Jianxin Shi, Ph.D. - Publications

Affiliations: 
2006 Stanford University, Palo Alto, CA 
Area:
Statistics, Genetics

108 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Hua X, Song L, Yu G, Vogtmann E, Goedert JJ, Abnet CC, Landi MT, Shi J. MicrobiomeGWAS: A Tool for Identifying Host Genetic Variants Associated with Microbiome Composition. Genes. 13. PMID 35886007 DOI: 10.3390/genes13071224  0.303
2022 Sang J, Zhang T, Kim J, Li M, Pesatori AC, Consonni D, Song L, Liu J, Zhao W, Hoang PH, Campbell DS, Feng J, D'Arcy ME, Synnott N, Chen Y, ... ... Shi J, et al. Rare germline deleterious variants increase susceptibility for lung cancer. Human Molecular Genetics. PMID 35717579 DOI: 10.1093/hmg/ddac123  0.308
2020 Zhang S, Zhang H, Zhou Y, Qiao M, Zhao S, Kozlova A, Shi J, Sanders AR, Wang G, Luo K, Sengupta S, West S, Qian S, Streit M, Avramopoulos D, et al. Allele-specific open chromatin in human iPSC neurons elucidates functional disease variants. Science (New York, N.Y.). 369: 561-565. PMID 32732423 DOI: 10.1126/Science.Aay3983  0.377
2020 Yuan F, Hung RJ, Walsh N, Zhang H, Platz EA, Wheeler W, Song L, Arslan AA, Beane Freeman LE, Bracci P, Canzian F, Du M, Gallinger S, Giles GG, Goodman PJ, ... ... Shi J, et al. Genome-wide association study data reveal genetic susceptibility to chronic inflammatory intestinal diseases and pancreatic ductal adenocarcinoma risk. Cancer Research. PMID 32641412 DOI: 10.1158/0008-5472.Can-20-0447  0.336
2020 Zhu B, Poeta ML, Costantini M, Zhang T, Shi J, Sentinelli S, Zhao W, Pompeo V, Cardelli M, Alexandrov BS, Otlu B, Hua X, Jones K, Brodie S, Dabrowska ME, et al. The genomic and epigenomic evolutionary history of papillary renal cell carcinomas. Nature Communications. 11: 3096. PMID 32555180 DOI: 10.1038/S41467-020-16546-5  0.323
2020 Hua X, Zhao W, Pesatori AC, Consonni D, Caporaso NE, Zhang T, Zhu B, Wang M, Jones K, Hicks B, Song L, Sampson J, Wedge DC, Shi J, Landi MT. Genetic and epigenetic intratumor heterogeneity impacts prognosis of lung adenocarcinoma. Nature Communications. 11: 2459. PMID 32424208 DOI: 10.1038/S41467-020-16295-5  0.354
2020 Landi MT, Bishop DT, MacGregor S, Machiela MJ, Stratigos AJ, Ghiorzo P, Brossard M, Calista D, Choi J, Fargnoli MC, Zhang T, Rodolfo M, Trower AJ, Menin C, Martinez J, ... ... Shi J, et al. Genome-wide association meta-analyses combining multiple risk phenotypes provide insights into the genetic architecture of cutaneous melanoma susceptibility. Nature Genetics. PMID 32341527 DOI: 10.1038/S41588-020-0611-8  0.414
2020 Cai N, Revez JA, Adams MJ, Andlauer TFM, Breen G, Byrne EM, Clarke TK, Forstner AJ, Grabe HJ, Hamilton SP, Levinson DF, Lewis CM, Lewis G, Martin NG, Milaneschi Y, ... ... Shi J, et al. Minimal phenotyping yields genome-wide association signals of low specificity for major depression. Nature Genetics. PMID 32231276 DOI: 10.1038/S41588-020-0594-5  0.387
2020 Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Mocci E, Zhang M, Song L, Chung CC, Zhang T, Xiao W, Albanes D, Andreotti G, Arslan AA, Babic A, ... ... Shi J, et al. A Transcriptome-Wide Association Study (TWAS) Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer. Journal of the National Cancer Institute. PMID 31917448 DOI: 10.1093/Jnci/Djz246  0.404
2020 Vogtmann E, Hua X, Yu G, Hullings A, Wan Y, Dagnall CL, Jones K, Hicks BD, Hutchinson A, Suman S, Zhu B, Graubard B, Gail MH, Caporaso JG, Wheeler W, ... ... Shi J, et al. Abstract A39: The human oral microbiota and risk of lung cancer: An analysis of three prospective cohort studies Cancer Research. 80. DOI: 10.1158/1538-7445.Mvc2020-A39  0.354
2020 Chen T, Chatterjee N, Landi MT, Shi J. A penalized regression framework for building polygenic risk models based on summary statistics from genome-wide association studies and incorporating external information Journal of the American Statistical Association. 1-19. DOI: 10.1080/01621459.2020.1764849  0.368
2019 Zhu B, Tse LA, Wang D, Koka H, Zhang T, Abubakar M, Lee P, Wang F, Wu C, Tsang KH, Chan WC, Law SH, Li M, Li W, Wu S, ... ... Shi J, et al. Immune gene expression profiling reveals heterogeneity in luminal breast tumors. Breast Cancer Research : Bcr. 21: 147. PMID 31856876 DOI: 10.1186/S13058-019-1218-9  0.306
2019 Vogtmann E, Han Y, Caporaso JG, Bokulich N, Mohamadkhani A, Moayyedkazemi A, Hua X, Kamangar F, Wan Y, Suman S, Zhu B, Hutchinson A, Dagnall C, Jones K, Hicks B, ... Shi J, et al. Oral microbial community composition is associated with pancreatic cancer: A case-control study in Iran. Cancer Medicine. PMID 31750624 DOI: 10.1002/Cam4.2660  0.31
