{"id":79,"date":"2015-12-24T13:55:15","date_gmt":"2015-12-24T18:55:15","guid":{"rendered":"https:\/\/my.vanderbilt.edu\/ericgamazon\/?page_id=79"},"modified":"2025-07-18T23:14:44","modified_gmt":"2025-07-19T04:14:44","slug":"software","status":"publish","type":"page","link":"https:\/\/my.vanderbilt.edu\/ericgamazon\/software\/","title":{"rendered":"Software"},"content":{"rendered":"<p>Please see lab&#8217;s <a href=\"https:\/\/github.com\/gamazonlab\" target=\"_blank\" rel=\"noopener\">github<\/a> page also.<\/p>\n<p>&nbsp;<\/p>\n<ul>\n<li class=\"TYR86d zfr3Q\"><a class=\"XqQF9c\" href=\"https:\/\/gamazonlab.shinyapps.io\/GeneMAP\/\" target=\"_blank\" rel=\"noopener\">GeneMAP<\/a>\n<ol>\n<li class=\"zfr3Q TYR86d lsiHE \">Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import. Artem Khan, Gokhan Unlu, Phillip Lin, Yuyang Liu, Ece Kilic, Timothy C. Kenny, K\u0131van\u00e7 Birsoy*, Eric R. Gamazon*. Nature Genetics. 2024. doi: <span class=\"C9DxTc \"><span class=\"c-bibliographic-information__value\">10.1038\/s41588-024-01827-2<\/span>. *Co-corresponding authors.<\/span><\/li>\n<\/ol>\n<\/li>\n<li><a class=\"XqQF9c\" href=\"https:\/\/cran.r-project.org\/web\/packages\/neuroimaGene\/index.html\" target=\"_blank\" rel=\"noopener\"><span class=\"C9DxTc aw5Odc \">NeuroimaGene<\/span><\/a>\n<ol>\n<li>\u00a0<span class=\"C9DxTc \">A transcriptomic atlas of the human brain reveals genetically determined aspects of neuropsychiatric health. Xavier Bledsoe, Eric R. Gamazon. American Journal of Human Genetics. 2024. doi: <\/span><a class=\"XqQF9c\" href=\"https:\/\/doi.org\/10.1016\/j.ajhg.2024.06.002\" target=\"_blank\" rel=\"noopener\"><span class=\"C9DxTc aw5Odc \">10.1016\/j.ajhg.2024.06.002<\/span><\/a><span class=\"C9DxTc \">.<\/span><\/li>\n<\/ol>\n<\/li>\n<li class=\"TYR86d zfr3Q\"><a href=\"https:\/\/github.com\/ericstrobl\/RCSP\">Root Causal Strength using Perturbations<\/a> (RCSP)\n<ol>\n<li class=\"TYR86d zfr3Q\">Discovering root causal genes with high throughput perturbations. Eric V. Strobl, Eric R. Gamazon. bioRxiv. 2024. doi: <a href=\"https:\/\/doi.org\/10.1101\/2024.01.13.574491\">10.1101\/2024.01.13.574491<\/a>.<\/li>\n<\/ol>\n<\/li>\n<li class=\"TYR86d zfr3Q\"><a class=\"XqQF9c\" href=\"https:\/\/github.com\/ericstrobl\/RTRE\" target=\"_blank\" rel=\"noopener\">Root and Treated Root causal Effects<\/a> (R-TRE)\n<ol>\n<li class=\"TYR86d zfr3Q\"><span class=\"C9DxTc \">Mitigating pathogenesis for target discovery and disease subtyping. Eric V. Strobl, Thomas A. Lasko, Eric R. Gamazon. medRxiv. 2023. doi: <\/span><a class=\"XqQF9c\" href=\"https:\/\/doi.org\/10.1101\/2023.08.12.23294026\" target=\"_blank\" rel=\"noopener\"><span class=\"C9DxTc aw5Odc \">10.1101\/2023.08.12.23294026<\/span><\/a><span class=\"C9DxTc \">.