Publications

PubMed Publication List:https://pubmed.ncbi.nlm.nih.gov/?term=Mulin+Jun+Li&sort=date

Google Scholar:https://scholar.google.com/citations?user=_efhuZ4AAAAJ&hl=en

# Co-first authors; * Corresponding/Co-corresponding authors

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2024

• Fu J#, Zhang Q#, Wang J#, Wang M, Zhang B, Zhu W, Qiu S, Geng Z, Cui G, Yu Y, Liao W, Zhang H, Gao B, Xu X, Han T, Yao Z, Qin W, Liu F, Liang M, Wang S, Xu Q, Xu J, Zhang P, Li W, Shi D, Wang C, Lui S, Yan Z, Chen F, Zhang J, Li J, Shen W, Miao Y, Wang D, Xian J, Gao J, Zhang X, Xu K, Zuo X, Zhang L, Ye Z, Chen J*, Li MJ*, Yu C*. Trans-ancestral genome-wide association studies of brain imaging phenotypes. Nat Genet. 2024 in press

  Full Paper

• Zhou Z#, Du J#, Wang J#, Liu L, Gordon MG, Ye CJ, Powell JE, Li MJ*, Rao S*. SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. Database (Oxford). 2024 Mar 9;2024:baae010.

  Abstract Full Paper

• Critical Assessment of Genome Interpretation Consortium (including Li MJ). CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. Genome Biol. 2024 Feb 22;25(1):53.

  Abstract

• Huang X#, Huang J#, Li X, Fan J, Zhou D, Qu HQ, Glessner JT, Ji D, Jia Q, Ding Z, Wang N, Wei W, Lyu X, Li MJ, Liu Z, Liu W, Wei Y, Hakonarson H, Xia Q*, Li J*. Target genes regulated by CLEC16A intronic region associated with common variable immunodeficiency. J Allergy Clin Immunol. 2024 Jan 6:S0091-6749(24)00030-7.

  Abstract

2023

• Wang Z#, Luo M#, Liang Q#, Zhao K, Hu Y, Wang W, Feng X, Hu B, Teng J, You T, Li R, Bao Z, Pan W, Yang T, Zhang C, Li T, Dong X, Yi X, Liu B, Zhao L, Li M, Chen K, Song W*, Yang J*, Li MJ*. Landscape of enhancer disruption and functional screen in melanoma cells. Genome Biol. 2023 Oct 30;24(1):248

  Abstract Full Paper

• Chang Y#, Zhou Y#, Zhou J#, Li W, Cao J, Jing Y, Zhang S, Shen Y, Lin Q, Fan X, Yang H, Dong X, Zhang S, Yi X, Shuai L, Shi L, Liu Z, Yang J, Ma X, Hao J, Chen K, Li MJ*, Wang F*, Huang D*. Unraveling the causal genes and transcriptomic determinants of human telomere length. Nat Commun. 2023 Dec 21;14(1):8517.

  Abstract Full Paper

• Xu H#, Yi X#, Fan X#, Wu C, Wang W, Chu X, Zhang S, Dong X, Wang Z, Wang J ,Zhou Y, Zhao K, Yao H, Nan Z, Wang J, Chen Y, Plewczynski D, Sham PC, Chen K*, Huang D*, Li MJ*. Inferring CTCF binding patterns and anchored loops across human tissues and cell types. Patterns. 2023 Jul 12;4(8):100798.

  Abstract Full Paper

• Li R#, Huang D#, Zhao Y, Yuan Y, Sun X, Dai Z, Huo D, Liu X, Helin K, Li MJ*, Wu X*. PR-DUB safeguards Polycomb repression through H2AK119ub1 restriction. Cell Prolif. 2023 Mar 23:e13457.

  Abstract Full Paper

• Wang Z#,*, Liang Q#, Qian X#, Hu B#, Zheng Z, Wang J, Hu Y, Bao Z, Zhao K, Zhou Y, Feng X, Yi X, Li J, Shi J, Liu Z, Hao J, Chen K, Yu Y, Sham PC, Lu W, Wang X*, Song W*, Li MJ*. An autoimmune pleiotropic SNP modulates IRF5 alternative promoter usage through ZBTB3-mediated chromatin looping. Nat Commun. 2023 Mar 3;14(1):1208.

