{"id":8,"date":"2024-01-24T16:25:25","date_gmt":"2024-01-24T16:25:25","guid":{"rendered":"https:\/\/keck.usc.edu\/statistical-genomics-center\/?page_id=8"},"modified":"2025-02-05T10:26:33","modified_gmt":"2025-02-05T18:26:33","slug":"publications","status":"publish","type":"page","link":"https:\/\/keck.usc.edu\/statistical-genomics-center\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"\n\n\n\n\n  \n\n  \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--hero-primary horizontal-navigation\"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--hero-primary\"\n    \n      >\n\n    \n  \n  <div class=\"inner-wrapper has-horizontal-nav\">\n\n          <div class=\"title-wrapper\">\n\n                  <div class=\"eyebrow-container\">\n                              \n<div class=\"f--field f--eyebrow\">\n\n    \n  <a href=\"https:\/\/keck.usc.edu\/statistical-genomics-center\/\"  aria-label=\"Read more about Center for Statistical Genomics\">Center for Statistical Genomics<\/a>\n\n\n\n<\/div>\n                      <\/div>\n        \n                      \n<div class=\"f--field f--page-title has-stripe\">\n\n    \n  <h1>Publications<\/h1>\n\n\n<\/div>\n        \n              <\/div>\n    \n              \n<div class=\"f--field f--link eyebrow-link\">\n\n    \n    \n  \n<a\n  class=\"link \"\n  href=\"https:\/\/github.com\/USCbiostats\/software-dev\/blob\/master\/happy_scientist\/README.md\"\n  target=\"_blank\"  aria-label=\"Read&#x20;more&#x20;about&#x20;Happy&#x20;Scientist&#x20;Seminars\">\n        Happy Scientist Seminars\n    <\/a>\n\n\n<\/div>\n    \n    \n      \n              <div class=\"horizontal-nav\">\n                      <div class=\"horizontal-menu-container\">\n              <button class=\"expand-menu\">\n                                  In This Section\n                                <svg class=\"menu\" version=\"1.1\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\" 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href=\"https:\/\/keck.usc.edu\/statistical-genomics-center\/projects\/project-2-integration-of-omic-data-in-the-analysis-of-gene-x-environment-interaction\/\" >Project 2:\u00a0Integration of Omic Data in the Analysis of Gene \u00d7 Environment Interaction<\/a>\n  \n  \n<\/li>\n                      <li class=\" menu-item menu-item-type-post_type menu-item-object-page menu-item-26\">\n      <a href=\"https:\/\/keck.usc.edu\/statistical-genomics-center\/projects\/project-3-statistical-methods-for-genome-characterization\/\" >Project 3:\u00a0Statistical Methods for Genome Characterization<\/a>\n  \n  \n<\/li>\n                  <\/ul>\n      <\/div>\n    <\/div>\n  \n<\/li>\n\n    \n      <li class=\" menu-item menu-item-type-custom menu-item-object-custom menu-item-30\">\n      <a href=\"https:\/\/github.com\/USCbiostats\" >Software<\/a>\n  \n  \n<\/li>\n\n    \n      <li class=\" menu-item menu-item-type-post_type menu-item-object-page menu-item-17\">\n      <a 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class=\"cc--component-container cc--accordions \"\n\n  \n   aria-label=\"Content Accordions\"\n  \n  \n  \n  \n  >\n  <div class=\"c--component c--accordions\"\n    \n      >\n\n    \n      <div class=\"header-container\">\n\n                  \n<div class=\"f--field f--section-title\">\n\n    \n  <h2>\n          Recent Research\n      <\/h2>\n\n\n<\/div>\n      \n      \n    <\/div>\n  \n      <ul>\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-1-B7RBMaaT4s\" aria-controls=\"section-1-1-B7RBMaaT4s\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">2025<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-1-B7RBMaaT4s\" role=\"region\" aria-labelledby=\"heading-1-1-B7RBMaaT4s\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n  <div class=\"inner-wrapper\">\n        \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <ul>\n<li><span style=\"font-weight: 400;\">Zhang Z, Kim A, Suboc N, Mancuso N, Gazal S. Efficient count-based models improve power and robustness for large-scale single-cell eQTL mapping. <\/span><a href=\"https:\/\/www.medrxiv.org\/content\/10.1101\/2025.01.18.25320755v1\"><span style=\"font-weight: 400;\">https:\/\/www.medrxiv.org\/content\/10.1101\/2025.01.18.25320755v1<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Zhao et al. LUCIDus: An R Package For Estimating Latent Unknown Clusters By Integrating Multi-omics Data (LUCID) With Phenotypic Traits. R Journal.