Recent Publications

2024

• Comprehensive and deep evaluation of structural variation detection pipelines with third-generation sequencing data
  Liu Z, Xie Z, Li M^†
  Genome Biol
• Application of GWAS summary data and drug-induced gene expression profiles of neural progenitor cells in psychiatric drug prioritization analysis
  Li X, Xue C, Zhu Z, Yu X, Yang Q, Cui L^†, Li M^†
  Mol Psychiatry

2023

• Reciprocal causation mixture model for robust Mendelian randomization analysis using genome-scale summary data
  Liu Z^*, Qin Y^*, Wu T, Tubbs JD, Baum L, Mak TSH, Li M^†, Zhang YD^†, Sham PC^†
  Nat Commun
• GBC: A parallel toolkit based on fast-accessible byte blocks for extremely large-scale genotypes of species
  Zhang L, Yuan Y, Peng W, Tang B, Li MJ, Gui H, Wang Q, Li M^†
  Genome Biol
• Dissecting the high-resolution genetic architecture of complex phenotypes by accurately estimating gene-based conditional heritability
  Miao L^*, Jiang L^*, Tang B, Sham PC, Li M^†
  Am J Hum Genet

2022

• Genome-Wide Association Study Identifies New Risk Loci for Progression of Schistosomiasis Among the Chinese Population
  Miao Zhou^*, Chao Xue^*, Xiaoying Wu, Zhongdao Wu^†, Miaoxin Li^†
  Front Cell Infect Microbiol.
• Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases
  Jiang L^*, Jiang H^*, Dai S, Chen Y, Song Y, Tang CS, Pang SY, Ho SL, Wang B, Garcia-Barcelo MM, Tam PK, Cherny SS, Li MJ, Sham PC^†, Li M^†
  Nucleic Acids Res
• A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia
  Li X^*, Jiang L^*, Xue C, Li MJ, Li M^†
  Elife
• PCGA: a comprehensive web server for phenotype-cell-gene association analysis
  Xue C^*, Jiang L^*, Zhou M, Long Q, Chen Y, Li X, Peng W, Yang Q, Li M^†
  Nucleic Acids Res
• Powerful and robust inference of complex phenotypes' causal genes with dependent expression quantitative loci by a median-based Mendelian randomization
  Jiang L, Miao L, Yi G, Li X, Xue C, Li MJ, Huang H, Li M^†
  Am J Hum Genet
• An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases
  Yuan Y, Zhang L, Long Q, Jiang H, Li M^†
  Comput Struct Biotechnol J
• RNA-SSNV: A Reliable Somatic Single Nucleotide Variant Identification Framework for Bulk RNA-Seq Data
  Long Q, Yuan Y, Li M^†
  Front Genet

2021

• Case report: exome sequencing achieved a definite diagnosis in a Chinese family with muscle atrophy
  Hui Jiang, Chunmiao Guo, Jie Xie, Jingxin Pan, Ying Huang, Miaoxin Li^†, Yibin Guo^†
  BMC Neurology

2020

• Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma
  Deke Jiang, Jiaen Deng, Changzheng Dong, Xiaopin Ma, Qianyi Xiao, Bin Zhou, Chou Yang, Lin Wei, Carly Conran, S. Lilly Zheng, Irene Oi-lin Ng, Long Yu, Jianfeng Xu, Pak C. Sham, Xiaolong Qi, Jinlin Hou, Yuan Ji, Guangwen Cao^†, Miaoxin Li^†
  BMC Cancer

2019

• A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia
  Li M, Jiang L, Mak TSH, Kwan JSH, Xue C, Chen P, Leung HC, Cui L, Li T, Li M^†, Sham PC^†
  Bioinformatics
• WITER: a powerful method for estimation of cancer-driver genes using a weighted iterative regression modelling background mutation counts
  Jiang L^*, Zheng J^*, Kwan JSH, Dai S, Li C, Li MJ, Yu B, To KF, Sham PC^†, Zhu Y^†, Li M^†
  Nucleic Acids Res
• DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits
  Jiang L^*, Xue C^*, Dai S, Chen S, Chen P, Sham PC, Wang H^†, Li M^†
  Genome Biol