2019 Schlafly A, Pfeiffer RM, Nagore E, Puig S, Calista D, Ghiorzo P, Menin C, Fargnoli MC, Peris K, Song L, Zhang T, Shi J, Landi MT, Sampson JN. Contribution of Common Genetic Variants to Familial Aggregation of Disease and Implications for Sequencing Studies. Plos Genetics. 15: e1008490. PMID 31730655 DOI: 10.1371/Journal.Pgen.1008490  0.347
2019 Glanville KP, Coleman JRI, Hanscombe KB, Euesden J, Choi SW, Purves KL, Breen G, Air TM, Andlauer TFM, Baune BT, Binder EB, Blackwood DHR, Boomsma DI, Buttenschøn HN, Colodro-Conde L, ... ... Shi J, et al. Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression. Biological Psychiatry. PMID 31570195 DOI: 10.1016/J.Biopsych.2019.06.031  0.322
2019 Wong JYY, Zhang H, Hsiung CA, Shiraishi K, Yu K, Matsuo K, Wong MP, Hong YC, Wang J, Seow WJ, Wang Z, Song M, Kim HN, Chang IS, Chatterjee N, ... ... Shi J, et al. Tuberculosis infection and lung adenocarcinoma: Mendelian randomization and pathway analysis of genome-wide association study data from never-smoking Asian women. Genomics. PMID 31306748 DOI: 10.1016/J.Ygeno.2019.07.008  0.344
2019 Zhang X, Abdellaoui A, Rucker J, de Jong S, Potash JB, Weissman MM, Shi J, Knowles JA, Pato C, Pato M, Sobell J, Smit JH, Hottenga JJ, de Geus EJC, Lewis CM, et al. Genome-wide Burden of Rare Short Deletions Is Enriched in Major Depressive Disorder in Four Cohorts. Biological Psychiatry. PMID 31003785 DOI: 10.1016/J.Biopsych.2019.02.022  0.353
2019 Hosgood HD, Mongodin EF, Wan Y, Hua X, Rothman N, Hu W, Vermeulen R, Seow WJ, Rohan T, Xu J, Li J, He J, Huang Y, Yang K, Wu G, ... ... Shi J, et al. The respiratory tract microbiome and its relationship to lung cancer and environmental exposures found in rural China. Environmental and Molecular Mutagenesis. PMID 30942501 DOI: 10.1002/Em.22291  0.315
2019 Landi MT, Zhang T, Garcia-Closas M, Bossé Y, Shi J, Zhu B, Lan Q, Rothman N, Choi J, Caporaso NE, Zhao W, Chen C, Ruppin E, Rosenbaum J, Gordenin D, et al. Abstract SY26-02: Sherlock-Lung: Tracing lung cancer mutational processes in never smokers Cancer Research. 79. DOI: 10.1158/1538-7445.Sabcs18-Sy26-02  0.31
2019 Blechter B, Hsiung CA, Yin Z, Shu X, Hosgood HD, Wong JYY, Shi J, Hu W, Bassig B, Seow WJ, Gao Ya, Cai Q, Xiang Y, Chang I, Zhou B, et al. Abstract 2682: Analysis of polygenic risk score interaction with coal use and risk of lung adenocarcinoma among never-smoking women in Asia Cancer Research. 79: 2682-2682. DOI: 10.1158/1538-7445.Sabcs18-2682  0.329
2019 Zhong J, Jermusyk A, Wu L, Hoskins JW, Collins I, Zhang M, Lei S, Chung CC, Zhang T, Xiao W, Stolzenberg-Solomon R, Klein AP, Wolpin BM, Shu X, Chanock SJ, ... ... Shi J, et al. Abstract 1591: Large-scale transcriptome-wide association study (TWAS) identifies novel candidate susceptibility genes for pancreatic cancer Epidemiology. DOI: 10.1158/1538-7445.Sabcs18-1591  0.349
2019 Zhao W, Hua X, Zhang T, Consonni D, Pesatori AC, Shi J, Landi MT. Abstract 1601: Genetic and epigenetic intratumor heterogeneity of lung adenocarcinoma Cancer Research. 79: 1601-1601. DOI: 10.1158/1538-7445.Am2019-1601  0.372
2019 Zhang S, Moy W, Zhang H, McGowan H, Shi J, Leites C, Pang Z, Sanders AR, Gejman PV, Duan J. Landscape Of Allele-Specific Open Chromatin In Human Ipsc-Differentiated Neurons And It Implication For Mental Disorders European Neuropsychopharmacology. 29. DOI: 10.1016/J.Euroneuro.2017.08.034  0.366
2019 Duan J, Forrest M, Zhang H, Moy W, McGowan H, Leites C, Shi J, Sanders A, Greenleaf W, Cowan C, Pang Z, Gejman P, Penzes P. Open Chromatin Profiling Identifies Functional Noncoding Risk Variants In Human Ipsc Model of Psychiatric Disorders European Neuropsychopharmacology. 29: S765. DOI: 10.1016/J.Euroneuro.2017.06.122  0.356
2018 Zhang T, Choi J, Kovacs MA, Shi J, Xu M, Goldstein AM, Trower AJ, Bishop DT, Iles MM, Duffy DL, MacGregor S, Amundadottir LT, Law MH, et al. Cell-type-specific eQTL of primary melanocytes facilitates identification of melanoma susceptibility genes. Genome Research. PMID 30333196 DOI: 10.1101/Gr.233304.117  0.391
2018 Gu F, Chen TH, Pfeiffer RM, Fargnoli MC, Calista D, Ghiorzo P, Peris K, Puig S, Menin C, De Nicolo A, Rodolfo M, Pellegrini C, Pastorino L, Evangelou E, Zhang T, ... ... Shi J, et al. Combining common genetic variants and non-genetic risk factors to predict risk of cutaneous melanoma. Human Molecular Genetics. PMID 30060076 DOI: 10.1093/Hmg/Ddy282  0.356
