xueying Qin,
    A Two-Stage Audio Retrieval Method for Searching Unannotated Audio Clips,
    in The IEEE International Symposium on Multimedia (ISM), (2008).
    Preprint - Full Text
  9. Kevin Y. Yip, Michael K. Ng and David W. Cheung,
    Input Validation for Semi-supervised Clustering,
    in Workshop on Foundations of Data Mining and Novel Techniques in High Dimensional Structural and Unstructured Data (FDM), (2006).
    Preprint - Full Text
  10. Wang Kay Ngai, Ben Kao, Chun Kit Chui, Reynold Cheng, Michael Chau and Kevin Y. Yip,
    Efficient Clustering of Uncertain Data,
    in IEEE International Conference on Data Mining (ICDM), (2006).
    Preprint - Full Text
  11. 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,
    in International Workshop on Semantic e-Science, (2006).
    Preprint
  12. Kevin Y. Yip, Peishen Qi, Martin Schultz, David W. Cheung and Kei-Hoi Cheung,
    SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services,
    in The Pacific Symposium on Biocomputing (PSB), (2006).
    Preprint - PDF
  13. 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,
    in International Conference on Intelligent Systems for Molecular Biology (ISMB), (2005).
    Preprint - Full Text
  14. Minghua Zhang, Ben Kao, David Cheung and Kevin Y. Yip,
    Mining Periodic Patterns with Gap Requirement from Sequences,
    in ACM SIGMOD International Conference on Management of Data, (2005).
    Preprint - Full Text
  15. Lin Cheung, Kevin Y. Yip, David W. Cheung, Ben Kao and Michael K. Ng,
    On Mining Micro-Array Data by Order-Preserving Submatrix,
    in International Workshop on Biomedical Data Engineering (BMDE), (2005).
    Preprint - Full Text
  16. Kevin Y. Yip, David W. Cheung and Michael K. Ng,
    On Discovery of Extremely Low-Dimensional Clusters using Semi-Supervised Projected Clustering,
    in IEEE International Conference on Data Engineering (ICDE), (2005).
    Preprint - Full Text
  17. Kei-Hoi Cheung, Andrew Smith, Kevin Y. Yip, Michael Seringhaus, Shawn M. Douglas and Mark Gerstein,
    A Semantic Web Approach to Integrating Heterogeneous Yeast Genome Data,
    in W3C Workshop on Semantic Web for Life Sciences (2004).
    Preprint - PDF
  18. Kevin Y. Yip, David W. Cheung, Michael K. Ng and Kei-Hoi Cheung,
    Identifying Projected Clusters from Gene Expression Profiles,
    in IEEE Symposium on BioInformatics and BioEngineering (BIBE), (2004).
    Preprint - Full Text
  19. Kevin Y. Yip, David W. Cheung and Michael K. Ng,
    A Highly-Usable Projected Clustering Algorithm for Gene Expression Profiles,
    in ACM SIGKDD Workshop on Data Mining in Bioinformatics (BIOKDD), (2003).
    Preprint - Full Text
 
Conference/workshop abstracts/posters:
  1. Zhewen Xiong, Stephen Lam Chan, Jingying Zhou, Xuezhen Zeng, Weiqin Yang, Haoran Wu, Jianquan Cao, Jie-Ting Low, Michael Wing-Yan Chan, Kevin Yuk-Lap Yip, Joseph Jao-Yiu Sung and Alfred Sze-Lok Cheng,
    Lipid-mediated Epigenetic Activation of PPAR-gamma Signaling Promotes Immune-Checkpoint Resistance in Hepatocellular Carcinoma,
    American Association of Cancer Research Annual Meeting (AACR), (2024).
  2. Alfred S. L. Cheng, Zhewen Xiong, Haoran Wu, Jianquan Cao, Zhixian Liang, Jingying Zhou, Joseph Jao-Yiu Sung, Kevin Yip and Stephen Chan,
    Single-Cell Dissection of Heterogeneity and Dynamics of Tumor Ecosystem upon Immune-Checkpoint Blockade in Hepatocellular Carcinoma,
    American Association of Cancer Research Annual Meeting (AACR), (2024).