\u00a0 (<\/span><i><span style=\"font-weight: 400;\">in press<\/span><\/i><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n\n\n\n<\/div>\n  <\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-2-B7RBMaaT4s\" aria-controls=\"section-1-2-B7RBMaaT4s\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">2024<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-2-B7RBMaaT4s\" role=\"region\" aria-labelledby=\"heading-1-2-B7RBMaaT4s\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n  <div class=\"inner-wrapper\">\n        \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <ul>\n<li><span style=\"font-weight: 400;\">Arai H, et al. Predictive value of CDC37 gene expression for targeted therapy in metastatic colorectal cancer. Eur J Cancer, 2024. Apr:201:113914. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38359495\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Battaglin F, et al. CCR5 and CCL5 gene expression in colorectal cancer: comprehensive profiling and clinical value. J Immunother Cancer, 2024. 12(1). (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38212126\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Bradfield JP, et al. Trans-ancestral genome-wide association study of longitudinal pubertal height growth and shared heritability with adult health outcomes. Genome Biol, 2024. 25(1):22 (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38773652\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Chen Z, et al. Fine-mapping analysis including over 254,000 East Asian and European descendants identifies 136 putative colorectal cancer susceptibility genes. Nat Commun, 2024. 15(1):3557. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38670944\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Drew DA, et al. Two genome-wide interaction loci modify the association of nonsteroidal anti-inflammatory drugs with colorectal cancer. Sci Adv, 2024. 10(22): eadk3121. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38809988\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Goodrich JA, et al. Integrating Multi-Omics with environmental data for precision health: A novel analytic framework and case study on prenatal mercury induced childhood fatty liver disease. Environ Int. 2024 Aug;190:108930. doi: 10.1016\/j.envint.2024.108930. Epub 2024 Aug 3. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39128376\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Goodrich J.A., et al. Postprandial Metabolite Profiles and Risk of Prediabetes in Young People: A Longitudinal Multicohort Study. Diabetes Care, 2024. 47(1):151-159. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/37971952\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Guirette M, et al.; CHARGE Gene-Lifestyle Interactions Working Group. Genome-Wide Interaction Analysis With DASH Diet Score Identified Novel Loci for Systolic Blood Pressure. Hypertension. 2024 Mar;81(3):552-560. doi: 10.1161\/HYPERTENSIONAHA.123.22334. Epub 2024 Jan 16. PMID: 38226488; PMCID: PMC10922535. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38226488\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Jiang L, Shen J, Darst BF, Haiman CA, Mancuso N, Conti DV. Hierarchical joint analysis of marginal summary statistics-Part II: High-dimensional instrumental analysis of omics data. Genet Epidemiol. 2024 Oct;48(7):291-309. doi: 10.1002\/gepi.22577. Epub 2024 Jun 17. PMID: 38887957. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38887957\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Lu Z, Wang X, Carr M, Kim A, Gazal S, Mohammadi P, Wu L, Gusev A, Pirruccello J, Kachuri L, Mancuso N. Improved multi-ancestry fine-mapping identifies cis-regulatory variants underlying molecular traits and disease risk, medRxiv, 2024 (<\/span><a href=\"https:\/\/www.medrxiv.org\/content\/10.1101\/2024.04.15.24305836v1\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Nagarajan P, et al. A Large-Scale Genome-Wide Study of Gene-Sleep Duration Interactions for Blood Pressure in 811,405 Individuals from Diverse Populations. medRxiv, 2024. