Analytic approaches to twin data using structural equation models. - F. V. Rijsdijk; Pak Chung Sham (Briefings Bioinform., 2002)

GENECOUNTING: haplotype analysis with missing genotypes. - Jing Hua Zhao; Sebastien Lissarrague; Laurent Essioux; Pak Chung Sham (Bioinform., 2002)

Genetic Power Calculator: design of linkage and association genetic mapping studies of complex traits. - Shaun Purcell; Stacey S. Cherny; Pak Chung Sham (Bioinform., 2003)

Generic number systems and haplotype analysis. - Jing Hua Zhao; Pak Chung Sham (Comput. Methods Programs Biomed., 2003)

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)

Clustering of SNP Data with Application to Genomics. - Michael K. Ng 001; Mark Junjie Li; Sio Iong Ao; Pak Chung Sham; Yiu-ming Cheung; Joshua Zhexue Huang (ICDM Workshops, 2006)

IGG: A tool to integrate GeneChips for genetic studies. - Miao-Xin Li; Lin Jiang; S.-L. Ho; You-Qiang Song; Pak Chung Sham (Bioinform., 2007)

WHAP: haplotype-based association analysis. - Shaun Purcell; Mark J. Daly; Pak Chung Sham (Bioinform., 2007)

Combining functional and linkage disequilibrium information in the selection of tag SNPs. - Pak Chung Sham; Sio Iong Ao; Johnny S. H. Kwan; P. Kao; F. Cheung; Pui-Yee Fong; Michael K. Ng 001 (Bioinform., 2007)

Constrained unidimensional scaling with application to genomics. - Sio Iong Ao; Michael K. Ng 001; Pak Chung Sham (Comput. Stat. Data Anal., 2007)

Unidimensional nonnegative scaling for genome-wide Linkage Disequilibrium maps. - Haiyong Liao; Michael K. Ng 001; Eric S. Fung; Pak Chung Sham (Int. J. Bioinform. Res. Appl., 2008)

IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. - Miao-Xin Li; Lin Jiang; Patrick Yu-Ping Kao; Pak Chung Sham; You-Qiang Song (Bioinform., 2009)

FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. - Mulin Jun Li; Pak Chung Sham; Junwen Wang (Bioinform., 2010)

SKM-SNP: SNP markers detection method. - Yang Liu 100; Mark Junjie Li; Yiu-ming Cheung; Pak Chung Sham; Michael K. Ng 001 (J. Biomed. Informatics, 2010)

Correlated evolution of transcription factors and their binding sites. - Shu Yang 009; Hari Krishna Yalamanchili; Xinran Li; Kwok-Ming Yao; Pak Chung Sham; Michael Q. Zhang; Junwen Wang (Bioinform., 2011)

GWASdb: a database for human genetic variants identified by genome-wide association studies. - Mulin Jun Li; Panwen Wang; Xiaorong Liu; Ee Lyn Lim; Zhangyong Wang; Meredith Yeager; Maria P. Wong; Pak Chung Sham; Stephen J. Chanock; Junwen Wang (Nucleic Acids Res., 2012)

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. - Mulin Jun Li; Lily Yan Wang; Zhengyuan Xia; Pak Chung Sham; Junwen Wang (Nucleic Acids Res., 2013)

dbPSHP: a database of recent positive selection across human populations. - Mulin Jun Li; Lily Yan Wang; Zhengyuan Xia; Maria P. Wong; Pak Chung Sham; Junwen Wang (Nucleic Acids Res., 2014)

Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. - Mulin Jun Li; Bin Yan; Pak Chung Sham; Junwen Wang (Briefings Bioinform., 2015)

MGAS: a powerful tool for multivariate gene-based genome-wide association analysis. - Sophie Van der Sluis; Conor V. Dolan; Jiang Li; You-Qiang Song; Pak Chung Sham; Danielle Posthuma; Miao-Xin Li (Bioinform., 2015)

Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes. - Jacob Shujui Hsu; Johnny S. H. Kwan; Zhicheng Pan; Maria-Mercè Garcia-Barcelo; Pak Chung Sham; Miao-Xin Li (Bioinform., 2016)