  Abstract Full Paper

• Qian Y#, Wang J#, Wang B, Wang W, Li P, Zhao Z, Jiang Y, Ren H, Huang D, Yang Y, Zhao Z, Zhang L, Shi J, Li MJ*, Lu W*. Systematic fine-mapping and functional studies of prostate cancer risk variants. iScience. 2023 Mar 26:S2589-0042(23)00574-6.

  Abstract Full Paper

• Yao X#, Yang H#, Han H, Kou X, Jiang Y, Luo M, Zhou Y, Wang J, Fan X, Wang X*, Li MJ*, Yan H*. Genome-wide analysis of genetic pleiotropy and causal genes across three age-related ocular disorders. Hum Genet. 2023 Mar 14;s00439-023-02542-4.

  Abstract Full Paper

• Meng X, Wang Q, Chen S, Zhang S, Yu J, Li H, Chen X, Wang Z, Yu W, Zheng Z, Zhou H, Luo J, Wang Z, Chen H, Wu N, Hu D, Chen S, Wei Y, Cui H, Song H, Chen H, Wang Y, Zhong J, Chen Z, Zhang H, Yang T, Li M, Liu Y, Dong X, Du M, Wang X, Yao X, Lin H*, Li MJ*, Yan H*. An interpretable model predicts visual outcomes of no light perception eyes after open globe injury. Br J Ophthalmol. 2023 Jan 3:bjo-2022-322753.

  Abstract Full Paper

• Huang D#, Feng X#, Yang H, Wang J, Zhang W, Fan X, Dong X, Chen K, Yu Y, Ma X*, Yi X*, Li MJ*. QTLbase2: an enhanced catalog of human quantitative trait loci on extensive molecular phenotypes. Nucleic Acids Res. 2023 Jan 6;51(D1):D1122-D1128.

  Abstract Full Paper Website

• Zhang L, Yuan Y, Peng W, Tang B, Li MJ, Gui H, Wang Q, Li M*. GBC: a parallel toolkit based on highly addressable byte-encoding blocks for extremely large-scale genotypes of species. Genome Biol. 2023 Apr 17;24(1):76.

  Abstract

• Liu N*, Zhang L*, Tian T, Cheng J, Zhang B, Qiu S, Geng Z, Cui G, Zhang Q, Liao W, Yu Y, Zhang H, Gao B, Xu X, Han T, Yao Z, Qin W, Liu F, Liang M, Xu Q, Fu J, Xu J, Zhu W, Zhang P, Li W, Shi D, Wang C, Lui S, Yan Z, Chen F, Li J, Zhang J, Wang D, Shen W, Miao Y, Xian J, Gao JH, Zhang X, Li MJ, Xu K, Zuo XN, Wang M, Ye Z*, Yu C*; CHIMGEN Consortium. Cross-ancestry genome-wide association meta- analyses of hippocampal and subfield volumes. Nat Genet. 2023 Jul;55(7):1126-1137.

  Abstract

• Lei X, Tian X, Wang H, Xu X, Li G, Liu W, Wang D, Xiao Z, Zhang M, Li MJ, Zhang Z, Ma Z*, Liu Z*. Noncoding SNP at rs1663689 represses ADGRG6 via interchromosomal interaction and reduces lung cancer progression. EMBO Rep. 2023 May 8:e56212.

  Abstract

• Xu H, Yi X, Cui Z, Li H, Zhu L, Zhang L, Chen J, Fan X, Zhou P, Li MJ, Yu Y, Liu Q, Huang D*, Yao Z*, Zhou J*. Maternal antibiotic exposure enhances ILC2 activation in neonates via downregulation of IFN1 signaling. Nat Commun. 2023 Dec 14;14(1):8332.

  Abstract

• Zhang B, Li Y, Zhang J, Wang Y, Liang C, Lu T, Zhang C, Liu L, Qin Y, He J, Zhao X, Yu J, Hao J, Yang J, Li MJ, Yao Z, Ma S*, Cheng H*, Cheng T*, Shi L*. ADAR1 links R-loop homeostasis to ATR activation in replication stress response. Nucleic Acids Res. 2023 Nov 27;51(21):11668-11687.