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38496537\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Papadimitriou N, et al. Genome-wide interaction study of dietary intake of fibre, fruits, and vegetables with risk of colorectal cancer. EBioMedicine, 2024. 104:105146. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38749303\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Shen J, Jiang L, Wang K, Wang A, Chen F, Newcombe PJ, Haiman CA, Conti DV. Hierarchical joint analysis of marginal summary statistics-Part I: Multipopulation fine mapping and credible set construction. Genet Epidemiol. 2024 Sep;48(6):241-257. doi: 10.1002\/gepi.22562. Epub 2024 Apr 12. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38606643\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Tian Y, et al. Genetic risk impacts the association of menopausal hormone therapy with colorectal cancer risk. Br J Cancer, 2024. 130(10): 1687-1696. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38561434\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Zhao Y, Jia Q, Goodrich J, Darst B, Conti DV. An extension of latent unknown clustering integrating multi-omics data (LUCID) incorporating incomplete omics data. Bioinform Adv. 2024 Aug 24;4(1):vbae123. doi: 10.1093\/bioadv\/vbae123 (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/39224838\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Zhu X, et al.; CHARGE Gene-Lifestyle Interactions Working Group. An approach to identify gene-environment interactions and reveal new biological insight in complex traits. Nat<\/span> <span style=\"font-weight: 400;\">Commun, 2024. Apr 22;15(1):3385. doi: 10.1038\/s41467-024-47806-3. (<\/span><a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38649715\/\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<\/ul>\n\n\n\n<\/div>\n  <\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n              <li>\n          <button type=\"button\" class=\"accordion-trigger \" id=\"heading-1-3-B7RBMaaT4s\" aria-controls=\"section-1-3-B7RBMaaT4s\" aria-expanded=\"false\" aria-disabled=\"false\">\n                          <span class=\"item-title\">2023<\/span>\n            \n                      <\/button>\n\n          <div id=\"section-1-3-B7RBMaaT4s\" role=\"region\" aria-labelledby=\"heading-1-3-B7RBMaaT4s\" class=\"accordion-panel\">\n\n                            \n    \n\n\n\n\n\n\n<div\n  class=\"cc--component-container cc--rich-text \"\n\n  \n  \n  \n  \n  \n  \n  >\n  <div class=\"c--component c--rich-text\"\n    \n      >\n\n    \n  <div class=\"inner-wrapper\">\n        \n<div class=\"f--field f--wysiwyg\">\n\n    \n  <ul>\n<li><span style=\"font-weight: 400;\">Aglago EK, et al. (2023). A genetic locus within the FMN1\/GREM1 gene region interacts with body mass index in colorectal cancer risk. Cancer Res. (<\/span><a href=\"https:\/\/aacrjournals.org\/cancerres\/article\/83\/15\/2572\/728086\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Carreras-Torres R, et al. (2023). Genome-wide Interaction Study with Smoking for Colorectal Cancer Risk Identifies Novel Genetic Loci Related to Tumor Suppression, Inflammation, and Immune Response. Cancer Epidemiol Biomarkers Prev 32, 315-328. (<\/span><a href=\"https:\/\/aacrjournals.org\/cebp\/article-abstract\/32\/3\/315\/718496\/Genome-wide-Interaction-Study-with-Smoking-for)\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Chen F, et al. (2023). Evidence of Novel Susceptibility Variants for Prostate Cancer and a Multiancestry Polygenic Risk Score Associated with Aggressive Disease in Men of African Ancestry. Eur Urol 84, 13-21. (<\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S0302283823025617?casa_token=HBpPPEmB3xAAAAAA:NFnDy--Ti64BV4ZeFZihSWVCh-tw0Kc2GkCObtXbXmF0K3jfPb4BUOSiEnKzNkRbgwJxExHhEQ\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Darst BF et al. (2023). Evaluating approaches for constructing polygenic risk scores for prostate cancer in men of African and European ancestry. Am J Hum Genet. 7:1200-1206. (<\/span><a href=\"https:\/\/www.cell.com\/ajhg\/pdf\/S0002-9297(23)00167-2.pdf\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Dimou N, et al. (2023). Probing the diabetes and colorectal cancer relationship using gene \u2013 environment interaction analyses. Br J Cancer. 