2018 Wray NR, Ripke S, Mattheisen M, Trzaskowski M, Byrne EM, Abdellaoui A, Adams MJ, Agerbo E, Air TM, Andlauer TMF, Bacanu SA, Bækvad-Hansen M, Beekman AFT, Bigdeli TB, Binder EB, ... ... Shi J, et al. Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression. Nature Genetics. PMID 29700475 DOI: 10.1038/S41588-018-0090-3  0.353
2018 Sinha R, Goedert JJ, Vogtmann E, Hua X, Porras C, Hayes R, Safaeian M, Yu G, Sampson J, Ahn J, Shi J. Quantification of Human Microbiome Stability Over Six Months: Implications for Epidemiologic Studies. American Journal of Epidemiology. PMID 29608646 DOI: 10.1093/Aje/Kwy064  0.31
2018 Bishop DT, Iles MM, Newton-Bishop JA, Barrett JH, Trouwer A, Law M, MacGregor S, Duffy D, Martin NG, Hayward N, Cust A, Landi MT, Goldstein A, Shi J, Machiela M, et al. Abstract 234: Understanding melanoma susceptibility through GWAS of risk phenotypes Epidemiology. DOI: 10.1158/1538-7445.Am2018-234  0.304
2018 Pellegrini C, Law M, Iles M, Machiela M, Stratigos A, Zhang T, Brown K, Newton-Bishop J, Hayward N, Martin N, Goldstein A, Yang R, Chanock S, Demenais F, Puig S, ... ... Shi J, et al. Abstract 228: Association analysis across different populations identifies 26 new cutaneous melanoma risk loci Epidemiology. DOI: 10.1158/1538-7445.Am2018-228  0.316
2018 Zhang T, Sampson J, Bertazzi PA, Pesatori A, Consonni D, Zhu B, Hicks B, Hua X, Shi J, Brown K, Chanock S, Landi MT. Abstract 1187: Comparison of intra-tumor heterogeneity and clonal evolution across lung cancer subtypes by multi-region whole genome sequencing Tumor Biology. DOI: 10.1158/1538-7445.Am2018-1187  0.313
2017 Stueve TR, Li WQ, Shi J, Marconett CN, Zhang T, Yang C, Mullen D, Yan C, Wheeler W, Hua X, Zhou B, Borok Z, Caporaso NE, Pesatori AC, Duan J, et al. Epigenome-wide analysis of DNA methylation in lung tissue shows concordance with blood studies and identifies tobacco smoke-inducible enhancers. Human Molecular Genetics. 26: 3014-3027. PMID 28854564 DOI: 10.1093/Hmg/Ddx188  0.32
2017 Forrest MP, Zhang H, Moy W, McGowan H, Leites C, Dionisio LE, Xu Z, Shi J, Sanders AR, Greenleaf WJ, Cowan CA, Pang ZP, Gejman PV, Penzes P, Duan J. Open Chromatin Profiling in hiPSC-Derived Neurons Prioritizes Functional Noncoding Psychiatric Risk Variants and Highlights Neurodevelopmental Loci. Cell Stem Cell. PMID 28803920 DOI: 10.1016/J.Stem.2017.07.008  0.354
2017 Gu F, Zhang H, Hyland PL, Berndt S, Gapstur SM, Wheeler W, Amos CI, Bezieau S, Bickeböller H, Brenner H, Brennan P, Chang-Claude J, Conti DV, Ann Doherty J, ... ... Shi J, et al. Inherited variation in circadian rhythm genes and risks of prostate cancer and three other cancer sites in combined cancer consortia. International Journal of Cancer. PMID 28699174 DOI: 10.1002/Ijc.30883  0.35
2017 Knowles DA, Davis JR, Edgington H, Raj A, Favé MJ, Zhu X, Potash JB, Weissman MM, Shi J, Levinson DF, Awadalla P, Mostafavi S, Montgomery SB, Battle A. Allele-specific expression reveals interactions between genetic variation and environment. Nature Methods. PMID 28530654 DOI: 10.1038/Nmeth.4298  0.32
2017 Hua X, Goedert JJ, Landi MT, Shi J. Identifying Host Genetic Variants Associated with Microbiome Composition by Testing Multiple Beta Diversity Matrices. Human Heredity. 81: 117-126. PMID 28076867 DOI: 10.1159/000448733  0.328
2016 Shi J, Hua X, Goedert JJ, Landi MT, Äijö T, Bonneau R, Zhou W, Sherwood B, Ji H, Zappala Z, Montgomery SB, Wang X, Xiao R, Zhu X, Li M, et al. SAGES 2015. Symposium of Advances in Genomics, Epidemiology and Statistics 2015: Abstracts Human Heredity. 81: 51-61. PMID 28076868 DOI: 10.1159/000447110  0.315
2016 Direk N, Williams S, Smith JA, Ripke S, Air T, Amare AT, Amin N, Baune BT, Bennett DA, Blackwood DH, Boomsma D, Breen G, Buttenschøn HN, Byrne EM, Børglum AD, ... ... Shi J, et al. An Analysis of Two Genome-wide Association Meta-analyses Identifies a New Locus for Broad Depression Phenotype. Biological Psychiatry. PMID 28049566 DOI: 10.1016/J.Biopsych.2016.11.013  0.317
2016 Shi J, Park JH, Duan J, Berndt ST, Moy W, Yu K, Song L, Wheeler W, Hua X, Silverman D, Garcia-Closas M, Hsiung CA, Figueroa JD, Cortessis VK, Malats N, et al. Winner's Curse Correction and Variable Thresholding Improve Performance of Polygenic Risk Modeling Based on Genome-Wide Association Study Summary-Level Data. Plos Genetics. 12: e1006493. PMID 28036406 DOI: 10.1371/Journal.Pgen.1006493  0.373