  3. Dennis C Otero, Jennifer L Hope, Ashley B Palete, Hannah A Faso, Michelle Lin, Sreeja Roy, Eric S Wang, Savio Chow, Kevin Yip, Alexandre Rosa Campos and Linda M Bradley,
    PSGL-1 Deficiency Re-wires T Cell Signaling to Support Development of Stem Cell Like Exhausted T Cells that Control PD-1 Blockade Resistant Melanoma Tumor Growth,
    Immunology, (2023).
  4. Y. Li, K. K. Wong, C. H. Tam, C. K. Lim, C. C. Wang, X. L. Yang, A. El-Osta, W. L. Lowe, W. H. Tam, K. Y. Yip and R. C. Ma,
    Whole Genome Bisulfite Sequencing Identifies Methylation Markers in Cord Blood Linked to Maternal Hyperglycaemia and Childhood Metabolic Abnormalities,
    American Society of Human Genetics (ASHG) Annual Meeting, (2022).
  5. 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,
    Cold Spring Harbor Laboratory Virtual Meeting on Biological Data Science, (2020).
  6. Zhewen Xiong, Stephen Chan, Jingying Zhou, Jianquan Cao, Joaquim SL Vong, Xuezhen Zeng, Yalin Tu, Yu Feng, Kevin Yip, Joseph JY Sung and Alfred Sze-Lok Cheng,
    Targeting Hepatoma-Intrinsic PPARγ Signaling Overcomes Immune Checkpoint Therapy Resistance by Inflaming the Tumor Microenvironment,
    International Digestive Disease Forum (IDDF), (2020).
  7. Weiqin Yang, Yu Feng, Jingying Zhou, Otto Ka Wing Cheung, Feng Wu, Zhiwu Tan, Liangliang Xu, Hanyong Sun, Yuan Tian, John Wong, Paul Bo San Lai, Stephen Lam Chan, Wing Hung Chan, Patrick Tan, Zhiwei Chen, Joseph Jao Yiu Sung, Kevin Yuk Lap Yip, Ka Fai To and Alfred Sze Lok Cheng,
    Enhancer Reprogramming by Selective HDAC8 Inhibition Potentiates Tumor Remission and Durable Benefit by PD-L1 Blockade,
    International Digestive Disease Forum (IDDF), (2020).
  8. Qin Cao*, Zhenghao Zhang*, Alexander Xi Fu, Qiong Wu, Tin-Lap Lee, Chao Cheng, Danny Leung and Kevin Y. Yip,
    A Semi-Supervised Framework for Heterogeneous Networks Reveals Relationships between Genome Architecture and Gene Expression,
    ENCODE Research Applications and Users Meeting, (2019).
  9. Weiqin Yang, Yu Feng, Jingying Zhou, Otto KW Cheung, Hanyong Sun, Stephen L Chan, Anthony WH Chan, Zhiwei Chen, Kevin YL Yip, Ka-Fai To, Joseph JY Sung and Alfred SL Cheng,
    Superior Efficacy and Long-term Survival Benefit of HDAC8 and PD-L1 Co-Blockade in Liver Cancer Immunotherapy,
    International Digestive Disease Forum (IDDF), (2019).
  10. NC Lui, AX Fu, PL Lai, CST Lau, P Li, KYL Yip and ESW Ngan,
    Functional Study of Non-coding Variants in Hirschsprung Disease using Human Pluripotent Stem Cell-based Model,
    International Society for Stem Cell Research (ISSCR) Annual Meeting, (2019).
  11. Steve Tin Chi Luk, Man Tong, Kai Yu Ng, Kevin Yuk-Lap Yip, Xin Yuan Guan and Stephanie Ma,
    Identification of ZFP42/REX1 as a Regulator of Cancer Stemness in CD133+ Liver Cancer Stem Cells by Genome-wide DNA Methylation Analysis,
    American Association of Cancer Research Annual Meeting (AACR), (2018).
  12. Ka-Hei Lam, Raymond Wai-Ming Lung, Pok-Man Hau, Kevin Yuk-Lap Yip, George Sai-Wah Tsao, Ken Hung-On Yu, Joanna Hung-Man Tong, Kwok-Wai Lo and Ka-Fai To,
    Epstein-Barr Virus-Encoded MicroRNAs Regulate the Expression of BRCA1 in Nasopharyngeal Carcinoma,
    American Association of Cancer Research Annual Meeting (AACR), (2018).