129:511-520. (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41416-023-02312-z\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Fernandez-Rozadilla C, et al. (2023). Deciphering colorectal cancer genetics through multi-omic analysis of 100,204 cases and 154,587 controls of European and east Asian ancestries. Nat Genet 55, 89-99. (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41588-022-01222-9\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Goodrich JA, et al. (2023). Metabolic Signatures of Youth Exposure to Mixtures of Per- and Polyfluoroalkyl Substances: A Multi-Cohort Study. Environ Health Perspect 131, 27005. (<\/span><a href=\"https:\/\/ehp.niehs.nih.gov\/doi\/full\/10.1289\/EHP11372\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Hou K, et al. (2023). Causal effects on complex traits are similar for common variants across segments of different continental ancestries within admixed individuals. Nat Genet 55, 549-558. (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41588-023-01338-6\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Kawaguchi ES, Kim AE, Lewinger JP, and Gauderman WJ. (2023). Improved two-step testing of genome-wide gene-environment interactions. Genet Epidemiol 47, 152-166. (<\/span><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/gepi.22509\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Mills C, Marconett CN, Lewinger JP, and Mi H. (2023). PEACOCK: a machine learning approach to assess the validity of cell type-specific enhancer-gene regulatory relationships. NPJ Syst Biol Appl 9, 9. (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41540-023-00270-z\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Queen K, Nguyen MN, Gilliland FD, Chun S, Raby BA, and Millstein J. (2023). ACDC: a general approach for detecting phenotype or exposure associated co-expression. Front Med (Lausanne) 10, 1118824. (<\/span><a href=\"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmed.2023.1118824\/full\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Sharma N and Millstein J. (2023). CausNet: generational orderings based search for optimal Bayesian networks via dynamic programming with parent set constraints. BMC Bioinformatics 24, 46. (<\/span><a href=\"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-023-05159-6\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Thomas M, et al. (2023). Combining Asian-European Genome-Wide Association Studies of Colorectal Cancer Improves Risk Prediction Across Race and Ethnicity. medRxiv. 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(2022). Transcriptomic Response to Calcium in Normal Colon Organoids is Impacted by Colon Location and Sex. Cancer Prev Res (Phila) 15, 679-688. (<\/span><a href=\"https:\/\/aacrjournals.org\/cancerpreventionresearch\/article\/15\/10\/679\/709273\/Transcriptomic-Response-to-Calcium-in-Normal-Colon\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Goodrich JA, Walker D, Lin X, Wang H, Lim T, McConnell R, Conti DV, Chatzi L, and Setiawan VW (2022). Exposure to perfluoroalkyl substances and risk of hepatocellular carcinoma in a multiethnic cohort. JHEP Rep 4, 100550. (<\/span><a href=\"https:\/\/www.sciencedirect.com\/science\/article\/pii\/S2589555922001227\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Haas CB, et al. (2022). Interactions between folate intake and genetic predictors of gene expression levels associated with colorectal cancer risk. Sci Rep 12, 18852. (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41598-022-23451-y\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Jordahl KM, et al. (2022). Beyond GWAS of Colorectal Cancer: Evidence of Interaction with Alcohol Consumption and Putative Causal Variant for the 10q24.2 Region. Cancer Epidemiol Biomarkers Prev 31, 1077-1089. (<\/span><a href=\"https:\/\/aacrjournals.org\/cebp\/article\/31\/5\/1077\/694750\/Beyond-GWAS-of-Colorectal-Cancer-Evidence-of\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Kawaguchi ES, Li G, Lewinger JP, and Gauderman WJ. (2022). Two-step hypothesis testing to detect gene-environment interactions in a genome-wide scan with a survival endpoint. Stat Med 41, 1644-1657. (<\/span><a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/full\/10.1002\/sim.9319?casa_token=NE0wQcM9j9MAAAAA%3AYSEwA7iLzm95BwOhlLT7CkpXcbRzjicCwwAwz8QlPGdAQWVFiUY6f9xL_zwHqOM7M2K0zVeIMV5YYdk\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Laville V, et