2016 Seow WJ, Matsuo K, Hsiung CA, Shiraishi K, Song M, Kim HN, Wong MP, Hong YC, Dean Hosgood H, Wang Z, Chang IS, Wang JC, Chatterjee N, Tucker M, Wei H, ... ... Shi J, et al. Association between GWAS-identified lung adenocarcinoma susceptibility loci and EGFR mutations in never-smoking Asian women, and comparison with findings from Western populations. Human Molecular Genetics. PMID 28025329 DOI: 10.1093/Hmg/Ddw414  0.347
2016 Shi J, Hua X, Zhu B, Ravichandran S, Wang M, Nguyen C, Brodie SA, Palleschi A, Alloisio M, Pariscenti G, Jones K, Zhou W, Bouk AJ, Boland J, Hicks B, et al. Somatic Genomics and Clinical Features of Lung Adenocarcinoma: A Retrospective Study. Plos Medicine. 13: e1002162. PMID 27923066 DOI: 10.1371/Journal.Pmed.1002162  0.325
2016 Power RA, Tansey KE, Buttenschøn HN, Cohen-Woods S, Bigdeli T, Hall LS, Kutalik Z, Lee SH, Ripke S, Steinberg S, Teumer A, Viktorin A, Wray NR, Arolt V, Baune BT, ... ... Shi J, et al. Genome-wide Association for Major Depression Through Age at Onset Stratification: Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium. Biological Psychiatry. PMID 27519822 DOI: 10.1016/J.Biopsych.2016.05.010  0.358
2016 Shi J, Zhou W, Zhu B, Hyland PL, Bennett H, Xiao Y, Zhang X, Burke LS, Song L, Hsu CH, Yan C, Chen Q, Meerzaman D, Dagnall CL, Burdette L, et al. Rare germline copy number variations and disease susceptibility in familial melanoma. The Journal of Investigative Dermatology. PMID 27476724 DOI: 10.1016/J.Jid.2016.07.023  0.38
2016 Zhu B, Mukherjee A, Machiela MJ, Song L, Hua X, Shi J, Garcia-Closas M, Chanock SJ, Chatterjee N. An investigation of the association of genetic susceptibility risk with somatic mutation burden in breast cancer. British Journal of Cancer. PMID 27467053 DOI: 10.1038/Bjc.2016.223  0.32
2016 Zhang H, Wheeler W, Hyland PL, Yang Y, Shi J, Chatterjee N, Yu K. A Powerful Procedure for Pathway-Based Meta-analysis Using Summary Statistics Identifies 43 Pathways Associated with Type II Diabetes in European Populations. Plos Genetics. 12: e1006122. PMID 27362418 DOI: 10.1371/Journal.Pgen.1006122  0.384
2016 Okbay A, Beauchamp JP, Fontana MA, Lee JJ, Pers TH, Rietveld CA, Turley P, Chen GB, Emilsson V, Meddens SF, Oskarsson S, Pickrell JK, Thom K, Timshel P, de Vlaming R, ... ... Shi J, et al. Genome-wide association study identifies 74 loci associated with educational attainment. Nature. 533: 539-42. PMID 27225129 DOI: 10.1038/Nature17671  0.391
2016 Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, et al. Impact of the X Chromosome and sex on regulatory variation. Genome Research. PMID 27197214 DOI: 10.1101/Gr.197897.115  0.352
2016 Vogtmann E, Hua X, Zeller G, Sunagawa S, Voigt AY, Hercog R, Goedert JJ, Shi J, Bork P, Sinha R. Colorectal Cancer and the Human Gut Microbiome: Reproducibility with Whole-Genome Shotgun Sequencing. Plos One. 11: e0155362. PMID 27171425 DOI: 10.1371/Journal.Pone.0155362  0.39
2016 Chatterjee N, Shi J, García-Closas M. Developing and evaluating polygenic risk prediction models for stratified disease prevention. Nature Reviews. Genetics. PMID 27140283 DOI: 10.1038/Nrg.2016.27  0.358
2016 Hua X, Hyland PL, Huang J, Song L, Zhu B, Caporaso NE, Landi MT, Chatterjee N, Shi J. MEGSA: A Powerful and Flexible Framework for Analyzing Mutual Exclusivity of Tumor Mutations. American Journal of Human Genetics. PMID 26899600 DOI: 10.1016/J.Ajhg.2015.12.021  0.345
2015 Winkler TW, Justice AE, Graff M, Barata L, Feitosa MF, Chu S, Czajkowski J, Esko T, Fall T, Kilpeläinen TO, Lu Y, Mägi R, Mihailov E, Pers TH, Rüeger S, ... ... Shi J, et al. The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study. Plos Genetics. 11: e1005378. PMID 26426971 DOI: 10.1371/Journal.Pgen.1005378  0.316
2015 Lee SH, Byrne EM, Hultman CM, Kähler A, Vinkhuyzen AA, Ripke S, Andreassen OA, Frisell T, Gusev A, Hu X, Karlsson R, Mantzioris VX, McGrath JJ, Mehta D, Stahl EA, ... ... Shi J, et al. New data and an old puzzle: the negative association between schizophrenia and rheumatoid arthritis. International Journal of Epidemiology. PMID 26286434 DOI: 10.1093/Ije/Dyv136  0.325
2015 Wang Y, Wei Y, Gaborieau V, Shi J, Han Y, Timofeeva MN, Su L, Li Y, Eisen T, Amos CI, Landi MT, Christiani DC, McKay JD, Houlston RS. Deciphering associations for lung cancer risk through imputation and analysis of 12 316 cases and 16 831 controls. European Journal of Human Genetics : Ejhg. PMID 25804397 DOI: 10.1038/Ejhg.2015.48  0.432
