Publication - Precision Medicine Genomics Lab

Selected Publications

Recent Publications

2023

Dissecting the high-resolution genetic architecture of complex phenotypes by accurately estimating gene-based conditional heritability

Lin Miao, Lin Jiang, Bin Tang, Pak Chung Sham, Miaoxin Li†
The American Journal of Human Genetics. 2023

Reciprocal causation mixture model for robust Mendelian randomization analysis using genome-scale summary data

Zipeng Liu, Yiming Qin, Tian Wu, Justin D. Tubbs, Larry Baum, Timothy Shin Heng Mak, Miaoxin Li†, Yan Dora Zhang†, Pak Chung Sham†.
Nature Communications. 2023

GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species

Liubin Zhang, Yangyang Yuan, Wenjie Peng, Bin Tang, Mulin Jun Li, Hongsheng Gui, Qiang Wang, Miaoxin Li†
Genome Biology. 2023

2022

An accurate prediction model of digenic interaction for estimating pathogenic gene pairs of human diseases

Yangyang Yuan, Liubin Zhang, Qihan Long, Hui Jiang et al, Miaoxin Li†
Comput. Struct. Biotechnol. J. 2022

PCGA: a comprehensive web server for phenotype-cell-gene association analysis

Chao Xue, Lin Jiang, Miao Zhou, Qihan Long, Ying Chen, Xiangyi Li, Wenjie Peng, Qi Yang, Miaoxin Li†
Nucleic Acids Research. 2022

Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases

Lin Jiang, Hui Jiang, Sheng Dai, Ying Chen et al, Miaoxin Li†
Nucleic Acids Research. 2022

Powerful and robust inference of causal genes of complex phenotypes with dependent expression quantitative loci by a novel median-based Mendelian randomization

Lin Jiang, Lin Miao, Guorong Yi, et al, Miaoxin Li†
The American Journal of Human Genetics. 2022

RNA-SSNV: A reliable Somatic Single Nucleotide Variants identification framework for RNA-seq data

Qihan Long, Yangyang Yuan, Miaoxin Li†.
Front. Genet. 2022

Genome-Wide Association Study Identifies New Risk Loci for Progression of Schistosomiasis Among the Chinese Population

Miao Zhou, Chao Xue et al, Miaoxin Li†
Front. Cell. Infect. Microbiol. 2022

A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia

Xiangyi Li, Lin Jiang, Chao Xue et al, Miaoxin Li†
eLife. 2022

2020

Knowledge-based analyses reveal new candidate genes associated with risk of hepatitis B virus related hepatocellular carcinoma

Deke Jiang et al, Guangwen Cao†, Miaoxin Li†
BMC cancer. 2020

2019

DESE: estimating driver tissues by selective expression of genes associated with complex diseases or traits.

Jiang L*, Xue C*, Dai S, Chen SZ, Chen PK, Sham P, Wang H†, Li M†.
Genome Biology. 2019

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 Research. 2019

A powerful conditional gene-based association approach implicated functionally important genes for schizophrenia

Miaoxin Li, Lin Jiang, Timothy Shin Heng Mak, Johnny Sheung Him Kwan, Chao Xue, Peikai Chen, Henry Chi-Ming Leung, Liqian Cui, Tao Li, Pak Chung Sham†.
Bioinformatics. 2019

2018

De novo mutations as causes of schizophrenia

Zhenxing Yang, Longkun Li, Miaoxin Li†
Psychiatry research. 2018

A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues

Dingge Ying, Mulin Jun Li, Pak Chung Sham, Miaoxin Li†.
Bioinformatics. 2018

2017

cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes.

Mulin Jun Li*, Miaoxin Li*, et al.
Genome biology. 2017

Sharing of genes and pathways across complex phenotypes: a multilevel genome-wide analysis.

Hongsheng Gui, Johnny S Kwan, Pak C Sham, Stacey S Cherny, Miaoxin Li†
Genetics. 2017

Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework.