al. (2022). Gene-lifestyle interactions in the genomics of human complex traits. Eur J Hum Genet 30, 730-739. (<\/span><a href=\"https:\/\/www.nature.com\/articles\/s41431-022-01045-6\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Liu Z, Mushayahama T, Queme B, Ebert D, Muruganujan A, Mills C, Thomas PD, and Mi H. (2022). Annotation Query (AnnoQ): an integrated and interactive platform for large-scale genetic variant annotation. Nucleic Acids Res 50, W57-W65. (<\/span><a href=\"https:\/\/academic.oup.com\/nar\/article\/50\/W1\/W57\/6595265\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Lu Z, Gopalan S, Yuan D, Conti DV, Pasaniuc B, Gusev A, and Mancuso, N. (2022). Multi-ancestry fine-mapping improves precision to identify causal genes in transcriptome-wide association studies. Am J Hum Genet 109, 1388-1404. (<\/span><a href=\"https:\/\/www.cell.com\/ajhg\/pdf\/S0002-9297(22)00306-8.pdf\"><span style=\"font-weight: 400;\">Read here<\/span><\/a><span style=\"font-weight: 400;\">)<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Midya V, et al. (2022). Association of Prenatal Exposure to Endocrine-Disrupting Chemicals With Liver Injury in Children. JAMA Netw Open 5, e2220176. 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Spatial mutation patterns as markers of early colorectal tumor cell mobility. Proc Natl Acad Sci U S A. 2018 May 29;115(22):5774-5779. <\/span><a href=\"https:\/\/doi.org\/10.1073\/pnas.1716552115\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Thomas DC.\u00a0 Estimating the effect of targeted screening strategies: an application to colonoscopy and colorectal cancer. Epidemiology 2017, 28: 470-476. <\/span><a href=\"https:\/\/dx.doi.org\/10.1097%2FEDE.0000000000000668\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Thomas DC. What Does \u201cPrecision Medicine\u201d Have to Say About Prevention? Epidemiology 2017;28(4): 479-483. <\/span><a href=\"https:\/\/dx.doi.org\/10.1097%2FEDE.0000000000000667\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Pereira M, Thompson JR, Weichenberger CX, Thomas DC, Minelli C.\u00a0 Inclusion of biological knowledge in a Bayesian shrinkage model for joint estimation of SNP effects. Genetic Epidemiology 2017, 41:320-31. <\/span><a href=\"https:\/\/doi.org\/10.1002\/gepi.22038\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">McAllister K, et al.\u00a0 Current challenges and new opportunities for gene-environment interaction studies of complex diseases.\u00a0 American Journal of Epidemiology 2017:186:753-761. <\/span><a href=\"https:\/\/doi.org\/10.1093\/aje\/kwx227\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Ritchie MD, et al. 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Volume 154, Issue 8, June 2018, Pages 2152-2164.e19. <\/span><a href=\"https:\/\/doi.org\/10.1053\/j.gastro.2018.02.021\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Manrai AK, et al. (2017) Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health. Annu Rev Public Health. 38(1), 279-294. <\/span><a href=\"https:\/\/doi.org\/10.1146\/annurev-publhealth-082516-012737\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Raskin L, Guo Y, Du L, Clendenning M, Rosty C; Colon Cancer Family Registry (CCFR), Lindor NM, Gruber SB, Buchanan DD. (2017) Targeted sequencing of established and candidate colorectal cancer genes in the Colon CancerFamily Registry Cohort. Oncotarget. 2017; 8(55):93450-93463. <\/span><a href=\"https:\/\/doi.org\/10.18632\/oncotarget.18596\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Stram, DO. (2017). Multi-SNP Haplotype Analysis Methods for Association Analysis. In R. C. Elston (Ed.), Statistical Human Genetics: Methods and Protocols (pp. 485-504). New York, NY: Springer New York. <\/span><a href=\"https:\/\/doi.org\/10.1007\/978-1-4939-7274-6_24\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Sun R, Hu Z, Sottoriva A, Graham TA, Harpak A, Ma Z, Fischer JM, Shibata D, Curtis C. (2017) Between-region genetic divergence reflects the mode and tempo of tumor evolution. Nature Genetics, 49(7), 1015-1024. <\/span><a href=\"https:\/\/doi.org\/10.1038\/ng.3891\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Gauderman WJ, et al. (2017). Update on the State of the Science for Analytical Methods for Gene-Environment Interactions (GxE). American Journal