2015 Maier R, Moser G, Chen GB, Ripke S, Coryell W, Potash JB, Scheftner WA, Shi J, Weissman MM, Hultman CM, Landén M, Levinson DF, Kendler KS, Smoller JW, et al. Joint analysis of psychiatric disorders increases accuracy of risk prediction for schizophrenia, bipolar disorder, and major depressive disorder. American Journal of Human Genetics. 96: 283-94. PMID 25640677 DOI: 10.1016/J.Ajhg.2014.12.006  0.327
2015 Yang X(, Shi J, Bennett H, Burke L, Dagnall C, Burdette L, Hicks B, Tucker M, Goldstein A. Abstract 2755: Germline copy number variations in melanoma families with/without CDKN2A/CDK4 mutations Cancer Research. 75: 2755-2755. DOI: 10.1158/1538-7445.Am2015-2755  0.354
2014 Goedert JJ, Hua X, Yu G, Shi J. Diversity and composition of the adult fecal microbiome associated with history of cesarean birth or appendectomy: Analysis of the American Gut Project. Ebiomedicine. 1: 167-172. PMID 25601913 DOI: 10.1016/J.Ebiom.2014.11.004  0.306
2014 Sampson JN, Wheeler B, Li P, Shi J. LEVERAGING LOCAL IDENTITY-BY-DESCENT INCREASES THE POWER OF CASE/CONTROL GWAS WITH RELATED INDIVIDUALS. The Annals of Applied Statistics. 8: 974-998. PMID 25544865 DOI: 10.1214/14-Aoas715  0.379
2014 Wood AR, Esko T, Yang J, Vedantam S, Pers TH, Gustafsson S, Chu AY, Estrada K, Luan J, Kutalik Z, Amin N, Buchkovich ML, Croteau-Chonka DC, Day FR, Duan Y, ... ... Shi J, et al. Defining the role of common variation in the genomic and biological architecture of adult human height. Nature Genetics. 46: 1173-86. PMID 25282103 DOI: 10.1038/Ng.3097  0.391
2014 Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, et al. Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis. 35: 2698-705. PMID 25239644 DOI: 10.1093/Carcin/Bgu203  0.387
2014 Wang Z, Zhu B, Zhang M, Parikh H, Jia J, Chung CC, Sampson JN, Hoskins JW, Hutchinson A, Burdette L, Ibrahim A, Hautman C, Raj PS, Abnet CC, Adjei AA, ... ... Shi J, et al. Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33. Human Molecular Genetics. 23: 6616-33. PMID 25027329 DOI: 10.1093/Hmg/Ddu363  0.389
2014 Kelley MJ, Shi J, Ballew B, Hyland PL, Li WQ, Rotunno M, Alcorta DA, Liebsch NJ, Mitchell J, Bass S, Roberson D, Boland J, Cullen M, He J, Burdette L, et al. Characterization of T gene sequence variants and germline duplications in familial and sporadic chordoma. Human Genetics. 133: 1289-97. PMID 24990759 DOI: 10.1007/S00439-014-1463-Z  0.343
2014 Shi J, Yang XR, Ballew B, Rotunno M, Calista D, Fargnoli MC, Ghiorzo P, Bressac-de Paillerets B, Nagore E, Avril MF, Caporaso NE, McMaster ML, Cullen M, Wang Z, Zhang X, et al. Rare missense variants in POT1 predispose to familial cutaneous malignant melanoma. Nature Genetics. 46: 482-6. PMID 24686846 DOI: 10.1038/Ng.2941  0.343
2014 Shi J, Yang XR, Caporaso NE, Landi MT, Li P. VTET: a variable threshold exact test for identifying disease-associated copy number variations enriched in short genomic regions. Frontiers in Genetics. 5: 53. PMID 24672538 DOI: 10.3389/Fgene.2014.00053  0.397
2014 Shi J, Marconett CN, Duan J, Hyland PL, Li P, Wang Z, Wheeler W, Zhou B, Campan M, Lee DS, Huang J, Zhou W, Triche T, Amundadottir L, Warner A, et al. Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue. Nature Communications. 5: 3365. PMID 24572595 DOI: 10.1038/Ncomms4365  0.369
2014 Ahsan H, Halpern J, Kibriya MG, Pierce BL, Tong L, Gamazon E, McGuire V, Felberg A, Shi J, Jasmine F, Roy S, Brutus R, Argos M, Melkonian S, Chang-Claude J, et al. A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 23: 658-69. PMID 24493630 DOI: 10.1158/1055-9965.Epi-13-0340  0.388
2014 Mostafavi S, Battle A, Zhu X, Potash JB, Weissman MM, Shi J, Beckman K, Haudenschild C, McCormick C, Mei R, Gameroff MJ, Gindes H, Adams P, Goes FS, Mondimore FM, et al. Type I interferon signaling genes in recurrent major depression: increased expression detected by whole-blood RNA sequencing. Molecular Psychiatry. 19: 1267-74. PMID 24296977 DOI: 10.1038/Mp.2013.161  0.394
2014 Battle A, Mostafavi S, Zhu X, Potash JB, Weissman MM, McCormick C, Haudenschild CD, Beckman KB, Shi J, Mei R, Urban AE, Montgomery SB, Levinson DF, Koller D. Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Research. 24: 14-24. PMID 24092820 DOI: 10.1101/Gr.155192.113  0.398