  13. Raymond W Lung, Po-Man Hau, Joanna H Tong, Ka-Hei Lam, Anthony W Chan, Kevin Y Yip, George S Tsao, Kwok-Wai Lo and Ka-Fai To,
    Epstein-Barr Virus-Encoded MiRNAs Target ATM-Mediated Response in Nasopharyngeal Carcinoma,
    American Association of Cancer Research Annual Meeting (AACR), (2018).
  14. Otto Ka Wing Cheung, Feng Wu, Sau-Dan Lee, Patrick Tan, Kevin Yuk-Lap Yip, Ka Fai To and Alfred Sze-Lok Cheng,
    Super-Enhancer-Associated Master Transcriptional Circuitry in NAFLD-HCC Development,
    International Digestive Disease Forum (IDDF), (2018).
  15. Tin-Lap Lee, Wai-Yee Chan, Yan Qian, Cao Qin, Kevin Yuk-Lap Yip, King Lau Chow, Nelson LS Tang, Jinyue Liao, Alfred Chun Shui Luk, Hoi Ching Suen, Wing Tung Lee, Ming Peng Zhao, Grace Wing Shan Kong, Hoi Sze Chung, David Chan Yiu Leung, Tak Yeung Leung and Tin Chiu Li,
    Predicting Mouse Oocyte Methylome from Polar Body by Single-cell Whole Genome Bisulfite Sequencing,
    Experimental Biology, (2018).
  16. Myth T. Mok, Ying-Ying Lee, Wei Kang, Weiqin Yang, Wenshu Tang, Feng Wu, Liangliang Xu, Zhou Yu, Sau-Dan Lee, Grace L. H. Wong, Kevin Y. L. Yip, Ka-Fai To and Alfred S. L. Cheng,
    Silencing of Tumor Suppressor IGFBP4 Constitutes EZH2-driven Epigenetic Reprogramming in Gepatocarcinogenesis,
    Annual Meeting of the Japanese Cancer Association (JCA), (2018).
  17. P. Kwok, C. Chu, A. Hastie, E. Lam, A. Leung, L. Li, J. McCaffrey, M. Levy-Sakin, Y. Mostovoy, S. Pastor, A. Poon, R. Rajagopalan, J. Sibert, W. Wang, E. Young, H. Cao, T. Chan, K. Yip and M. Xiao,
    Single-Molecule Mapping of Complex Genomic Regions across 26 Human Populations reveals Population Specific Variation Patterns,
    American Society of Human Genetics (ASHG) Annual Meeting, (2017).
  18. T.L. Lee, Y. Qian, J.Y. Liao, W.Y. Chan, C. Ling, G.W.S. Kong, C.H.S. Chung, K.Y.L. Yip, K.L. Chow and T.C. Li,
    Revealing Transcriptome and Methylome Landscapes in a Human Oocyte by Parallel Sequencing,
    American Society of Human Genetics (ASHG) Annual Meeting, (2017).
  19. Steve Tin-Chi Luk, Man Tong, Kai Yu Ng, Kevin Yuk-Lap Yip, Xin Yuan Guan and Stephanie Ma,
    Identification of ZFP42/REX1 as a Regulator of Cancer Stemness in CD133+ Liver Cancer Stem Cells by Genome-wide DNA Methylation Analysis,
    American Association of Cancer Research Annual Meeting (AACR), (2017).
  20. Alden King-Yung Leung, Nana Jin, Kevin Y. Yip and Ting-Fung Chan,
    OMView: A Comprehensive Visualization Suite for Interpreting Optical Mapping Data The 21st Annual International Conference on Research in Computational Molecular Biology (RECOMB), (2017).
  21. Guozhi Jiang, Claudia HT Tam, Andrea O Luk, Heung Man Lee, Cadmon KP Lim, Xiaodan Fan, Si Lok, Ting Fung Chan, Kevin Yuk-Lap Yip, Nelson Tang, Stephen KW Tsui, Weichuan Yu, Brian Tomlinson, Yu Huang, Huiyao Lan, Cheuk-Chun Szeto, Wing Yee So, Juliana CN Chan and Ronald CW Ma,
    Genome-wide Association Study in Chinese Identifies New Susceptibility Loci Associated with Chronic Kidney Disease in Type 2 Diabetes,
    The 11th International Diabetes Federation World Diabetes Congress (IDF-WPR), (2016).