  Abstract

• Han L, Zhang C, Wang D, Zhang J, Tang Q, Li MJ, Sack MN, Wang L*, Zhu L*. Retrograde regulation of mitochondrial fission and epithelial to mesenchymal transition in hepatocellular carcinoma by GCN5L1. Oncogene. 2023 Mar;42(13):1024-1037.

  Abstract

• Yuan J#, Tong Y#, Liu X, Li MJ, Zhang Q*, Yang Y*. eaQTLdb: An atlas of enhancer activity quantitative trait loci across cancer types. Int J Cancer. 2023 Feb 25;ijc.34481.

  Abstract

• Liu W, Yu X, Yuan Y, Feng Y, Wu C, Huang C, Xie P, Li S, Li X, Wang Z, Qi L, Chen Y, Shi L, Li MJ, Huang Z, Tang B, Chang A, Hao J*. CD73, a Promising Therapeutic Target of Diclofenac, Promotes Metastasis of Pancreatic Cancer through a Nucleotidase Independent Mechanism. Adv Sci. 2023 Feb;10(6):e2206335.

  Abstract

2022

• Xu J#, Xia X#, Li Q#, Dou Y#, Suo X, Sun Z, Liu N, Han Y, Sun X, He Y, Qin W, Zhang S, Banaschewski T, Flor H, Grigis A, Gowland P, Heinz A, Brühl R, Martinot JL, Artiges E, Nees F, Paus T, Poustka L, Hohmann S, Walter H, Sham PC, Schumann G, Wu X*, Li MJ*, Yu C*; Alzheimer’s Disease Neuroimaging Initiative; IMAGEN Consortia. A causal association of ANKRD37 with human hippocampal volume. Mol Psychiatry. 2022 Nov;27(11):4432-4445.

  Abstract Full Paper

• Wang J#, Liu J#, Luo M, Cui H, Zhang W, Zhao K, Dai H, Song F, Chen K, Yu Y, Zhou D*, Li MJ*, Yang H*. Rational drug repositioning for coronavirus-associated diseases using directional mapping and side-effect inference. iScience. 2022 Nov 18;25(11):105348.

  Abstract Full Paper

• Yi X*, Luo M, Feng X, Zhou Y, Wang J, Li MJ*. 3DCoop: An approach for computational inference of cell-type-specific transcriptional regulators cooperation in 3D chromatin. STAR Protoc. 2022 May 11;3(2):101382.

  Abstract Full Paper Website

• Huang D#, Zhou Y#, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ*. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Res. 2022 Jan 7;50(D1):D1408-D1416..

  Abstract Full Paper Website

• Cao C#, Wang J#, Kwok D, Cui F, Zhang Z, Zhao D, Li MJ, Zou Q*. webTWAS: a resource for disease candidate susceptibility genes identified by transcriptome-wide association study. Nucleic Acids Res. 2022 Jan 7;50(D1):D1123-D1130.

  Abstract

• Li X, Jiang L, Xue C, Li MJ, Li M*. A conditional gene-based association framework integrating isoform-level eQTL data reveals new susceptibility genes for schizophrenia. Elife. 2022 Apr 12;11:e70779.

  Abstract

• 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*. Deviation from baseline mutation burden provides powerful and robust rare-variants association test for complex diseases. Nucleic Acids Res. 2022 Apr 8;50(6):e34.

  Abstract

• Jiang L, Miao L, Yi G, Li X, Xue C, Li MJ, Huang H, Li M*. Powerful and robust inference of complex phenotypes' causal genes with dependent expression quantitative loci by a median-based Mendelian randomization. Am J Hum Genet. 2022 May 5;109(5):838-856.

  Abstract

• Wang C, Zhou J, Wang L, Xing T, Dai H, Zhou Y, Qi L, Zhao Y, Huang C, Li D, Li H, Li MJ, Liu B, Zheng H, Chen K, Li L*. ABO blood groups and expression of blood group antigens of epithelial ovarian cancer in Chinese women. Cancer Med. 2022 Nov 22.