2014 Zhang H, Shi J, Liang F, Wheeler W, Stolzenberg-Solomon R, Yu K. A fast multilocus test with adaptive SNP selection for large-scale genetic-association studies. European Journal of Human Genetics : Ejhg. 22: 696-702. PMID 24022295 DOI: 10.1038/Ejhg.2013.201  0.425
2014 Shi J, Yang XR, Ballew B, Rotunno M, Calista D, Fargnoli MC, Ghiorzo P, Paillerets BB, Nagore E, Hua X, Hyland P, Yin J, Vallabhaneni H, Chai W, Ravichandran S, et al. Abstract 941: Exome sequencing identifiedPOT1, a telomere shelterin gene, as a major susceptibility gene for familial cutaneous malignant melanoma Cancer Research. 74: 941-941. DOI: 10.1158/1538-7445.Am2014-941  0.324
2014 Shi J, Marconett C, Duan J, Hyland P, Li P, Wang Z, Wheeler W, Campan M, Huang J, Zhou W, Triche T, Amundadottir L, Hutchinson A, Chen P, Zhou B, et al. Abstract 287: Characterizing the genetic basis of methylome diversity in histologically normal human lung tissue Cancer Research. 74: 287-287. DOI: 10.1158/1538-7445.Am2014-287  0.372
2014 Li W, Shi J, Wheeler W, Caporaso N, Laird-Offspringa I, Landi MT. Abstract 286: Epigenome-wide association study of normal lung tissues identifies hypomethylation of multiple CpG sites associated with cigarette smoking Cancer Research. 74: 286-286. DOI: 10.1158/1538-7445.Am2014-286  0.302
2013 Ahn J, Sinha R, Pei Z, Dominianni C, Wu J, Shi J, Goedert JJ, Hayes RB, Yang L. Human gut microbiome and risk for colorectal cancer. Journal of the National Cancer Institute. 105: 1907-11. PMID 24316595 DOI: 10.1093/Jnci/Djt300  0.324
2013 Sanders AR, Göring HH, Duan J, Drigalenko EI, Moy W, Freda J, He D, Shi J, Gejman PV. Transcriptome study of differential expression in schizophrenia. Human Molecular Genetics. 22: 5001-14. PMID 23904455 DOI: 10.1093/Hmg/Ddt350  0.372
2013 Randall JC, Winkler TW, Kutalik Z, Berndt SI, Jackson AU, Monda KL, Kilpeläinen TO, Esko T, Mägi R, Li S, Workalemahu T, Feitosa MF, Croteau-Chonka DC, Day FR, Fall T, ... ... Shi J, et al. Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. Plos Genetics. 9: e1003500. PMID 23754948 DOI: 10.1371/Journal.Pgen.1003500  0.34
2013 Berndt SI, Gustafsson S, Mägi R, Ganna A, Wheeler E, Feitosa MF, Justice AE, Monda KL, Croteau-Chonka DC, Day FR, Esko T, Fall T, Ferreira T, Gentilini D, Jackson AU, ... ... Shi J, et al. Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture. Nature Genetics. 45: 501-12. PMID 23563607 DOI: 10.1038/Ng.2606  0.35
2013 Li WQ, Hu N, Hyland PL, Gao Y, Wang ZM, Yu K, Su H, Wang CY, Wang LM, Chanock SJ, Burdett L, Ding T, Qiao YL, Fan JH, Wang Y, ... ... Shi JX, et al. Genetic variants in DNA repair pathway genes and risk of esophageal squamous cell carcinoma and gastric adenocarcinoma in a Chinese population. Carcinogenesis. 34: 1536-42. PMID 23504502 DOI: 10.1093/Carcin/Bgt094  0.392
2013 Guha S, Rees E, Darvasi A, Ivanov D, Ikeda M, Bergen SE, Magnusson PK, Cormican P, Morris D, Gill M, Cichon S, Rosenfeld JA, Lee A, Gregersen PK, Kane JM, ... ... Shi J, et al. Implication of a rare deletion at distal 16p11.2 in schizophrenia. Jama Psychiatry. 70: 253-60. PMID 23325106 DOI: 10.1001/2013.Jamapsychiatry.71  0.374
2013 Ripke S, Wray NR, Lewis CM, Hamilton SP, Weissman MM, Breen G, Byrne EM, Blackwood DH, Boomsma DI, Cichon S, Heath AC, Holsboer F, Lucae S, Madden PA, ... ... Shi J, et al. A mega-analysis of genome-wide association studies for major depressive disorder. Molecular Psychiatry. 18: 497-511. PMID 22472876 DOI: 10.1038/Mp.2012.21  0.391
2012 Fanous AH, Zhou B, Aggen SH, Bergen SE, Amdur RL, Duan J, Sanders AR, Shi J, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, et al. Genome-wide association study of clinical dimensions of schizophrenia: polygenic effect on disorganized symptoms. The American Journal of Psychiatry. 169: 1309-17. PMID 23212062 DOI: 10.1176/Appi.Ajp.2012.12020218  0.375
2012 Shiels MS, Engels EA, Shi J, Landi MT, Albanes D, Chatterjee N, Chanock SJ, Caporaso NE, Chaturvedi AK. Genetic variation in innate immunity and inflammation pathways associated with lung cancer risk. Cancer. 118: 5630-6. PMID 23044494 DOI: 10.1002/Cncr.27605  0.352
2012 Levinson DF, Shi J, Wang K, Oh S, Riley B, Pulver AE, Wildenauer DB, Laurent C, Mowry BJ, Gejman PV, Owen MJ, Kendler KS, Nestadt G, Schwab SG, Mallet J, et al. Genome-wide association study of multiplex schizophrenia pedigrees. The American Journal of Psychiatry. 169: 963-73. PMID 22885689 DOI: 10.1176/Appi.Ajp.2012.11091423  0.61
