Kevin Y. Yip

发表

Mining Order-Preserving Submatrices from Data with Repeated Measurements

David Wai-Lok Cheung, Sau Dan Lee, Ben Kao, 2013, IEEE Trans. Knowl. Data Eng..

SemBiosphere: A Semantic Web Approach to Recommending Microarray Clustering Services

Kei-Hoi Cheung, Peishen Qi, David Wai-Lok Cheung, 2005, Pacific Symposium on Biocomputing.

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

Mark Gerstein, Martin H. Schultz, Kevin Y. Yip, 2006, Bioinform..

Metric and trigonometric pruning for clustering of uncertain data in 2D geometric space

Reynold Cheng, David Wai-Lok Cheung, Michael Chau, 2011, Inf. Syst..

YeastHub: a semantic web use case for integrating data in the life sciences domain

Kei-Hoi Cheung, Mark Gerstein, Andrew K. Smith, 2005, ISMB.

CLUSTAG: hierarchical clustering and graph methods for selecting tag SNPs

Sio Iong Ao, Michael K. Ng, David Wai-Lok Cheung, 2005, Bioinform..

Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

Mark Gerstein, Drew McDermott, Kevin Y. Yip, 2009, BMC Bioinformatics.

Mining periodic patterns with gap requirement from sequences

David Wai-Lok Cheung, Ben Kao, Minghua Zhang, 2005, SIGMOD '05.

Progressive skylining over Web-accessible databases

David Wai-Lok Cheung, Eric Lo, King-Ip Lin, 2006, Data Knowl. Eng..

OMTools: a software package for visualizing and processing optical mapping data

Nana Jin, Alden King-Yung Leung, Ting-Fung Chan, 2017, Bioinform..

Training set expansion: an approach to improving the reconstruction of biological networks from limited and uneven reliable interactions

Mark Gerstein, Kevin Y. Yip, M. Gerstein, 2008, Bioinform..

Table of Contents International Workshop on Biomedical Data Engineering (BMDE2005)

Claudia Täubner, Ben Kao, David W. Cheung, 2005 .

A unified framework for integrative study of heterogeneous gene regulatory mechanisms

Alfred S. L. Cheng, Qiong Wu, Danny Leung, 2020 .

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module

Ting-Fung Chan, Kevin Y. Yip, King Ming Chan, 2014, Front. Bioeng. Biotechnol..

Efficient Clustering of Uncertain Data

Reynold Cheng, Michael Chau, Ben Kao, 2006, Sixth International Conference on Data Mining (ICDM'06).

A Two-Stage Audio Retrieval Method for Searching Unannotated Audio Clips

Francis C. M. Lau, Xueying Qin, Songhua Xu, 2008, 2008 Tenth IEEE International Symposium on Multimedia.

A comprehensive web tool for toehold switch design

Siu-Kai Kong, Ting-Fung Chan, Kevin Y. Yip, 2018, Bioinform..

Faculty Opinions recommendation of Assessment of computational methods for the analysis of single-cell ATAC-seq data.

Kevin Y. Yip, 2019 .

On Mining Micro-array data by Order-Preserving Submatrix

Michael K. Ng, David Wai-Lok Cheung, Ben Kao, 2005, 21st International Conference on Data Engineering Workshops (ICDEW'05).

An integrated system for studying residue coevolution in proteins

Mark Gerstein, Drew McDermott, Kevin Y. Yip, 2008, Bioinform..

K-mer counting with low memory consumption enables fast clustering of single-cell sequencing data without read alignment

Kevin Y. Yip, Christina Huan Shi, 2019, bioRxiv.

Case Report: Development of Grid-like Applications for Public Health Using Web 2.0 Mashup Techniques

Kei-Hoi Cheung, Matthew Scotch, Kevin Y. Yip, 2008, J. Am. Medical Informatics Assoc..

Faculty Opinions recommendation of Exploring single-cell data with deep multitasking neural networks.

Kevin Y. Yip, 2019 .

A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps

Kevin Y. Yip, Xihao Hu, Christina Huan Shi, 2016, Bioinform..

On discovery of extremely low-dimensional clusters using semi-supervised projected clustering

Michael K. Ng, David Wai-Lok Cheung, Kevin Y. Yip, 2005, 21st International Conference on Data Engineering (ICDE'05).