  Abstract

2021

• Dai H#, Chu X#, Liang Q#, Wang M#, Li L, Zhou Y, Zheng Z, Wang W, Wang Z, Li H, Wang J, Zheng H, Zhao Y, Liu L, Yao H, Luo M, Wang Q, Kang S, Li Y, Wang K, Song F, Zhang R, Wu X, Cheng X, Zhang W, Wei Q*, Li MJ*, Chen K*. Genome-wide association and functional interrogation identified a variant at 3p26.1 modulating ovarian cancer survival among Chinese women. Cell Discov. 2021 Dec 21;7(1):121.

  Abstract Full Paper

• Yi X, Zheng Z, Xu H, Zhou Y, Huang D, Wang J, Feng X, Zhao K, Fan X, Zhang S, Dong X, Wang Z, Shen Y, Cheng H, Shi L, Li MJ*. Interrogating cell type-specific cooperation of transcriptional regulators in 3D chromatin. iScience. 2021 Nov18;24(12):103468.

  Abstract Full Paper Code and Data

• Zhou Y, Qian X, Liu Z, Yang H, Liu T, Chen K, Wang Y, Sham PC, Yu Y, Li MJ*. Coagulation factors and the incidence of COVID-19 severity: Mendelian randomization analyses and supporting evidence. Signal Transduct Target Ther. 2021 Jun 7;6(1):222.

  Abstract Full Paper

• Liu N#, Xu J#, Liu H#, Zhang S, Li M, Zhou Y, Qin W, Li MJ*, Yu C*; Alzheimer’s disease Neuroimaging Initiative. Hippocampal transcriptome-wide association study and neurobiological pathway analysis for Alzheimer's disease. PLoS Genet. 2021 Feb 25;17(2):e1009363.

  Abstract Full Paper

• Huang D#, Wang Z#, Zhou Y#, Liang Q, Sham PC, Yao H*, Li MJ*. vSampler: fast and annotation-based matched variant sampling tool. Bioinformatics. 2021 Jul 27;37(13):1915-1917.

  Abstract Full Paper Website Code and Data

• Chen L*, Li MJ*. Deciphering Non-Coding Regulatory Variants: Computational and Functional Validation. Front Bioeng Biotechnol. 2021 Nov 3;9:769614. doi: 10.3389/fbioe.2021.769614.

  Abstract Full Paper

• Shen L, Hu P, Zhang Y, Ji Z, Shan X, Ni L, Ning N, Wang J, Tian H, Shui G, Yuan Y, Li G, Zheng H, Yang XP, Huang D, Feng X, Li MJ, Liu Z, Wang T*, Yu Q*. Serine metabolism antagonizes antiviral innate immunity by preventing ATP6V0d2-mediated YAP lysosomal degradation. Cell Metab. 2021 May 4;33(5):971-987.e6.

  Abstract

• Zheng Y, Dong H, Bai X, Cui H, Li MJ, Wu HY, Zhang K*. Effects of lysine 2-hydroxyisobutyrylation on bacterial FabI activity and resistance to triclosan. Biochimie. 2021 Mar;182:197-205.

  Abstract

• Dai Z, Li R, Hou Y, Li Q, Zhao K, Li T, Li MJ, Wu X*. Inducible CRISPRa screen identifies putative enhancers. J Genet Genomics. 2021 Oct 20;48(10):917-927.