2012 Hartz SM, Short SE, Saccone NL, Culverhouse R, Chen L, Schwantes-An TH, Coon H, Han Y, Stephens SH, Sun J, Chen X, Ducci F, Dueker N, Franceschini N, Frank J, ... ... Shi J, et al. Increased genetic vulnerability to smoking at CHRNA5 in early-onset smokers. Archives of General Psychiatry. 69: 854-60. PMID 22868939 DOI: 10.1001/Archgenpsychiatry.2012.124  0.301
2012 Gladwin TE, Derks EM, Rietschel M, Mattheisen M, Breuer R, Schulze TG, Nöthen MM, Levinson D, Shi J, Gejman PV, Cichon S, Ophoff RA. Segment-wise genome-wide association analysis identifies a candidate region associated with schizophrenia in three independent samples. Plos One. 7: e38828. PMID 22723893 DOI: 10.1371/Journal.Pone.0038828  0.308
2012 Shi J, Chatterjee N, Rotunno M, Wang Y, Pesatori AC, Consonni D, Li P, Wheeler W, Broderick P, Henrion M, Eisen T, Wang Z, Chen W, Dong Q, Albanes D, et al. Inherited variation at chromosome 12p13.33, including RAD52, influences the risk of squamous cell lung carcinoma. Cancer Discovery. 2: 131-9. PMID 22585858 DOI: 10.1158/2159-8290.Cd-11-0246  0.371
2012 Spitz MR, Gorlov IP, Dong Q, Wu X, Chen W, Chang DW, Etzel CJ, Caporaso NE, Zhao Y, Christiani DC, Brennan P, Albanes D, Shi J, Thun M, Landi MT, et al. Multistage analysis of variants in the inflammation pathway and lung cancer risk in smokers. Cancer Epidemiology, Biomarkers & Prevention : a Publication of the American Association For Cancer Research, Cosponsored by the American Society of Preventive Oncology. 21: 1213-21. PMID 22573796 DOI: 10.1158/1055-9965.Epi-12-0352-T  0.317
2012 Chen LS, Saccone NL, Culverhouse RC, Bracci PM, Chen CH, Dueker N, Han Y, Huang H, Jin G, Kohno T, Ma JZ, Przybeck TR, Sanders AR, Smith JA, Sung YJ, ... ... Shi J, et al. Smoking and genetic risk variation across populations of European, Asian, and African American ancestry--a meta-analysis of chromosome 15q25. Genetic Epidemiology. 36: 340-51. PMID 22539395 DOI: 10.1002/Gepi.21627  0.338
2012 Flores R, Shi J, Gail MH, Gajer P, Ravel J, Goedert JJ. Assessment of the human faecal microbiota: II. Reproducibility and associations of 16S rRNA pyrosequences. European Journal of Clinical Investigation. 42: 855-63. PMID 22385292 DOI: 10.1111/J.1365-2362.2012.02659.X  0.301
2012 Shi J, Chatterjee N, Rotunno M, Wang Y, Pesatori AC, Consonni D, Li P, Broderick P, Henrion M, Eisen T, Wang Z, Chen W, Dong Q, Albanes D, Thun M, et al. Abstract 2931: Inherited variation at chromosome 12p13.33 includingRAD52influences squamous cell lung carcinoma risk Cancer Research. 72: 2931-2931. DOI: 10.1158/1538-7445.Am2012-2931  0.373
2011 Zhou B, Shi J, Whittemore AS. Optimal methods for meta-analysis of genome-wide association studies. Genetic Epidemiology. 35: 581-91. PMID 21922536 DOI: 10.1002/Gepi.20603  0.331
2011 Kendler KS, Kalsi G, Holmans PA, Sanders AR, Aggen SH, Dick DM, Aliev F, Shi J, Levinson DF, Gejman PV. Genomewide association analysis of symptoms of alcohol dependence in the molecular genetics of schizophrenia (MGS2) control sample. Alcoholism, Clinical and Experimental Research. 35: 963-75. PMID 21314694 DOI: 10.1111/J.1530-0277.2010.01427.X  0.397
2011 Levinson DF, Duan J, Oh S, Wang K, Sanders AR, Shi J, Zhang N, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, Byerley WF, Black DW, et al. Copy number variants in schizophrenia: confirmation of five previous findings and new evidence for 3q29 microdeletions and VIPR2 duplications. The American Journal of Psychiatry. 168: 302-16. PMID 21285140 DOI: 10.1176/Appi.Ajp.2010.10060876  0.565
2011 Peterson RE, Maes HH, Holmans P, Sanders AR, Levinson DF, Shi J, Kendler KS, Gejman PV, Webb BT. Genetic risk sum score comprised of common polygenic variation is associated with body mass index. Human Genetics. 129: 221-30. PMID 21104096 DOI: 10.1007/S00439-010-0917-1  0.402
2011 Chen X, Lee G, Maher BS, Fanous AH, Chen J, Zhao Z, Guo A, van den Oord E, Sullivan PF, Shi J, Levinson DF, Gejman PV, Sanders A, Duan J, Owen MJ, et al. GWA study data mining and independent replication identify cardiomyopathy-associated 5 (CMYA5) as a risk gene for schizophrenia. Molecular Psychiatry. 16: 1117-29. PMID 20838396 DOI: 10.1038/Mp.2010.96  0.387
2011 Shi J, Potash JB, Knowles JA, Weissman MM, Coryell W, Scheftner WA, Lawson WB, DePaulo JR, Gejman PV, Sanders AR, Johnson JK, Adams P, Chaudhury S, Jancic D, Evgrafov O, et al. Genome-wide association study of recurrent early-onset major depressive disorder. Molecular Psychiatry. 16: 193-201. PMID 20125088 DOI: 10.1038/Mp.2009.124  0.4