<\/span><span class=\"C9DxTc \">\u00a0<\/span><\/li>\n<\/ol>\n<\/li>\n<li class=\"TYR86d zfr3Q\"><a href=\"https:\/\/github.com\/rvinas\/HYFA\" target=\"_blank\" rel=\"noopener\">HYFA<\/a>\n<ol>\n<li class=\"TYR86d zfr3Q\">\u00a0Hypergraph factorisation for multi-tissue gene expression imputation. Vi\u00f1as R, Joshi CK, Georgiev D, Lin P, Dumitrascu B*, Gamazon ER*, and Li\u00f2 P*. Nature Machine Intelligence. 2023. <span class=\"C9DxTc \">doi: <\/span><a class=\"XqQF9c\" href=\"https:\/\/doi.org\/10.1038\/s42256-023-00684-8\" target=\"_blank\" rel=\"noopener\"><span class=\"C9DxTc aw5Odc \">10.1038\/s42256-023-00684-8<\/span><\/a><span class=\"C9DxTc \">. <\/span>*Co-corresponding authors.<\/li>\n<\/ol>\n<\/li>\n<li class=\"TYR86d zfr3Q\"><a class=\"XqQF9c\" href=\"https:\/\/github.com\/gamazonlab\/MR-JTI\" target=\"_blank\" rel=\"noopener\">MR-JTI<\/a>\n<ol class=\"n8H08c BKnRcf\">\n<li class=\"TYR86d zfr3Q\">\u00a0<a class=\"XqQF9c\" href=\"https:\/\/www.nature.com\/articles\/s41588-020-0706-2\" target=\"_blank\" rel=\"noopener\">A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis<\/a>. Zhou D, Jiang Y, Zhong X, Cox NJ, Liu C, Gamazon ER. Nature Genetics. 2020. doi: <span class=\" aw5Odc\"><a class=\"XqQF9c\" href=\"https:\/\/www.nature.com\/articles\/s41588-020-0706-2\" target=\"_blank\" rel=\"noopener\">10.1038\/s41588-020-0706-2<\/a> <\/span><\/li>\n<\/ol>\n<\/li>\n<li><a href=\"https:\/\/github.com\/gamazonlab\/PrediXcan\" target=\"_blank\" rel=\"noopener\">PrediXcan<\/a>\n<ol>\n<li>\u00a0<a href=\"https:\/\/www.nature.com\/articles\/ng.3367\" target=\"_blank\" rel=\"noopener\">A gene-based association method for mapping traits using reference transcriptome data<\/a>. Gamazon ER, Wheeler HE, Shah KP, Mozaffari SV, Aquino-Michaels K, Carroll RJ, Eyler AE, Denny JC; GTEx Consortium, Nicolae DL, Cox NJ, Im HK. Nature Genetics. 2015 Aug 10. doi: 10.1038\/ng.3367. [Epub ahead of print] PMID: 26258848.<\/li>\n<\/ol>\n<\/li>\n<li><a class=\"dhtgD\" href=\"https:\/\/github.com\/gamazonlab\/Local_ancestry\" target=\"_blank\" rel=\"noopener\">Local_ancestry<\/a>\n<ol class=\"n8H08c BKnRcf\">\n<li id=\"h.p_z44oZ_pOqWjA\" class=\"zfr3Q TYR86d\">\u00a0On using local ancestry to characterize the genetic architecture of human phenotypes: Genetic regulation of gene expression in multiethnic or admixed populations as a model.\u00a0Zhong Y, Perera M, Gamazon ER. American Journal of Human Genetics. 2019. 104(6):1097-1115. doi: <span class=\" aw5Odc\"><a class=\"XqQF9c\" href=\"https:\/\/www.cell.com\/ajhg\/fulltext\/S0002-9297(19)30155-7\" target=\"_blank\" rel=\"noopener\">10.1016\/j.ajhg.2019.04.009<\/a><\/span>.<\/li>\n<\/ol>\n<\/li>\n<li><a class=\"dhtgD aw5Odc\" href=\"https:\/\/github.com\/gamazonlab\/neanderthal_predixcan_manuscript\" target=\"_blank\" rel=\"noopener\">neanderthal_predixcan_manuscript<\/a>\n<ol>\n<li>\u00a0<a class=\"dhtgD aw5Odc\" href=\"https:\/\/www.nature.com\/articles\/s41559-019-0996-x\" target=\"_blank\" rel=\"noopener\">Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences<\/a>. Colbran LL, Gamazon ER, Zhou D, et al. Nature Ecology &amp; Evolution. 