  Abstract

• Xu J, Liu X, Li Q, Goldblatt R, Qin W, Liu F, Chu C, Luo Q, Ing A, Guo L, Liu N, Liu H, Huang C, Cheng J, Wang M, Geng Z, Zhu W, Zhang B, Liao W, Qiu S, Zhang H, Xu X, Yu Y, Gao B, Han T, Cui G, Chen F, Xian J, Li J, Zhang J, Zuo XN, Wang D, Shen W, Miao Y, Yuan F, Lui S, Zhang X, Xu K, Zhang L, Ye Z, Banaschewski T, Barker GJ, Bokde ALW, Flor H, Grigis A, Garavan H, Gowland P, Heinz A, Brühl R, Martinot JL, Artiges E, Nees F, Orfanos DP, Lemaitre H, Paus T, Poustka L, Robinson L, Hohmann S, Fröhner JH, Smolka MN, Walter H, Whelan R, Winterer J, Patrick K, Calhoun V, Li MJ, Liang M, Gong P, Barker ED, Clinton N, Marquand A, Yu L, Yu C*, Schumann G*; CHIMGEN; IMAGEN Consortia. Global urbanicity is associated with brain and behaviour in young people. Nat Hum Behav. 2021 Oct 28.

  Abstract

2020

• Huang D, Yi X, Zhou Y, Yao H, Xu H, Wang J, Zhang S, Nong W, Wang P, Shi L, Xuan C, Li M, Wang J, Li W, Kwan HS, Sham PC, Wang K, Li MJ*. Ultrafast and scalable variant annotation and prioritization with big functional genomics data. Genome Res. 2020 Dec;30(12):1789-1801.

  Abstract Full Paper Website Code and Data

• Cui H#, Zuo S#, Liu Z, Liu H, Wang J, You T, Zheng Z, Zhou Y, Qian X, Yao H, Xie L, Liu T, Sham PC, Yu Y*, Li MJ*. The support of genetic evidence for cardiovascular risk induced by antineoplastic drugs. Sci Adv. 2020 Oct 14;6(42):eabb8543.

  Abstract Full Paper Website

• Zhu X#, Lan B#, Yi X#, He C, Dang L, Zhou X, Lu Y, Sun Y, Liu Z, Bai X, Zhang K, Li B, Li MJ*, Chen Y*, Zhang L*. HRP2-DPF3a-BAF complex coordinates histone modification and chromatin remodeling to regulate myogenic gene transcription. Nucleic Acids Res. 2020 Jul 9;48(12):6563-6582.

  Abstract Full Paper

• Xu H, Zhang S, Yi X, Plewczynski D, Li MJ*. Exploring 3D chromatin contacts in gene regulation: The evolution of approaches for the identification of functional enhancer-promoter interaction. Comput Struct Biotechnol J. 2020 Feb 28;18:558-570.

  Abstract Full Paper

• Zhou Y, Sun Y, Huang D, Li MJ*. epiCOLOC: Integrating Large-Scale and Context-Dependent Epigenomics Features for Comprehensive Colocalization Analysis. Front Genet. 2020 Feb 12;11:53.

  Abstract Full Paper Website Code and Data

• Dong X*, Huang D, Yi X, Zhang S, Wang Z, Yan B, Sham PC, Chen K, Li MJ*. Diversity spectrum analysis identifies mutation-specific effects of cancer driver genes. Commun Biol. 2020 Jan 7;3(1):6.

  Abstract Full Paper Website

• Yao H#, Liang Q#, Qian X, Wang J, Sham PC, Li MJ*. Methods and resources to access mutation-dependent effects on cancer drug treatment. Brief Bioinform. 2020 Dec 1;21(6):1886-1903.

  Abstract Full Paper

• Wang J#, Huang D#, Zhou Y, Yao H, Liu H, Zhai S, Wu C, Zheng Z, Zhao K, Wang Z, Yi X, Zhang S, Liu X, Liu Z, Chen K, Yu Y, Sham PC, Li MJ*. CAUSALdb: a database for disease/trait causal variants identified using summary statistics of genome-wide association studies. Nucleic Acids Res. 2020 Jan 8;48(D1):D807-D816.

  Abstract Full Paper Website Code and Data

• Zheng Z#, Huang D#, Wang J, Zhao K, Zhou Y, Guo Z, Zhai S, Xu H, Cui H, Yao H, Wang Z, Yi X, Zhang S, Sham PC, Li MJ*. QTLbase: an integrative resource for quantitative trait loci across multiple human molecular phenotypes. Nucleic Acids Res. 2020 Jan 8;48(D1):D983-D991.