of Epidemiology 2017; 186:762-770. <\/span><a href=\"https:\/\/doi.org\/10.1093\/aje\/kwx228\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Zhang Z, et al. (2017) Correction of confidence intervals in excess relative risk models using Monte Carlo dosimetry systems with shared errors. PLoS ONE, 12(4), e0174641. <\/span><a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0174641\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Zhao, J., Salomon, M. P., Shibata, D., Curtis, C., Siegmund, K., &amp; Marjoram, P. (2017). Early mutation bursts in colorectal tumors. PLoS ONE, 12(3), e0172516. <\/span><a href=\"https:\/\/doi.org\/10.1371\/journal.pone.0172516\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Reiner A, et al. Breast cancer family history and contralateral breast cancer risk in young women: An update from the Women\u2019s Environmental Cancer and Radiation Epidemiology Study. Journal of clinical oncology : official journal of the American Society of Clinical Oncology, 36(15), 1513\u20131520. <\/span><a href=\"https:\/\/doi.org\/10.1200\/JCO.2017.77.3424\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Assi N, et al. Metabolic signature of healthy lifestyle and its relationship with risk of hepatocellular carcinoma in a large European cohort. The American Journal of Clinical Nutrition, Volume 108, Issue 1, July 2018, Pages 117\u2013126, <\/span><a href=\"https:\/\/doi.org\/10.1093\/ajcn\/nqy074\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Dadaev, T, et al. Fine-mapping of Prostate Cancer Susceptibility Loci in a Large Meta-Analysis Identifies Candidate Causal Variants. Nature Communications volume 9, Article number: 2256 (2018). <\/span><a href=\"https:\/\/doi.org\/10.1038\/s41467-018-04109-8\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Gauderman, WJ, Lewinger JP, Conti, DV, Morrison, J, Kim, A, &amp; Thomas, DC (2017). A unified model for the analysis of gene environment interaction. American Journal of Epidemiology, Volume 188, Issue 4, April 2019, Pages 760\u2013767. <\/span><a href=\"https:\/\/doi.org\/10.1093\/aje\/kwy278\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Du M, et al. Genetic predisposition modifies the effect of multiple environmental factors on risk of colorectal tumors. JNCI.<\/span><\/li>\n<li><span style=\"font-weight: 400;\">Schmit SL, et al. Novel genetic susceptibility loci for colorectal cancer. JNCI: Journal of the National Cancer Institute, Volume 111, Issue 2, February 2019, Pages 146\u2013157. <\/span><a href=\"https:\/\/doi.org\/10.1093\/jnci\/djy099\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<li><span style=\"font-weight: 400;\">Huyghe JR, et al.. Discovery of common and rare risk loci for colorectal cancer. Nature Genetics volume 51, pages76\u201387(2019). <\/span><a href=\"https:\/\/doi.org\/10.1038\/s41588-018-0286-6\"><span style=\"font-weight: 400;\">(Read here)<\/span><\/a><\/li>\n<\/ul>\n\n\n\n<\/div>\n  <\/div>\n\n\n  <\/div><\/div>\n            \n                      <\/div>\n        <\/li>\n\n          <\/ul>\n  \n\n  <\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":5,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":true,"footnotes":""},"class_list":["post-8","page","type-page","status-publish","hentry"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.5 (Yoast SEO v27.5) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>Publications - Center for Statistical Genomics<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/keck.usc.edu\/statistical-genomics-center\/publications\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Publications\" \/>\n<meta property=\"og:url\" content=\"https:\/\/keck.usc.edu\/statistical-genomics-center\/publications\/\" \/>\n<meta property=\"og:site_name\" content=\"Center for Statistical Genomics\" \/>\n<meta property=\"article:modified_time\" content=\"2025-02-05T18:26:33+00:00\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:label1\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data1\" content=\"16 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/keck.usc.edu\\\/statistical-genomics-center\\\/publications\\\/\",\"url\":\"https:\\\/\\\/keck.usc.edu\\\/statistical-genomics-center\\\/publications\\\/\",\"name\":\"Publications - 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