Miaoxin Li, Jiang Li, Mulin Jun Li, Zhicheng Pan, Jacob Shujui Hsu, Dajiang J Liu, Xiaowei Zhan, Junwen Wang, Youqiang Song, Pak Chung Sham†
Nucleic acids research. 2017

2016

Inheritance-mode specific pathogenicity prioritization (ISPP) for human protein coding genes.

Jacob Shujui Hsu, Johnny SH Kwan, Zhicheng Pan, Maria-Mercè Garcia-Barcelo, Pak Chung Sham, Miaoxin Li†
Bioinformatics. 2016

FAPI: Fast and accurate P-value Imputation for genome-wide association study.

Johnny SH Kwan, Miao-Xin Li†, Jia-En Deng, Pak C Sham†
European Journal of Human Genetics. 2016

SNPTracker: a swift tool for comprehensive tracking and unifying dbSNP rs IDs and genomic coordinates of massive sequence variants.

Jia-En Deng, Pak C Sham†, Miao-Xin Li†
G3: Genes, Genomes, Genetics. 2016

Other Publications

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. cepip: context-dependent epigenomic weighting for prioritization of regulatory variants and disease-associated genes. Genome Biol. 2017 Mar 16;18(1):52.
Van der Sluis S, Dolan CV, Li J, Song Y, Sham P, Posthuma D, Li MX†. MGAS: a powerful tool for multivariate gene-based genome-wide association analysis. Bioinformatics. Bioinformatics. 2015 Apr 1;31(7):1007-15
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†.Predicting regulatory variants with composite statistic.Bioinformatics. 2016 Sep 15;32(18):2729-36.
Li MJ, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J†, Li MX†. wKGGSeq: A comprehensive strategy-based and disease-targeted online framework to facilitate exome sequencing studies of inherited disorders. Hum Mutat. 2015 Feb 10. doi: 10.1002/humu.2276
Gui H, Kwan JS, Sham PC, Cherny SS†,Li M†. Sharing of Genes and Pathways Across Complex Phenotypes: A Multilevel Genome-Wide Analysis.Genetics. 2017 May 11. pii: genetics.116.198150
Li J,Sham PC,Song Y†, Li MX†. SPS: a simulation tool for calculating power of set-based genetic association tests. Genet Epidemiol. 2015 Jul;39(5):395-7
Wang Q*, Cheng W*, Li M*, Ren H, Hu X, Deng W, Ma X, Zhao L, Wang Y, Xiang B, Wu HM, Sham PC, Feng J, Li T. The CHRM3 gene is implicated in abnormal thalamo-orbital frontal cortex functional connectivity in first-episode treatment-naive patients with schizophrenia. Psychol Med. 2016 May;46(7):1523-34
Wang Q*, Li MX*, Yang Z, Hu X, Wu HM, Ni P, Ren H, Deng W, Li M, Ma X, Guo W, Zhao L, Wang Y, Xiang B, Lei W, Sham PC, Li T. Increased co-expression of genes harboring the damaging de novo mutations in Chinese schizophrenic patients during prenatal development. Sci Rep. 2015 Dec 15;5:18209.
Deng JE, Sham PC,Li MX†. SNPTracker: A Swift Tool for Comprehensive Tracking and Unifying dbSNP rs IDs and Genomic Coordinates of Massive Sequence Variants. G3 (Bethesda). 2015 Nov 19;6(1):205-7.
Kwan JS, Li M*†, Deng JE, Sham PC. FAPI: Fast and accurate P-value Imputation for genome-wide association study. Eur J Hum Genet. 2016 May;24(5):761-6
Schizophrenia Working Group of the Psychiatric Genomics Consortium. Biological insights from 108 schizophrenia-associated genetic loci. Nature. 2014 Jul 24;511(7510):421-7.