  Abstract Full Paper Website

• Xu Q, Guo L, Cheng J, Wang M, Geng Z, Zhu W, Zhang B, Liao W, Qiu S, Zhang H, Xu X, Yu Y, Gao B, Han T, Yao Z, Cui G, Liu F, Qin W, Zhang Q, Li MJ, Liang M, Chen F, Xian J, Li J, Zhang J, Zuo XN, Wang D, Shen W, Miao Y, Yuan F, Lui S, Zhang X, Xu K, Zhang LJ, Ye Z, Yu C*; CHIMGEN Consortium. CHIMGEN: a Chinese imaging genetics cohort to enhance cross-ethnic and cross-geographic brain research. Mol Psychiatry. 2020 Mar;25(3):517-529

  Abstract

2019

• Zhang S#, He Y#, Liu H, Zhai H, Huang D, Yi X, Dong X, Wang Z, Zhao K, Zhou Y, Wang J, Yao H, Xu H, Yang Z, Sham PC, Chen K, Li MJ*. regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants. Nucleic Acids Res. 2019 Dec 2;47(21):e134.

  Abstract Full Paper Code and Data

• Huo D, Chen H, Cheng Y, Song X, Zhang K, Li MJ, Xuan C*. JMJD6 modulates DNA damage response through downregulating H4K16ac independently of its enzymatic activity. Cell Death Differ. 2020 Mar;27(3):1052-1066.

  Abstract

• Jiang L, Zheng J, Kwan JSH, Dai S, Li C, Li MJ, Yu B, To KF, Sham PC, Zhu Y, Li M*. WITER: a powerful method for estimation of cancer-driver genes using a weighted iterative regression modelling background mutation counts. Nucleic Acids Res. 2019 Sep 19;47(16):e96.

  Abstract

• Sun Y#, Liu Z#, Cao X, Lu Y, Mi Z, He C, Liu J, Zheng Z, Li MJ, Li T, Xu D, Wu M, Cao Y, Li Y, Yang B, Mei C*, Zhang L*, Chen Y*. Activation of P-TEFb by cAMP-PKA signaling in autosomal dominant polycystic kidney disease. Sci Adv. 2019 Jun 5;5(6):eaaw3593.

  Abstract

• Cao X, Dang L, Zheng X, Lu Y, Lu Y, Ji R, Zhang T, Ruan X, Zhi J, Hou X, Yi X, Li MJ, Gu T, Gao M, Zhang L*, Chen Y*. Targeting Super-Enhancer-Driven Oncogenic Transcription by CDK7 Inhibition in Anaplastic Thyroid Carcinoma. Thyroid. 2019 Jun;29(6):809-823.

  Abstract

2018

• Huang D#, Yi X#, Zhang S, Zheng Z, Wang P, Xuan C, Sham PC, Wang J, Li MJ*. GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits. Nucleic Acids Res. 2018 Jul 2;46(W1):W114-W120.

  Abstract Full Paper Website

• Xu J#, Li Q#, Qin W#, Li MJ, Zhuo C, Liu H, Liu F, Wang J, Schumann G, Yu C*. Neurobiological substrates underlying the effect of genomic risk for depression on the conversion of amnestic mild cognitive impairment. Brain. 2018 Dec 1;141(12):3457-3471.

  Abstract

• Ying D, Li MJ, Sham PC, Li M*. A powerful approach reveals numerous expression quantitative trait haplotypes in multiple tissues. Bioinformatics. 2018 Sep 15;34(18):3145-3150.

  Abstract

• Poon EN, Hao B, Guan D, Li MJ, Lu J, Yang Y, Wu B, Wu SC, Webb SE, Liang Y, Miller AL, Yao X, Wang J, Yan B*, Boheler KR*. Integrated transcriptomic and regulatory network analyses identify microRNA-200c as a novel repressor of human pluripotent stem cell-derived cardiomyocyte differentiation and maturation. Cardiovasc Res. 2018 May 1;114(6):894-906.

  Abstract

2017

• 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.