Predicting regulatory variants with composite statistic. - Mulin Jun Li; Zhicheng Pan; Zipeng Liu; Jiexing Wu; Panwen Wang; Yun Zhu; Feng Xu; Zhengyuan Xia; Pak Chung Sham; Jean-Pierre A. Kocher; Miao-Xin Li; Jun S. Liu; et al. (Bioinform., 2016)

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. - Mulin Jun Li; Zipeng Liu; Panwen Wang; Maria P. Wong; Matthew R. Nelson; Jean-Pierre A. Kocher; Meredith Yeager; Pak Chung Sham; Stephen J. Chanock; Zhengyuan Xia; Junwen Wang (Nucleic Acids Res., 2016)

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. - Mulin Jun Li; Hongcheng Yao; Dandan Huang; Huanhuan Liu; Zipeng Liu; Hang Xu; Yiming Qin; Jeanette Prinz; Weiyi Xia; Panwen Wang; Bin Yan; Nhan L. Tran; et al. (Nucleic Acids Res., 2017)

A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues. - Dingge Ying; Mulin Jun Li; Pak Chung Sham; Miao-Xin Li (Bioinform., 2018)

GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits. - Dandan Huang; Xianfu Yi; Shijie Zhang; Zhanye Zheng; Panwen Wang; Chenghao Xuan; Pak Chung Sham; Junwen Wang; Mulin Jun Li (Nucleic Acids Res., 2018)

Evaluation of tools for highly variable gene discovery from single-cell RNA-seq data. - Shun H. Yip; Pak Chung Sham; Junwen Wang (Briefings Bioinform., 2019)

A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia. - Miao-Xin Li; Lin Jiang; Timothy Shin Heng Mak; Johnny S. H. Kwan; Chao Xue; Peikai Chen; Henry Chi-Ming Leung; Liqian Cui; Tao Li 034; Pak Chung Sham (Bioinform., 2019)

Methods and resources to access mutation-dependent effects on cancer drug treatment. - Hongcheng Yao; Qian Liang; Xinyi Qian; Junwen Wang; Pak Chung Sham; Mulin Jun Li (Briefings Bioinform., 2020)

CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies. - Jianhua Wang; Dandan Huang; Yao Zhou; Hongcheng Yao; Huanhuan Liu; Sinan Zhai; Chengwei Wu; Zhanye Zheng; Ke Zhao; Zhao Wang; Xianfu Yi; Shijie Zhang; et al. (Nucleic Acids Res., 2020)

QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes. - Zhanye Zheng; Dandan Huang; Jianhua Wang; Ke Zhao; Yao Zhou; Zhenyang Guo; Sinan Zhai; Hang Xu; Hui Cui; Hongcheng Yao; Zhao Wang; Xianfu Yi; et al. (Nucleic Acids Res., 2020)

vSampler: fast and annotation-based matched variant sampling tool. - Dandan Huang; Zhao Wang; Yao Zhou; Qian Liang; Pak Chung Sham; Hongcheng Yao; Mulin Jun Li (Bioinform., 2021)

A framework to decipher the genetic architecture of combinations of complex diseases: applications in cardiovascular medicine. - Liangying Yin; Carlos Kwan-Long Chau; Yu-Ping Lin; Shitao Rao; Yong Xiang; Pak Chung Sham; Hon-Cheong So (Bioinform., 2021)

VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. - Dandan Huang; Yao Zhou; Xianfu Yi; Xutong Fan; Jianhua Wang; Hongcheng Yao; Pak Chung Sham; Jihui Hao; Kexin Chen; Mulin Jun Li (Nucleic Acids Res., 2022)

Inferring CTCF-binding patterns and anchored loops across human tissues and cell types. - Hang Xu; Xianfu Yi; Xutong Fan; Chengyue Wu; Wei Wang; Xinlei Chu; Shijie Zhang; Xiaobao Dong; Zhao Wang; Jianhua Wang; Yao Zhou; Ke Zhao; et al. (Patterns, 2023)

Estimation of causal effects of genes on complex traits using a Bayesian-network-based framework applied to GWAS data. - Liangying Yin; Yaning Feng; Yujia Shi; Alexandria Lau; Jinghong Qiu; Pak Chung Sham; Hon-Cheong So (Nat. Mac. Intell., 2024)