  22. Feng Wu, Yingying Lee, Sau Dan Lee, Patrick Tan, Nathalie Wong, Kevin Yuk-Lap Yip, Kai F To and Alfred Sze Lok Cheng,
    Nanoscale ChIP-seq Analysis in Primary Hepatocellular Carcinoma Tissues Reveals Tumor-specific Chromatin Deregulation for Oncogene Activation,
    American Association of Cancer Research Annual Meeting (AACR), (2016).
  23. Raymond Wai-Ming Lung, Tom Pok-Man Hau, Wing-Po Chak, Joanna Hung-Man Tong, Ken Hung-On Yu, Sai-Wah Tsao, Kevin Yuk-Lap Yip, Ka-Fai To and Kwok-Wai Lo,
    The Role of Epstein-Barr Virus-Encoded miRNAs in ATM Regulating DNA Damage Response in Nasopharyngeal Carcinoma,
    American Association of Cancer Research Annual Meeting (AACR), (2016).
  24. Pok Man Hau, Grace Chung, Raymond Lung, Samantha Lun, Chit Chow, Alice Wong, Fei-Fei Liu, George Tsao, Kevin Yip, Ka Fai To and Kwok Wai Lo,
    The Identification of UBR5-ZNF423 Recurrent Fusion Gene in EBV-associated Nasopharyngeal Carcinoma,
    American Association of Cancer Research Annual Meeting (AACR), (2016).
  25. Qin Cao and Kevin Y Yip,
    Construction and Analysis of Active Enhancer-Target Networks in 935 Samples of Human Primary Cells, Tissues and Cell Lines,
    The 24th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), (2016).
  26. TL. Lee, J. Liao, SH. Ng, K. Yip, Q. Cao and WY. Chan,
    Delineating Epigenetic Dynamics in Spermatogonial Stem Cell during Neonatal Development at Single-Base Resolution,
    American Society of Human Genetics (ASHG) Annual Meeting, (2015).
  27. Ma RC, So WY, Tam CH, Jiang GZ, Luk AO, Lee HM, Lim KP, Wang X, Kong AP, Ng AC, Fan X, Lok S, Chan TF, Yip K, Tang N, Tsui S, Yu W, Tomlinson BT, Lan HY, Huang Y, Szeto CC, Chan JC, on behalf of the TRANSCEND Consortium,
    Genome-wide Association Study Identifies Novel Loci Associated with Coronary Heart Disease in Type 2 Diabetes,
    International Diabetes Federation World Diabetes Congress (IDF-WPR), (2015).
  28. Yao Fu, Zhu Liu, Shaoke Lou, Vincenza Colonna, Jason Bedford, Xinmeng Mu, Kevin Y Yip, Hyun Min Kang, Tuuli Lappalainen, Andrea Sboner, Haiyuan Yu, Mark Rubin, Chris Tyler-Smith, Ekta Khurana, Mark Gerstein and 1000 Genomes Project Consortium,
    A Computational Framework for Prioritizing Noncoding Regulatory Variants in Cancer,
    American Association of Cancer Research Annual Meeting (AACR), (2015).
  29. Xihao Hu and Kevin Y. Yip,
    Learning Nucleotide Groups from RNA Structure-Probing Data,
    The Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, (2014).
  30. Qin Cao and Kevin Y. Yip,
    Evaluation of the Accuracy of Enhancer-Target Associations,
    The Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, (2014).
  31. 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,
    The Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, (2014).
  32. 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,
    The Seventh Annual RECOMB/ISCB Conference on Regulatory and Systems Genomics, with DREAM Challenges and Cytoscape Workshops, (2014).
  33. Cathy Ka Yan Mak, Tin Yun Grace Chung, Kevin Y. Yip, Kai Yuen Tso, Sau Dan Lee, Ka Fai To and Kwok Wai Lo,
    Whole-transcriptome Analyses of EBV-associated Nasopharyngeal Carcinoma using Next-Generation Transcriptome Sequencing,
    American Association of Cancer Research Annual Meeting (AACR), (2014).