ACT: aggregation and correlation toolbox for analyses of genome tracks

Lucas Lochovsky, Mark Gerstein, Jie Wang, 2011, Bioinform..

Faculty Opinions recommendation of Prioritization of cancer therapeutic targets using CRISPR-Cas9 screens.

Kevin Y. Yip, 2019 .

A semi-supervised approach to projected clustering with applications to microarray data

Michael K. Ng, David Wai-Lok Cheung, Liping Jing, 2009, Int. J. Data Min. Bioinform..

Integrating Information in Biological Ontologies and Molecular Networks to Infer Novel Terms

Kevin Y. Yip, Le Li, Le Li, 2016, Scientific Reports.

HARP: a practical projected clustering algorithm

Michael K. Ng, David Wai-Lok Cheung, Kevin Y. Yip, 2004, IEEE Transactions on Knowledge and Data Engineering.

A highly-usable projected clustering algorithm for gene expression profiles

Michael K. Ng, David Wai-Lok Cheung, Kevin Y. Yip, 2003, BIOKDD.

Input Validation for Semi-supervised Clustering

Michael K. Ng, David Wai-Lok Cheung, Kevin Y. Yip, 2006, Sixth IEEE International Conference on Data Mining - Workshops (ICDMW'06).

LinkHub: a Semantic Web system that facilitates cross-database queries and information retrieval in proteomics

Kei-Hoi Cheung, Mark Gerstein, Andrew K. Smith, 2007, BMC Bioinformatics.

Identifying projected clusters from gene expression profiles

Kei-Hoi Cheung, Michael K. Ng, David Wai-Lok Cheung, 2004, J. Biomed. Informatics.

Flexible k-mers with variable-length indels for identifying binding sequences of protein dimers

Kevin Y. Yip, Chenyang Hong, 2020, Briefings Bioinform..

A web services choreography scenario for interoperating bioinformatics applications

Kei-Hoi Cheung, Jin-long Li, David Wai-Lok Cheung, 2003, BMC Bioinformatics.

Computational identification of protein binding sites on RNAs using high-throughput RNA structure-probing data

Siu-Ming Yiu, Ting-Fung Chan, Thomas K. F. Wong, 2014, Bioinform..

HCLS 2.0/3.0: Health care and life sciences data mashup using Web 2.0/3.0

Kei-Hoi Cheung, Jeffrey P. Townsend, Matthew Scotch, 2008, J. Biomed. Informatics.

Analysis of sequencing data for probing RNA secondary structures and protein-RNA binding in studying posttranscriptional regulations

Kevin Y. Yip, Xihao Hu, Yang Wu, 2015, Briefings Bioinform..

Faculty Opinions recommendation of Consistent RNA sequencing contamination in GTEx and other data sets.

Kevin Y. Yip, 2020 .

Decision Trees for Uncertain Data

Sau Dan Lee, Wai-Shing Ho, Ben Kao, 2011, IEEE Transactions on Knowledge and Data Engineering.

Towards a More Accurate Error Model for BioNano Optical Maps

Ming Xiao, Siu-Ming Yiu, Ting-Fung Chan, 2016, ISBRA.

The tYNA platform for comparative interactomics: a web tool for managing, comparing and mining multiple networks

Mark Gerstein, Martin H. Schultz, Kevin Y. Yip, 2006, Bioinform..

Identifying projected clusters from gene expression profiles

Kei-Hoi Cheung, Michael K. Ng, David Wai-Lok Cheung, 2004, Proceedings. Fourth IEEE Symposium on Bioinformatics and Bioengineering.

OMBlast: alignment tool for optical mapping using a seed-and-extend approach

Ming Xiao, Alden King-Yung Leung, Ting-Fung Chan, 2016, Bioinform..

A network approach to exploring the functional basis of gene‐gene epistatic interactions in disease susceptibility

Wei Jiang, Weichuan Yu, Nelson L. S. Tang, 2018, Bioinform..

ECplot: an online tool for making standardized plots from large datasets for bioinformatics publications

Sau Dan Lee, Kevin Y. Yip, Alex Chun-Hong Fok, 2014, Bioinform..

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

Siu-Ming Yiu, Alden King-Yung Leung, Ting-Fung Chan, 2017 .

Semantic Web Approach to Database Integration in the Life Sciences

Mark Gerstein, Kei-Hoi Cheung, Kevin Y. Yip, 2007 .