Li MX, Ho PW, Pang SY, Tse ZH, Kung MH, Sham PC, Ho SL. PMCA4 (ATP2B4) Mutation in Familial Spastic Paraplegia. PLoS One. 2014 Aug 13;9(8):e104790.
Peng L, Zhao Q, Li Q, Li MX, Li C, Xu T, Jing X, Zhu X, Wang Y, Li F, Liu R, Zhong C, Pan Q, Zeng B, Liao Q, Hu B, Hu ZX, Huang YS, Sham P, Liu J, Xu S, Wang J, Gao ZL, Wang Y. The p.Ser267Phe variant in SLC10A1 is associated with resistance to chronic hepatitis B. Hepatology. 2014 Nov 21. doi: 10.1002/hep.27608.
Wong EH,So HC,Li MX, et al. Common Variants on Xq28 Conferring Risk of Schizophrenia in Han Chinese. Schizophrenia Bulletin 2013 Sep 16.
Li MX*, Kwan JS*, Bao SY, Yang W, Ho SL, Song YQ, Sham PC. Predicting Mendelian disease-causing non-synonymous single nucleotide variants in exome sequencing studies. PLoS Genet. 2013 Jan;9(1):e1003143
Li MX*, Kwan JS*, Sham PC. HYST: A hybrid set-based test for genome-wide association studies, with application to protein-protein interaction-based association analysis. Am J Hum Genet. 2012 Sep 7;91(3):478-88
Li MX, Gui HS, Kwan JS, Sham PC. GATES: a rapid and powerful gene-based association test using extended Simes procedure. Am J Hum Genet. 2011 Mar 11;88(3):283-93..
Li MX†, Gui HS, Kwan JS, Bao SY, Sham PC†. A comprehensive framework for prioritizing variants in exome sequencing studies of rare monogenic diseases. Nucleic Acids Res. 2012 Apr 1;40(7):e53. Epub 2012 Jan 12.
Li MX, Yeung MY, Cherny SS, Sham PC. Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets.Hum Genet. 2012 May;131(5):747-56. Epub 2011 Dec 6.
Li MX, Sham PC, Cherny SS, Song YQ. A knowledge-based weighting framework to boost the power of genome-wide association studies.PLoS One. 2010 Dec 31;5(12):e14480.
Li MX†, Jiang L, Kao PYP, Sham PC, Song YQ†. IGG3: A tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis. Bioinformatics. 2009 Jun 1;25(11):1449-50.
Li MX, Jiang L, Song YQ, Sham PC. Power of transmission/disequilibrium tests in admixed populations. Genet Epidemiol. 2008 Jul;32(5):434-44.
Li MX, Jiang L, Ho SL, Song YQ, Sham PC. IGG: A tool to integrate GeneChips for genetic studies. Bioinformatics. 2007 Nov 15;23(22):3105-7.
Zhao LJ*, Li MX*, Guo YF, Xu FH, Li JL, Deng HW. SNPP: automating large-scale SNP genotype data management. Bioinformatics. 2005 Jan 15;21(2):266-8.
Li MX*, Cheng TS*, Ho PWL, Chan KH, Mak W, Cheung RTF, Ramsden DB, Sham PC, Song YQ, Ho SL. (2008) -459C>T point mutation in 5′ non-coding region of human Connexin-32 gene is linked to X-linked Charcot-Marie-Tooth neuropathy. J Peripher Nerv Syst. 2009 Mar;14(1):14-21.
Li MX*, Pang SY, Song YQ, Kung HW, Ho SL, Sham. Whole exome sequencing identifies a novel mutation in the transglutaminase 6 gene for spinocerebellar ataxia in a Chinese family. (In press)
Li MX, PY Liu, YM Li, YJ Qin, YZ L, HW Deng. A major gene model of adult height is suggested in Chinese. J Hum Genet. 2004; 49(3): 148-53.
Li JL, Li MX, Guo YF, Deng HY, Deng HW. JADE: a distributed Java application for deleterious genomic mutation (DGM) estimation. Bioinformatics. 2006 Aug 1;22(15):1926-7.
So HC, Li MX, Sham PC Uncovering the total heritability explained by all true susceptibility variants in a genome-wide association study. Genet Epidemiol. 2011 Sep;35(6):447-56.