2010 Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, Jackson AU, Lango Allen H, Lindgren CM, Luan J, Mägi R, Randall JC, Vedantam S, Winkler TW, Qi L, Workalemahu T, ... ... Shi J, et al. Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature Genetics. 42: 937-48. PMID 20935630 DOI: 10.1038/Ng.686  0.34
2010 Lango Allen H, Estrada K, Lettre G, Berndt SI, Weedon MN, Rivadeneira F, Willer CJ, Jackson AU, Vedantam S, Raychaudhuri S, Ferreira T, Wood AR, Weyant RJ, Segrè AV, Speliotes EK, ... ... Shi J, et al. Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 467: 832-8. PMID 20881960 DOI: 10.1038/Nature09410  0.421
2010 Dao DT, Mahon PB, Cai X, Kovacsics CE, Blackwell RA, Arad M, Shi J, Zandi PP, O'Donnell P, Knowles JA, Weissman MM, Coryell W, Scheftner WA, Lawson WB, et al. Mood disorder susceptibility gene CACNA1C modifies mood-related behaviors in mice and interacts with sex to influence behavior in mice and diagnosis in humans. Biological Psychiatry. 68: 801-10. PMID 20723887 DOI: 10.1016/J.Biopsych.2010.06.019  0.314
2010 Gerstenblith MR, Shi J, Landi MT. Genome-wide association studies of pigmentation and skin cancer: A review and meta-analysis Pigment Cell and Melanoma Research. 23: 587-606. PMID 20546537 DOI: 10.1111/J.1755-148X.2010.00730.X  0.35
2010 Sanders AR, Levinson DF, Duan J, Dennis JM, Li R, Kendler KS, Rice JP, Shi J, Mowry BJ, Amin F, Silverman JM, Buccola NG, Byerley WF, Black DW, Freedman R, et al. The Internet-based MGS2 control sample: self report of mental illness. The American Journal of Psychiatry. 167: 854-65. PMID 20516154 DOI: 10.1176/Appi.Ajp.2010.09071050  0.314
2010 Furberg H, Kim Y, Dackor J, Boerwinkle E, Franceschini N, Ardissino D, Bernardinelli L, Mannucci PM, Mauri F, Merlini PA, Absher D, Assimes TL, Fortmann SP, Iribarren C, Knowles JW, ... ... Shi J, et al. Genome-wide meta-analyses identify multiple loci associated with smoking behavior Nature Genetics. 42: 441-447. PMID 20418890 DOI: 10.1038/Ng.571  0.346
2010 Gerstenblith MR, Shi J, Landi MT. Abstract 4719: Genome-wide association studies of pigmentation and skin cancer: A meta-analysis Cancer Research. 70: 4719-4719. DOI: 10.1158/1538-7445.Am10-4719  0.372
2010 Derks EM, Gladwin T, Rietschel M, Mattheisen M, Breuer R, Schulze TG, Nothen MM, Levinson D, Shi J, Cichon S, Freimer NB, Cantor R, Ophoff RA. SEGMENT-WISE GENOME-WIDE ASSOCIATION ANALYSIS IDENTIFIES A LIMITED NUMBER OF REPLICABLE CANDIDATE REGIONS ASSOCIATED WITH SCHIZOPHRENIA Schizophrenia Research. 117: 219. DOI: 10.1016/J.Schres.2010.02.312  0.325
2009 Mahon PB, Payne JL, MacKinnon DF, Mondimore FM, Goes FS, Schweizer B, Jancic D, Coryell WH, Holmans PA, Shi J, Knowles JA, Scheftner WA, Weissman MM, et al. Genome-wide linkage and follow-up association study of postpartum mood symptoms. The American Journal of Psychiatry. 166: 1229-37. PMID 19755578 DOI: 10.1176/Appi.Ajp.2009.09030417  0.359
2009 Shi J, Levinson DF, Duan J, Sanders AR, Zheng Y, Pe'er I, Dudbridge F, Holmans PA, Whittemore AS, Mowry BJ, Olincy A, Amin F, Cloninger CR, Silverman JM, Buccola NG, et al. Common variants on chromosome 6p22.1 are associated with schizophrenia. Nature. 460: 753-7. PMID 19571809 DOI: 10.1038/Nature08192  0.39
2009 Dupuis J, Shi J, Manning AK, Benjamin EJ, Meigs JB, Cupples LA, Siegmund D. Mapping quantitative traits in unselected families: algorithms and examples. Genetic Epidemiology. 33: 617-27. PMID 19278016 DOI: 10.1002/Gepi.20413  0.632
2008 Sanders AR, Duan J, Levinson DF, Shi J, He D, Hou C, Burrell GJ, Rice JP, Nertney DA, Olincy A, Rozic P, Vinogradov S, Buccola NG, Mowry BJ, Freedman R, et al. No significant association of 14 candidate genes with schizophrenia in a large European ancestry sample: implications for psychiatric genetics. The American Journal of Psychiatry. 165: 497-506. PMID 18198266 DOI: 10.1176/Appi.Ajp.2007.07101573  0.384
2007 Shi J, Siegmund DO, Levinson DF. Statistical corrections of linkage data suggest predominantly cis regulations of gene expression. Bmc Proceedings. 1: S145. PMID 18466489 DOI: 10.1186/1753-6561-1-S1-S145  0.638
2007 Shi J, Siegmund D, Yakir B. Importance Sampling for Estimating p Values in Linkage Analysis Journal of the American Statistical Association. 102: 929-937. DOI: 10.1198/016214507000000680  0.619
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