Decision Trees for Uncertain Data

Sau Dan Lee, Wai-Shing Ho, Ben Kao, 2011, IEEE Trans. Knowl. Data Eng..

Mining Order-Preserving Submatrices from Data with Repeated Measurements

Sau Dan Lee, Ben Kao, Kevin Y. Yip, 2008, IEEE Transactions on Knowledge and Data Engineering.

Mining periodic patterns with gap requirement from sequences

Kevin Y. Yip, D. Cheung, Minghua Zhang, 2007 .

Extensive In Vivo Metabolite-Protein Interactions Revealed by Large-Scale Systematic Analyses

Kevin Y. Yip, M. Gerstein, M. Snyder, 2010, Cell.

Architecture of the human regulatory network derived from ENCODE data

David Z. Chen, Kevin Y. Yip, Timothy E. Reddy, 2012, Nature.

Improved Reconstruction of In Silico Gene Regulatory Networks by Integrating Knockout and Perturbation Data

Kevin Y. Yip, M. Gerstein, Koon-Kiu Yan, 2010, PloS one.

An Integrated Encyclopedia of DNA Elements in the Human Genome

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2012, Nature.

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

Raymond K. Auerbach, Kevin Y. Yip, Stefan R. Henz, 2010, Science.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

Kevin Y. Yip, M. Gerstein, J. Rozowsky, 2011, Genome Biology.

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

Raymond K. Auerbach, William Stafford Noble, Stephen C. J. Parker, 2011, PLoS biology.

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y. Yip, James B. Brown, P. Bickel, 2012, Genome Biology.

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Kevin Y. Yip, E. Birney, M. Gerstein, 2012, Genome research.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer

Kevin Y. Yip, M. Gerstein, X. Mu, 2014, Genome Biology.

Reconstruction of enhancer–target networks in 935 samples of human primary cells, tissues and cell lines

Kevin Y. Yip, M. Gerstein, A. Cheng, 2017, Nature Genetics.

Machine learning and genome annotation: a match meant to be?

Kevin Y. Yip, M. Gerstein, Chao Cheng, 2013, Genome Biology.

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Kevin Y. Yip, Tyler H. Garvin, M. Gerstein, 2018, Nature Methods.

Comparative Analysis of the Transcriptome across Distant Species

Peter J. Bickel, Raymond K. Auerbach, Peter J. Park, 2014, Nature.

On mining micro-array data by Order-Preserving Submatrix.

Kevin Y Yip, Ben Kao, Kevin Y. Yip, 2007, International journal of bioinformatics research and applications.

New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation.

Kevin Y. Yip, A. Cheng, Le Li, 2019, Genome research.

New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation

Kevin Y. Yip, A. Cheng, Le Li, 2018, bioRxiv.

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation

Kevin Y. Yip, Jun Wang, S. Lok, 2014, Genome Biology.

A common set of distinct features that characterize noncoding RNAs across multiple species

Michael Q. Zhang, Kevin Y. Yip, Yu-Cheng T. Yang, 2014, Nucleic acids research.

Improved prediction of RNA secondary structure by integrating the free energy model with restraints derived from experimental probing data

Kevin Y. Yip, D. Mathews, Z. Lu, 2015, Nucleic acids research.

Interactome-transcriptome analysis discovers signatures complementary to GWAS Loci of Type 2 Diabetes

Kevin Y. Yip, S. Lok, S. Tsui, 2016, Scientific Reports.

Genome-Wide Structural Variation Detection by Genome Mapping on Nanochannel Arrays

Kevin Y. Yip, Jacob J. K. Wu, A. Pang, 2015, Genetics.

Whole-genome analysis of noncoding genetic variations identifies multiscale regulatory element perturbations associated with Hirschsprung disease

Kevin Y. Yip, Alexander Xi Fu, P. Sham, 2020, bioRxiv.

Analysis of membrane proteins in metagenomics: networks of correlated environmental features and protein families.

Kevin Y. Yip, M. Gerstein, D. Engelman, 2010, Genome research.

LinkHub : a Semantic Web System for Efficiently Handling Complex Graphs of Proteomics Identifier Relationships that Facilitates Cross-database Queries and Information Retrieval

Kei-Hoi Cheung, Kevin Y. Yip, Mark B. Gerstein, 2006 .