  Abstract Full Paper Website Code and Data

• Li MJ#, Zhang J#, Liang Q, Xuan C, Wu J, Jiang P, Li W, Zhu Y, Wang P, Fernandez D, Shen Y, Chen Y, Kocher JA, Yu Y, Sham PC, Wang J*, Liu JS*, Liu XS*. Exploring genetic associations with ceRNA regulation in the human genome. Nucleic Acids Res. 2017 Jun 2;45(10):5653-5665.

  Abstract Full Paper

• Li MJ#, Yao H#, Huang D#, Liu H, Liu Z, Xu H, Qin Y, Prinz J, Xia W, Wang P, Yan B, Tran NL, Kocher JP, Sham PC, Wang J*. mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers. Nucleic Acids Res. 2017 Jul 3;45(W1):W215-W221.

  Abstract Full Paper Website

• Zhang DD, Wang WT, Xiong J, Xie XM, Cui SS, Zhao ZG, Li MJ, Zhang ZQ, Hao DL, Zhao X, Li YJ, Wang J, Chen HZ, Lv X*, Liu DP*. Long noncoding RNA LINC00305 promotes inflammation by activating the AHRR-NF-κB pathway in human monocytes. Sci Rep. 2017 Apr 10;7:46204.

  Abstract

• Li M#,*, Li J#, Li MJ, Pan Z, Hsu JS, Liu DJ, Zhan X, Wang J, Song Y, Sham PC*. Robust and rapid algorithms facilitate large-scale whole genome sequencing downstream analysis in an integrative framework. Nucleic Acids Res. 2017 May 19;45(9):e75.

  Abstract

2016

• 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.

  Abstract Full Paper Code and Data

• Li MJ#, Liu Z#, Wang P, Wong MP, Nelson MR, Kocher JP, Yeager M, Sham PC, Chanock SJ, Xia Z*, Wang J*. GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2016 Jan 4;44(D1):D869-76.

  Abstract Full Paper

• Cheng TH, Thompson DJ, O'Mara TA, Painter JN, Glubb DM, Flach S, Lewis A, French JD, Freeman-Mills L, Church D, Gorman M, Martin L; National Study of Endometrial Cancer Genetics Group (NSECG), Hodgson S, Webb PM; Australian National Endometrial Cancer Study Group (ANECS), Attia J, Holliday EG, McEvoy M, Scott RJ, Henders AK, Martin NG, Montgomery GW, Nyholt DR, Ahmed S, Healey CS, Shah M, Dennis J, Fasching PA, Beckmann MW, Hein A, Ekici AB, Hall P, Czene K, Darabi H, Li J, Dörk T, Dürst M, Hillemanns P, Runnebaum I, Amant F, Schrauwen S, Zhao H, Lambrechts D, Depreeuw J, Dowdy SC, Goode EL, Fridley BL, Winham SJ, Njølstad TS, Salvesen HB, Trovik J, Werner HM, Ashton K, Otton G, Proietto T, Liu T, Mints M, Tham E; RENDOCAS, Consortium C, Li MJ, Yip SH, Wang J, Bolla MK, Michailidou K, Wang Q, Tyrer JP, Dunlop M, Houlston R, Palles C, Hopper JL; AOCS Group, Peto J, Swerdlow AJ, Burwinkel B, Brenner H, Meindl A, Brauch H, Lindblom A, Chang-Claude J, Couch FJ, Giles GG, Kristensen VN, Cox A, Cunningham JM, Pharoah PDP, Dunning AM, Edwards SL, Easton DF, Tomlinson I, Spurdle AB*. Five endometrial cancer risk loci identified through genome-wide association analysis. Nat Genet. 2016 Jun;48(6):667-674.

  Abstract

2015

• Li MJ, Yan B, Sham PC, Wang J*. Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression. Brief Bioinform. 2015 May;16(3):393-412.

  Abstract Full Paper

• Li MJ, Wang J*. Current trend of annotating single nucleotide variation in humans-A case study on SNVrap. Methods. 2015 Jun;79-80:32-40.

  Abstract Full Paper

• Li MJ, Deng J, Wang P, Yang W, Ho SL, Sham PC, Wang J*, Li M*. wKGGSeq: A Comprehensive Strategy-Based and Disease-Targeted Online Framework to Facilitate Exome Sequencing Studies of Inherited Disorders. Hum Mutat. 2015 May;36(5):496-503.