Gui H, Li M, Sham PC, Cherny SS. Comparisons of seven algorithms for pathway analysis using the WTCCC Crohn’s Disease dataset.BMC Res Notes. 2011 Oct 7;4:386.
Deng HW, Li YM, Li MX, Liu PY. Robust Indices of Hardy-Weinberg Disequilibrium for QTL Fine Mapping. Hum Hered. 2003; 56(4): 160-5.
Li JL, Li MX, Deng HY, Duffy PE, Deng HW. PhD: a web database application for phenotype data management. Bioinformatics. 2005 Aug 15;21(16):3443-4.
He QY, Cao J, Liu XH, Li MX, Liu YS, Xie JY, Liang SP. DEPD: a novel database for differentially expressed proteins. Bioinformatics. 2005 Sep 15;21(18):3694-6.
Jiang DK, Shen H, Li MX, Jiang C, Yang N, Zhu J, Wu Y, Qin YJ, Zhou Q, Deng HW. No major effect of the insulin-like growth factor I gene on bone mineral density in premenopausal Chinese women. Bone. 2005 Apr;36(4):694-9.
Liu PY, Li YM, Li MX, Malkin I, Qin YJ, Chen XD, Liu YJ, Deng HW. Lack of evidence for a major gene in the Mendelian transmission of BMI in Chinese. Obes Res. 2004 Dec;12 (12):1967-73.
Yang YJ, Liu YZ, Li MX, Lei SF, Chen XD, Sun X, Deng HW. Linkage exclusion analysis of two important chromosomal regions for height. Biochem Biophys Res Commun. 2005 Oct 7;335(4):1287-92.
Guo JJ, Liu YJ, Li MX, Yang YJ, Recker RR, Deng HW. Linkage exclusion analysis of two candidate regions on chromosomes 7 and 11: leptin and UCP2/UCP3 are not QTLs for obesity in US Caucasians. Biochem Biophys Res Commun. 2005 Jul 1;332(2):602-8.
Deng FY, Liu MY, Li MX, Lei SF, Qin YJ, Zhou Q, Liu YJ, Deng HW. Tests of linkage and association of the COL1A2 gene with bone phenotypes’ variation in Chinese nuclear families. Bone. 2003 Oct; 33(4): 614-619.
Deng FY, Lei SF, Li MX, Jiang C, Dvornyk V, Deng HW. Genetic determination and correlation of body mass index and bone mineral density at the spine and hip in Chinese Han ethnicity. Osteoporos Int. 2006 Jan;17(1):119-24.
Zhou XG, Liu YZ, Li MX, Jian WX, Lei SF, Qin YJ, Zhou Q, Deng HW. Parathyroid hormone gene with bone phenotypes in Chinese. Biochem Biophys Res Commun. 2003 Aug 1; 307(3): 666-71.
Jian WX, Long JR, Li MX, Liu XH, Deng HW. Genetic determination of variation and covariation of bone mineral density at the hip and spine in a Chinese population. J Bone Miner Metab. 2005;23(2):181-5.
Lei SF, Deng FY, Li MX, Dvornyk V, Deng HW. Bone mineral density in elderly Chinese: effects of age, sex, weight, height, and body mass index. J Bone Miner Metab. 2004; 22(1): 71-8.
Xu H, Long JR, Li MX, Deng HW. Interaction effects between estrogen receptor alpha and vitamin D receptor genes on age at menarche in Chinese women. Acta Pharmacol Sin. 2005 Jul;26(7):860-4.
Chen XD, Shen H, Lei SF, Li MX, Yang YJ, Deng HW. Exclusion mapping of chromosomes 1, 4, 6 and 14 with bone mineral density in 79 Caucasian pedigrees. Bone. 2006 Mar;38(3):450-5.
Lei SF, Liu YZ, Deng FY, Li YM, Li MX, Deng HW. Association and linkage analyses of interleukin-6 gene 634C/G polymorphism and bone phenotypes in Chinese. J Bone Miner Metab. 2005;23(4):323-8.