START: a system for flexible analysis of hundreds of genomic signal tracks in few lines of SQL-like queries

Eric Lo, Chris Liu, Kevin Y. Yip, 2017, BMC Genomics.

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.

Kevin Y. Yip, Christina Huan Shi, 2020, Bioinformatics.

A survey on computational methods for enhancer and enhancer target predictions

Kevin Y. Yip, Qin Cao, Qin Cao, 2015 .

Identification of specificity determining residues in peptide recognition domains using an information theoretic approach applied to large-scale binding maps

Kevin Y. Yip, Philip M. Kim, M. Gerstein, 2011, BMC Biology.

A Survey of the Computational Methods for Enhancers and Enhancer-target Predictions

Kevin Y. Yip, Qin Cao, Kevin Y. Yip, 2016 .

throughput sequencing and array data by integrating conservation , secondary structure and high Prediction and characterization of non-coding RNAs in C . elegans

Raymond K. Auerbach, Kevin Y. Yip, M. Gerstein, 2010 .

Title Identifying projected clusters from gene expression profiles

Kevin Y. Yip, 2001 .

Identification of Genes Associated With Hirschsprung Disease, Based on Whole-Genome Sequence Analysis, and Potential Effects on Enteric Nervous System Development.

Kevin Y. Yip, Alexander Xi Fu, P. Sham, 2018, Gastroenterology.

Title HARP : A practical projected clustering algorithm

Kevin Y. Yip, M. Ng, D. Cheung, 2004 .

Simultaneous transcriptome and methylome profiles of single mouse oocytes provide novel insights on maturation and aging

Kevin Y. Yip, T. Leung, Tin-Lap Lee, 2020, bioRxiv.

Racial, ethnic, and healthcare disparities in rheumatoid arthritis.

Kevin Y. Yip, I. Navarro-Millán, Kevin Y. Yip, 2020, Current opinion in rheumatology.

maps across 26 human populations reveal population-specific patterns of structural

Kevin Y. Yip, E. Y. Chow, P. Kwok, 2019 .

Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C666-1

Kevin Y. Yip, S. Cheung, K. To, 2013, Infectious Agents and Cancer.

Complete genomic sequence of Epstein-Barr virus in nasopharyngeal carcinoma cell line C 666-1

Kevin Y. Yip, S. Cheung, K. To, 2013 .

Identification of a Major Determinant for Serine-Threonine Kinase Phosphoacceptor Specificity

Kevin Y. Yip, Philip M. Kim, M. Gerstein, 2014, Molecular cell.

Characterization of Azotobacter vinelandii and Kits for Its Synthetic Biology Applications

Kevin Y. Yip, S. Kong, T. Chan, 2017, bioRxiv.

Why are we still using opioids for osteoarthritis?

Kevin Y. Yip, J. Oettinger, 2020, International journal of clinical practice.

Shaping the nebulous enhancer in the era of high-throughput assays and genome editing

Mark Gerstein, Qiong Wu, Kevin Y Yip, 2020, Briefings Bioinform..

Supervised enhancer prediction with epigenetic pattern recognition and targeted validation

Mark Gerstein, Chengfei Yan, Axel Visel, 2018, Nature Methods.

Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation

Kevin Y. Yip, Jun Wang, S. Lok, 2014, Genome Biology.

Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data.

Raymond K. Auerbach, Kevin Y Yip, Zhi John Lu, 2011, Genome research.

Genome maps across 26 human populations reveal population-specific patterns of structural variation

Kevin Y. Yip, E. Y. Chow, P. Kwok, 2019, Nature Communications.

A proof-of-concept study for the pathogenetic role of enhancer hypomethylation of MYBPHL in multiple myeloma

Kevin Y. Yip, A. Cheng, G. Morgan, 2021, Scientific Reports.

Horseshoe crab genomes reveal the evolution of genes and microRNAs after three rounds of whole genome duplication

Kevin Y. Yip, P. Qian, J. Qiu, 2021, Communications biology.

Horseshoe crab genomes reveal the evolutionary fates of genes and microRNAs after three rounds (3R) of whole genome duplication

Kevin Y. Yip, P. Qian, J. Qiu, 2020, bioRxiv.

A semantic web approach to integrating heterogeneous yeast genome data

Kevin Y. Yip, Shawn M. Douglas, Michael R. Seringhaus, 2004 .

Machine learning and genome annotation: a match meant to be?