  Abstract Full Paper

• Nelson MR, Tipney H, Painter JL, Shen J, Nicoletti P, Shen Y, Floratos A, Sham PC, Li MJ, Wang J, Cardon LR, Whittaker JC, Sanseau P*. The support of human genetic evidence for approved drug indications. Nat Genet. 2015 Aug;47(8):856-60.

  Abstract

• Xiao B, Gu SM, Li MJ, Li J, Tao B, Wang Y, Wang Y, Zuo S, Shen Y, Yu Y, Chen D, Chen G, Kong D, Tang J, Liu Q, Chen DR, Liu Y, Alberti S, Dovizio M, Landolfi R, Mucci L, Miao PZ, Gao P, Zhu DL, Wang J, Li B, Patrignani P, Yu Y*. Rare SNP rs12731181 in the miR-590-3p Target Site of the Prostaglandin F2α Receptor Gene Confers Risk for Essential Hypertension in the Han Chinese Population. Arterioscler Thromb Vasc Biol. 2015 Jul;35(7):1687-95.

  Abstract

• Wang P, Qin J, Qin Y, Zhu Y, Wang LY, Li MJ, Zhang MQ, Wang J*. ChIP-Array 2: integrating multiple omics data to construct gene regulatory networks. Nucleic Acids Res. 2015 Jul 1;43(W1):W264-9.

  Abstract

2014

• Li MJ, Wang LY, Xia Z, Wong MP, Sham PC, Wang J*. dbPSHP: a database of recent positive selection across human populations. Nucleic Acids Res. 2014 Jan;42(Database issue):D910-6.

  Abstract Full Paper

• Yalamanchili HK, Yan B, Li MJ, Qin J, Zhao Z, Chin FY, Wang J*. DDGni: dynamic delay gene-network inference from high-temporal data using gapped local alignment. Bioinformatics. 2014 Feb 1;30(3):377-83.

  Abstract

2013

• Li MJ, Wang LY, Xia Z, Sham PC, Wang J*. GWAS3D: Detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications. Nucleic Acids Res. 2013 Jul;41(Web Server issue):W150-8.

  Abstract Full Paper

• Wang P, Lai WF, Li MJ, Xu F, Yalamanchili HK, Lovell-Badge R, Wang J*. Inference of gene-phenotype associations via protein-protein interaction and orthology. PLoS One. 2013 Oct 23;8(10):e77478.

  Abstract

• Qin J, Li MJ, Wang P, Wong NS, Wong MP, Xia Z, Tsao GS, Zhang MQ, Wang J*. ProteoMirExpress: inferring microRNA and protein-centered regulatory networks from high-throughput proteomic and mRNA expression data. Mol Cell Proteomics. 2013 Nov;12(11):3379-87.

  Abstract

2012

• Li MJ, Sham PC, Wang J*. Genetic variant representation, annotation and prioritization in the post-GWAS era. Cell Res. 2012 Oct;22(10):1505-8.

  Abstract Full Paper

• Li MJ, Wang P, Liu X, Lim EL, Wang Z, Yeager M, Wong MP, Sham PC, Chanock SJ, Wang J*. GWASdb: a database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res. 2012 Jan;40(Database issue):D1047-54.

  Abstract Full Paper

• Xu F#, Wang W#, Wang P, Li MJ, Sham PC, Wang J*. A fast and accurate SNP detection algorithm for next-generation sequencing data. Nat Commun. 2012;3:1258.

  Abstract

2011

• Qin J, Li MJ, Wang P, Zhang MQ, Wang J*. ChIP-Array: combinatory analysis of ChIP-seq/chip and microarray gene expression data to discover direct/indirect targets of a transcription factor. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W430-6.

  Abstract

• Wang LY, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J*. EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans. Epigenetics. 2011 Dec;6(12):1505-12.

  Abstract

2010

• Li MJ, Sham PC, Wang J*. FastPval: a fast and memory efficient program to calculate very low P-values from empirical distribution. Bioinformatics. 2010 Nov 15;26(22):2897-9.

  Abstract Full Paper