Xu H, Zhao LJ, Lei SF, Li MX, Sun X, Deng FY, Jiang DK, Deng HW. The (CA)n polymorphism of the TNFR2 gene is associated with peak bone density in Chinese nuclear families. J Hum Genet. 2005;50(6):301-4.
Deng FY, Long JR, Lei SF, Li MX, Deng HW.Potential effect of inter-genic action on peak bone mass (PBM) in Chinese females. Yi Chuan Xue Bao. 2005 Oct;32(10):1003-10.
Jiang DK, Xu FH, Liu MY, Chen XD, Li MX, Liu YJ, Shen H, Deng HW. No evidence of association of the osteocalcin gene HindIII polymorphism with bone mineral density in Chinese women. J Musculoskelet Neuronal Interact. 2007 Apr-Jun;7(2):149-54.
Liu XH, Liu YJ, Jiang DK, Li YM,Li MX, Qin YJ, Jian WX, Zhou Q, Deng HW. No evidence for linkage and/or association of human alpha2-HS glycoprotein gene with bone mineral density variation in Chinese nuclear families. Calcif Tissue Int. 2003 Sep; 73(3): 244-50.
Liu YJ, Liu XH, Lei SF, Li MX, Deng HW. Alpha2-HS glycoprotein gene is associated with bone size at the hip in Chinese. Yi Chuan Xue Bao. 2005 Nov;32(11):1128-35.
Mo XY, Cao CK , Xu FH , Liu MY, Li MX, Qin YJ , Zhou Q, Zhang YY, Deng HW. Lack of association between the HindIII RFLP of the osteocalcin (BGP) gene and bone mineral density (BMD) in healthy pre- and post-menopausal Chinese women. J Bone Miner Metab. 2004;22(3):264-9.
Huang QY, Xu FH, Shen H, Deng HY, Conway T, Liu YJ, Liu YZ, Li JL, Li MX, Davies KM, Recker RR, Deng HW. Genome Scan for QTLs Underlying Bone Size Variation at Ten Refined Skeletal Sites:Genetic Heterogeneity and the Significance of Phenotype Refinement. Physiol Genomics. 2004 May 19;17(3):326-31
Zhang YY, Lei SF, Mo XY, Wang YB, Li MX, Deng HW. The -1997 G/T Polymorphism in the COLIA1 Upstream Regulatory Region is Associated with Hip Bone Mineral Density (BMD) in Chinese Nuclear Families. Calcif Tissue Int. 2005 Feb;76(2):107-12.
Wang YB, Lei SF, Dvornyk V, Sun X, Jiang DK, Li MX, Deng HW. The genetic, environmental and phenotypic correlations of bone phenotypes at the spine and hip in Chinese. Ann Hum Biol. 2006 Jul-Aug;33(4):500-9.
Qin YJ, Shen H, Huang QR, Zhao LJ, Zhou Q, Li MX, He JW, Mo XY, Lu JH, Recker RR, Deng HW. Estrogen receptor alpha gene polymorphisms and peak bone density in Chinese nuclear families. J Bone Miner Res. 2003 Jun; 18(6): 1028-35.
Li Y, Fu L, Wong AM, Fan YH, Li MX, Bei JX, Jia WH, Zeng YX, Chan D, Cheung KM, Sham P, Chua D, Guan XY, Song YQ. Identification of genes with allelic imbalance on 6p associated with nasopharyngeal carcinoma in southern Chinese. PLoS One. 2011 Jan 20;6(1):e14562.
Xia LQ, Li MX, Qiu W, Zou XQ, Mo XT, Chen Y. Studies on the Fermentation Monitoring of Bacillus Thuringiensis. Jour Nat Scie Hunan Norm Uni?2002 Jun?25 (2).
Liu C, Saffen D, Schulze TG, Burmeister M, Sham PC, Yao YG, Kuo PH, Chen C, An Y, Dai J, Yue W, Li MX, Xue H, Su B, Chen L, Shi Y, Qiao M, Liu T, Xia K, Chan RC. Psychiatric genetics in China: achievements and challenges.Mol Psychiatry. 2016 Jan;21(1):4-9.
Zhao Q*, Peng L*, Huang W*. Li Q*, …, Li MX et al. Rare inborn errors associated with chronic hepatitis B virus infection. Hepatology. 2012;56(5):1661-70.

*: Joint First Author ; †: Corresponding Author