2019 Oct 7. doi: 10.1038\/s41559-019-0996-x. PMID: 31591491.<\/li>\n<\/ol>\n<\/li>\n<li style=\"text-align: left\"><a href=\"http:\/\/www.scandb.org\" target=\"_blank\" rel=\"noopener\">SCAN<\/a>: SNP and CNV annotation database (GEO:\u00a0<a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE9703\" target=\"_blank\" rel=\"noopener\">GSE9703<\/a>, <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE39672\" target=\"_blank\" rel=\"noopener\">GSE39672)<\/a>\n<ol>\n<li>\u00a0SCAN: SNP and copy number annotation. Gamazon ER, Zhang W, Konkashbaev A, Duan S, Kistner EO, et al. Bioinformatics. 2010 Jan 15;26(2):259-62. PMID: 19933162.<\/li>\n<li>\u00a0<a href=\"http:\/\/www.plosgenetics.org\/article\/info%3Adoi%2F10.1371%2Fjournal.pgen.1000888\" target=\"_blank\" rel=\"noopener\">Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS<\/a>. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. PLoS Genetics. 2010 Apr 1;6(4):e1000888. PMID: 20369019.<\/li>\n<li>\u00a0SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. Zhang W*, Gamazon ER*, Zhang X*, Konkashbaev A, Liu C, Szil\u00e1gyi KL, Dolan ME, Cox NJ. Database (Oxford). 2015 Mar 27;2015. pii: bav025. doi: 10.1093\/database\/bav025. Print 2015. PMID: 25818895. *Contributed equally.<\/li>\n<\/ol>\n<\/li>\n<li><a href=\"http:\/\/www.pacdb.org\" target=\"_blank\" rel=\"noopener\">PACdb<\/a>: a pharmacogenetics-cell line database\n<ol>\n<li>\u00a0PACdb: a database for cell-based pharmacogenomics. Gamazon ER, Duan S, Zhang W, Huang RS, Kistner EO, et al. Pharmacogenet Genomics. 2010 Apr;20(4):269-73. PMID: 20216476.<\/li>\n<li>\u00a0Chemotherapeutic drug susceptibility associated SNPs are enriched in expression quantitative trait loci. Gamazon ER, Huang RS, Cox NJ, Dolan ME. Proceedings of the National Academy of Sciences. 2010 May 18;107(20):9287-92. Epub 2010 May 4. PMID: 20442332.<\/li>\n<\/ol>\n<\/li>\n<li><a href=\"https:\/\/github.com\/egamazon\/ExprTargetDB\" target=\"_blank\" rel=\"noopener\">ExprTargetDB<\/a>: An expression-corroborated catalogue of human microRNA targets (GEO: <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/geo\/query\/acc.cgi?acc=GSE34406\" target=\"_blank\" rel=\"noopener\">GSE34406<\/a>)\n<ol>\n<li>\u00a0Exprtarget: an integrative approach to predicting human microRNA targets. Gamazon ER, Im HK, Duan S, Lussier YA, Cox NJ, et al. PLoS One. 2010 Oct 21;5(10):e13534. PMID: 20975837.<\/li>\n<\/ol>\n<\/li>\n<li><a href=\"http:\/\/www.scandb.org\/newinterface\/tools\/OmicKriging.html\" target=\"_blank\" rel=\"noopener\">OmicKriging<\/a> R package\n<ol>\n<li>\u00a0<a href=\"http:\/\/onlinelibrary.wiley.com\/doi\/10.1002\/gepi.21808\/abstract\" target=\"_blank\" rel=\"noopener\">Poly-Omic Prediction of Complex Traits: OmicKriging<\/a>. Wheeler HE, Aquino-Michaels K, Gamazon ER, Trubetskoy VV, Dolan ME, Huang RS, Cox NJ and Im HK. (2014), Poly-Omic Prediction of Complex Traits: OmicKriging. Genetic Epidemiology. doi: 10.1002\/gepi.21808.