A highly-usable projected clustering algorithm for gene expression profiles. - Kevin Y. Yip; David W. Cheung; Michael K. Ng 001 (BIOKDD, 2003)

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; Kei-Hoi Cheung (BMC Bioinform., 2004)

Identifying projected clusters from gene expression profiles. - Kevin Y. Yip; David W. Cheung; Michael K. Ng 001; Kei-Hoi Cheung (J. Biomed. Informatics, 2004)

HARP: A Practical Projected Clustering Algorithm. - Kevin Y. Yip; David W. Cheung; Michael K. Ng 001 (IEEE Trans. Knowl. Data Eng., 2004)

On Discovery of Extremely Low-Dimensional Clusters using Semi-Supervised Projected Clustering. - Kevin Y. Yip; David W. Cheung; Michael K. Ng 001 (ICDE, 2005)

YeastHub: a semantic web use case for integrating data in the life sciences domain. - Kei-Hoi Cheung; Kevin Y. Yip; Andrew K. Smith; Remko de Knikker; Andy Masiar; Mark Gerstein (ISMB (Supplement of Bioinformatics), 2005)

CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs. - Sio Iong Ao; Kevin Y. Yip; Michael K. Ng 001; David Wai-Lok Cheung; Pui-Yee Fong; Ian Melhado; Pak Chung Sham (Bioinform., 2005)

Efficient Clustering of Uncertain Data. - Wang Kay Ngai; Ben Kao; Chun Kit Chui; Reynold Cheng; Michael Chau; Kevin Y. Yip (ICDM, 2006)

Input Validation for Semi-supervised Clustering. - Kevin Y. Yip; Michael K. Ng 001; David W. Cheung (ICDM Workshops, 2006)

SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services. - Kevin Y. Yip; Peishen Qi; Martin H. Schultz; David W. Cheung; Kei-Hoi Cheung (Pacific Symposium on Biocomputing, 2006)

Progressive skylining over Web-accessible databases. - Eric Lo 001; Kevin Y. Yip; King-Ip Lin; David W. Cheung (Data Knowl. Eng., 2006)

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 H. Schultz; Mark Gerstein (Bioinform., 2007)

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 H. Schultz; Mark Gerstein (BMC Bioinform., 2007)

On mining micro-array data by Order-Preserving Submatrix. - Lin Cheung; David W. Cheung; Ben Kao; Kevin Y. Yip; Michael K. Ng 001 (Int. J. Bioinform. Res. Appl., 2007)

Mining periodic patterns with gap requirement from sequences. - Minghua Zhang; Ben Kao; David W. Cheung; Kevin Y. Yip (ACM Trans. Knowl. Discov. Data, 2007)

Mining Order-Preserving Submatrices from Data with Repeated Measurements. - Chun Kit Chui; Ben Kao; Kevin Y. Yip; Sau Dan Lee (ICDM, 2008)

A Two-Stage Audio Retrieval Method for Searching Unannotated Audio Clips. - Songhua Xu; Suchao Chen; Kevin Y. Yip; Francis C. M. Lau 001; Xueying Qin (ISM, 2008)

An integrated system for studying residue coevolution in proteins. - Kevin Y. Yip; Prianka Patel; Philip M. Kim; Donald M. Engelman; Drew McDermott; Mark Gerstein (Bioinform., 2008)

Case Report: Development of Grid-like Applications for Public Health Using Web 2.0 Mashup Techniques. - Matthew Scotch; Kevin Y. Yip; Kei-Hoi Cheung (J. Am. Medical Informatics Assoc., 2008)

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; Matthew Scotch (J. Biomed. Informatics, 2008)

Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions. - Kevin Y. Yip; Mark Gerstein (Bioinform., 2009)

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; Mark Gerstein (BMC Bioinform., 2009)

A semi-supervised approach to projected clustering with applications to microarray data. - Kevin Y. Yip; Lin Cheung; David W. Cheung; Liping Jing; Michael K. Ng 001 (Int. J. Data Min. Bioinform., 2009)