  34. King-Yung Leung, Tsz-Piu Kwok, Jikun Wu, Siu-Ming Yiu, Kevin Yip and Ting-Fung Chan,
    OMSuite: A Software Platform for Structural Variation Detection using Optical Mapping Data,
    The 14th International Meeting on Human Genome Variation and Complex Genome Analysis (HGV), (2013).
  35. Angel CY Mak, Jacob JK Wu, Yvonne YY Lai, Ernest T Lam, Ming Xiao, Pui-Yan Kwok, Ting-Fung Chan, Kevin Y Yip, Tsz-Piu Kwok, Jing-Woei Li, Alden KY Leung, Aldrin KY Yim and Siu-Ming Yiu,
    Genome-wide Structural Variation Analysis with Genome Mapping on Nanochannel Arrays,
    21st Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 12th European Conference on Computational Biology (ECCB), (2013).
  36. A. C. Y. Mak, J. J. K. Wu, Y. Y. Y. Lai, K. Y. Yip, T. F. Chan, E. T. Lam, T. P. Kwok, J. W. Li, A. K. Y. Leung, A. K. Y. Yim, M. Xiao, P. Y. Kwok and S. M. Yiu,
    Genome-wide Structural Variation Analysis with Genome Mapping on Nanochannel Arrays,
    American Society of Human Genetics (ASHG) Annual Meeting, (2013).
  37. H. M. Lee, Z. Gao, R. Ma, X. Liu, J. Luan, V. Lam, C. Tam, Y. Wang, J. Ho, W. Leung, K. Yip, T. F. Chan, S. Tsui, W. So , J. Chan and J. Wang,
    Discovery of Type 2 Diabetes Genes using a Multiomic Analysis in a Family Trio,
    Joint Conference of Human Genome Meeting (HGM) 2013 and 21st International Congress of Genetics (ICG), (2013).
  38. 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).
  39. Michael Snyder, Xiyan Li, Tara Gianoulis, Kevin Yip and Mark Gerstein,
    Extensive In vivo Metabolite-Protein Interactions Revealed by Large-scale Sysdstematic Analyses,
    Experimental Biology, (2012).
 
Book chapters:
  1. Qin Cao and Kevin Y. Yip,
    A Survey on Computational Methods for Enhancer and Enhancer Target Predictions,
    in Computational Biology and Bioinformatics: Gene Regulation (ed. Ka-Chun Wong, CRC Press), (2015).
    Preprint
  2. Kei-Hoi Cheung, Andrew K. Smith, Kevin Y. L. Yip, Christopher J. O. Baker and Mark B. Gerstein,
    Semantic Web Approach to Database Integration in the Life Sciences,
    in Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences (eds. C Baker and K Cheung, Springer, NY), (2007).
 
Theses:
  1. Yuk Lap Yip,
    Computational Reconstruction of Biological Networks,
    PhD Thesis, Yale University, (2009).
    Preprint
  2. Kevin Yuk-Lap Yip,
    HARP: A Practical Projected Clustering Algorithm for Mining Gene Expression Data,
    Master Thesis, Department of Computer Science, The University of Hong Kong, (2003).
    Preprint - Full Text
 
Technical reports:
  1. Chun Kit Chui, Ben Kao, Kevin Y. Yip and Sau Dan Lee,
    Mining Order-Preserving Submatrices from Data with Repeated Measurements,
    Technical Report TR-2008-16, Department of Computer Science, The University of Hong Kong, (2008).
    Preprint - PDF
  2. Kevin Yuk-Lap Yip,
    Learning from Instance-level Relationships,
    Technical Report, Department of Computer Science, Yale University, (2006).
    Preprint
  3. Kevin Y. Yip, David W. Cheung and Michael K. Ng,
    On Discovery of Extremely Low-Dimensional Clusters using Semi-Supervised Projected Clustering,
    Technical Report TR-2004-08, Department of Computer Science, The University of Hong Kong, (2004).
    Preprint - PDF
 
Others:
  1. 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
  2. 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