<\/li>\n<\/ol>\n<\/li>\n<li><a href=\"http:\/\/www.scandb.org\/newinterface\/empiricalFDR.R\" target=\"_blank\" rel=\"noopener\">eFDR<\/a>\n<ol>\n<li>\u00a0Integrative Genomics: Quantifying significance of phenotype-genotype relationships from multiple sources of high-throughput data. Gamazon ER, Huang RS, Dolan ME, Cox NJ, Im HK. Frontiers in Statistical Genetics and Methodology. 3:202. doi: 10.3389\/fgene.2012.00202. PMID: 23755062.<\/li>\n<\/ol>\n<\/li>\n<li><a href=\"https:\/\/github.com\/gamazonlab\/GxTheta\" target=\"_blank\" rel=\"noopener\">GxTheta<\/a>\n<ol>\n<li>\u00a0<a href=\"https:\/\/onlinelibrary.wiley.com\/doi\/abs\/10.1002\/gepi.22087\" target=\"_blank\" rel=\"noopener\">An ancestry based approach for detecting interactions<\/a>. Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, et al.<\/li>\n<\/ol>\n<\/li>\n<li><a href=\"https:\/\/github.com\/randel\/MixRF\" target=\"_blank\" rel=\"noopener\">MixRF<\/a>\n<ol>\n<li>\u00a0<a href=\"http:\/\/www.cell.com\/ajhg\/fulltext\/S0002-9297%2816%2900071-9\" target=\"_blank\" rel=\"noopener\">Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx<\/a>. Wang J, Gamazon ER, Pierce BL, Stranger BE, Im HK, Gibbons RD, Cox NJ, Nicolae DL, Chen LS. American Journal of Human Genetics. 2016 Mar 29. pii: S0002-9297(16)00071-9. doi: 10.1016\/j.ajhg.2016.02.020. [Epub ahead of print] PMID: 27040689.<\/li>\n<\/ol>\n<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Please see lab&#8217;s github page also. &nbsp; GeneMAP Metabolic gene function discovery platform GeneMAP identifies SLC25A48 as necessary for mitochondrial choline import. Artem Khan, Gokhan Unlu, Phillip Lin, Yuyang Liu, Ece Kilic, Timothy C. Kenny, K\u0131van\u00e7 Birsoy*, Eric R. Gamazon*. Nature Genetics. 2024. doi: 10.1038\/s41588-024-01827-2. *Co-corresponding authors. NeuroimaGene \u00a0A transcriptomic atlas of the human brain&#8230;<\/p>\n","protected":false},"author":3547,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"tags":[],"class_list":["post-79","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/pages\/79","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/users\/3547"}],"replies":[{"embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/comments?post=79"}],"version-history":[{"count":43,"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/pages\/79\/revisions"}],"predecessor-version":[{"id":1327,"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/pages\/79\/revisions\/1327"}],"wp:attachment":[{"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/media?parent=79"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/my.vanderbilt.edu\/ericgamazon\/wp-json\/wp\/v2\/tags?post=79"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}