ACT: aggregation and correlation toolbox for analyses of genome tracks. - Justin Jee; Joel S. Rozowsky; Kevin Y. Yip; Lucas Lochovsky; Robert D. Bjornson; Guoneng Zhong; Zhengdong D. Zhang; Yutao Fu; Jie Wang; Zhiping Weng; Mark Gerstein (Bioinform., 2011)

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; Kevin Y. Yip (Inf. Syst., 2011)

Decision Trees for Uncertain Data. - Smith Tsang; Ben Kao; Kevin Y. Yip; Wai-Shing Ho; Sau Dan Lee (IEEE Trans. Knowl. Data Eng., 2011)

Mining Order-Preserving Submatrices from Data with Repeated Measurements. - Kevin Y. Yip; Ben Kao; Xinjie Zhu; Chun Kit Chui; Sau Dan Lee; David W. Cheung (IEEE Trans. Knowl. Data Eng., 2013)

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; Kevin Y. Yip (Bioinform., 2014)

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; Kevin Y. Yip (Bioinform., 2014)

Towards a More Accurate Error Model for BioNano Optical Maps. - Menglu Li; Angel C. Y. Mak; Ernest T. Lam; Pui-Yan Kwok; Ming Xiao; Kevin Y. Yip; Ting-Fung Chan; Siu-Ming Yiu (ISBRA, 2016)

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations. - Xihao Hu; Yang Wu; Zhi John Lu; Kevin Y. Yip (Briefings Bioinform., 2016)

A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps. - Xihao Hu; Christina Huan Shi; Kevin Y. Yip (Bioinform., 2016)

OMTools: a software package for visualizing and processing optical mapping data. - Alden King-Yung Leung; Nana Jin; Kevin Y. Yip; Ting-Fung Chan (Bioinform., 2017)

OMBlast: alignment tool for optical mapping using a seed-and-extend approach. - Alden King-Yung Leung; Tsz-Piu Kwok; Raymond Wan 001; Ming Xiao; Pui-Yan Kwok; Kevin Y. Yip; Ting-Fung Chan (Bioinform., 2017)

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; Kevin Y. Yip (Bioinform., 2018)

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 019; Nelson L. S. Tang; Weichuan Yu; Kevin Y. Yip (Bioinform., 2018)

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; Kevin Y. Yip (Briefings Bioinform., 2020)

Flexible k-mers with variable-length indels for identifying binding sequences of protein dimers. - Chenyang Hong; Kevin Y. Yip (Briefings Bioinform., 2020)

A general near-exact k-mer counting method with low memory consumption enables de novo assembly of 106× human sequence data in 2.7 hours. - Christina Huan Shi; Kevin Y. Yip (Bioinform., 2020)

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 001; Alfred S. L. Cheng; Chao Cheng; Danny Leung; Kevin Y. Yip (Nat. Mach. Intell., 2020)

Deep learning identifies and quantifies recombination hotspot determinants. - Yu Li 006; Siyuan Chen; Trisevgeni Rapakoulia; Hiroyuki Kuwahara; Kevin Y. Yip; Xin Gao 001 (Bioinform., 2022)

Reusability report: Capturing properties of biological objects and their relationships using graph neural networks. - Chenyang Hong; Qin Cao; Zhenghao Zhang; Stephen Kwok-Wing Tsui; Kevin Y. Yip (Nat. Mach. Intell., 2022)

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; et al. (Briefings Bioinform., 2024)

Driving Accurate Allergen Prediction with Protein Language Models and Generalization-Focused Evaluation. - Brian Shing-Hei Wong; Joshua Mincheol Kim; Sin-Hang Fung; Qing Xiong; Kelvin Fu-Kiu Ao; Junkang Wei; Ran Wang; Dan Michelle Wang; Jingying Zhou; Bo Feng; Alfred Sze-Lok Cheng; Kevin Y. Yip; et al. (CoRR, 2025)