Kevin Y. Yip, M. Gerstein, Chao Cheng, 2013, Genome Biology.

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

Kevin Y Yip, Kevin Y. Yip, Chong Shou, 2011, Genome Biology.

FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer

Kevin Y. Yip, M. Gerstein, X. Mu, 2014, Genome Biology.

Comparing classical pathways and modern networks: towards the development of an edge ontology.

Kevin Y Yip, Yuanpeng J Huang, Gaetano T Montelione, 2007, Trends in biochemical sciences.

An integrative ENCODE resource for cancer genomics

Jie Xu, Lucas Lochovsky, Donghoon Lee, 2019, Nature Communications.

modENCODE Project Genome by the Caenorhabditis elegans Integrative Analysis of the

Raymond K. Auerbach, Kevin Y. Yip, Stefan R. Henz, 2011 .

Sustained Antidiabetic Effects of a Berberine-Containing Chinese Herbal Medicine Through Regulation of Hepatic Gene Expression

Kevin Y. Yip, Jennifer J. Siu, S. Tsui, 2012, Diabetes.

G9a Plays Distinct Roles in Maintaining DNA Methylation, Retrotransposon Silencing, and Chromatin Looping.

Kevin Y. Yip, D. Leung, Qin Cao, 2020, Cell reports.

Quantifying full-length circular RNAs in cancer

Kevin Y. Yip, Christina Huan Shi, Yat-Yuen Lim, 2021, bioRxiv.

OMSV enables accurate and comprehensive identification of large structural variations from nanochannel-based single-molecule optical maps

Kevin Y. Yip, Iris K. Pang, P. Kwok, 2017, bioRxiv.

Reply to ‘Inflated performance measures in enhancer–promoter interaction-prediction methods’

Kevin Y Yip, Kevin Y. Yip, Qin Cao, 2019, Nature Genetics.

OMMA enables population-scale analysis of complex genomic features and phylogenomic relationships from nanochannel-based optical maps

Catherine Chu, Alden King-Yung Leung, Melissa Chun-Jiao Liu, 2019, GigaScience.

A selective HDAC8 inhibitor potentiates antitumor immunity and efficacy of immune checkpoint blockade in hepatocellular carcinoma

Kevin Y. Yip, A. Cheng, J. Sung, 2021, Science Translational Medicine.

Reusability report: Capturing properties of biological objects and their relationships using graph neural networks

Kevin Y. Yip, S. Tsui, Qin Cao, 2022, Nature Machine Intelligence.

Jellyfish genomes reveal distinct homeobox gene clusters and conservation of small RNA processing

Kevin Y. Yip, P. Holland, Jin Sun, 2020, Nature Communications.

Systematic exploration of autonomous modules in noisy microRNA-target networks for testing the generality of the ceRNA hypothesis

Kevin Y Yip, Kevin Y. Yip, Danny Kit-Sang Yip, 2014, BMC Genomics.

Targeting PPAR-gamma counteracts tumour adaptation to immune-checkpoint blockade in hepatocellular carcinoma

Kevin Y. Yip, Wenshu Tang, K. To, 2023, Gut.

Abstract 4854: A computational framework for prioritizing noncoding regulatory variants in cancer

Kevin Y. Yip, H. Kang, M. Gerstein, 2015 .

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

Kevin Y. Yip, James B. Brown, E. Birney, 2012, Genome Biology.

Biosphere: the interoperation of web services in microarray cluster analysis.

Kei-Hoi Cheung, Kevin Y Yip, Kevin Y. Yip, 2004, Applied bioinformatics.

Genome maps across 26 human populations reveal population-specific patterns of structural variation

Pui-Yan Kwok, Catherine Chu, Kevin Y Yip, 2019, Nature Communications.

Supplementary information

Kevin Y. Yip, Lauren A. Cowley, Zhi John Lu, 2008 .

Decision Trees for Uncertain Data

Kevin Y. Yip, B. Kao, Wai-Shing Ho, 2009, IEEE International Conference on Data Engineering.

Genome-wide analysis of chromatin features identifies histone modification sensitive and insensitive yeast transcription factors

Kevin Y. Yip, M. Gerstein, C. Shou, 2011, Genome Biology.

A statistical framework for modeling gene expression using chromatin features and application to modENCODE datasets

Kevin Y. Yip, M. Gerstein, J. Rozowsky, 2011, Genome Biology.