2018

• A rare variant in MLKL confers susceptibility to ApoE ɛ4-negative Alzheimer's disease in Hong Kong Chinese population
  Binbin Wang^*, Suying Bao^*, Zhigang Zhang^*, Xueya Zhou, Jing Wang, Yanhui Fan, Yan Zhang, Yan Li, Luhua Chen, Yizhen Jia, Jiang Li, Miaoxin Li, et al, Xu Ma^†, Leung Wing Chu^†, You-Qiang Song^†
  Neurobiol Aging.
• A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues
  Ying D, Li MJ, Sham PC, Li M^†
  Bioinformatics

2017

• Dysfunction of Myosin Light-Chain 4 (MYL4) Leads to Heritable Atrial Cardiomyopathy With Electrical, Contractile, and Structural Components: Evidence From Genetically-Engineered Rats
  Wenhui Peng, Miaoxin Li, Hailing Li, Kai Tang, Jianhui Zhuang, Jianguo Zhang, Jingjing Xiao, Hui Jiang, Dali Li, Yongchun Yu, Pak C. Sham, Stanley Nattel, Yawei Xu^†
  J Am Heart Assoc
• Sharing of Genes and Pathways Across Complex Phenotypes: A Multilevel Genome-Wide Analysis
  Gui H, Kwan JS, Sham PC, Cherny SS^†, Li M^†
  Genetics
• cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes
  Li MJ^*, Li M^*, Liu Z^*, Yan B, Pan Z, Huang D, Liang Q, Ying D, Xu F, Yao H, Wang P, Kocher JA, Xia Z, Sham PC, Liu JS, Wang J, Li MJ^†, Li M^†
  Genome Biol
• Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework
  Li M^*, Li J^*, Li MJ, Pan Z, Hsu JS, Liu DJ, Zhan X, Wang J, Song Y, Li M^†, Sham PC^†
  Nucleic Acids Res

2016

• FAPI: Fast and Accurate P-value Imputation for genome-wide association study
  Kwan SH^*, Li M^*, Deng JE, Li M^†, Sham PC^†
  European Journal of Human Genetics
• Predicting regulatory variants with composite statistic
  Li MJ, Pan Z, Liu Z, Wu J, Wang P, Zhu Y, Xu F, Xia Z, Sham PC, Kocher JP, Li M^†, Liu JS^†, Wang J^†
  Bioinformatics
• Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes
  Hsu JS, Kwan JS, Pan Z, Garcia-Barcelo MM, Sham PC, Li M^†
  Bioinformatics

2015

• wKGGSeq: A comprehensive strategy-based and disease-targeted online framework to facilitate exome sequencing studies of inherited disorders
  Li MJ, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J^†, Li MX^†
  Hum Mutat
• SPS: a simulation tool for calculating power of set-based genetic association tests
  Li J, Song Y, Sham PC, Wang J, Li MX^†
  Genet Epidemiol
• SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rsIDs and Genomic Coordinates of Massive Sequence Variants
  Deng JE, Sham PC, Li MX^†
  G3 (Bethesda)
• MGAS: a powerful tool for multivariate gene-based genome-wide association analysis
  Van der Sluis S, Dolan CV, Li J, Song Y, Sham P, Posthuma D, Li M^†
  Bioinformatics

2013

• Predicting Mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies
  Li MX^*, Kwan JS^*, Bao SY, Yang W, Ho SL, Song YQ, Sham PC^†
  PLoS Genet

2012

• HYST: A hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis
  Li MX^*, Kwan JS^*, Li MX^†, Sham PC^†
  Am J Hum Genet
• A comprehensive framework for prioritizing variants in exome sequencing studies of rare monogenic diseases
  Li MX, Gui HS, Kwan JS, Bao SY, Li MX^†, Sham PC^†
  Nucleic Acids Res

2011

• GATES: a rapid and powerful gene-based association test using extended Simes procedure
  Li MX, Gui HS, Kwan JS, Sham PC, Li MX^†
  Am J Hum Genet