Software

Please see lab’s github page also.

 

• GeneMAP
  1. GeneMAP: A discovery platform for metabolic gene function. Artem Khan, Gokhan Unlu, Phillip Lin, Yuyang Liu, Ece Kilic, Timothy C. Kenny, Kıvanç Birsoy*, Eric R. Gamazon*. bioRxiv. 2024. doi: 10.1101/2023.12.07.570588. *Co-corresponding authors.
• NeuroimaGene
  1.  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: 10.1016/j.ajhg.2024.06.002.
• Root Causal Strength using Perturbations (RCSP)
  1. Discovering root causal genes with high throughput perturbations. Eric V. Strobl, Eric R. Gamazon. bioRxiv. 2024. doi: 10.1101/2024.01.13.574491.
• Root and Treated Root causal Effects (R-TRE)
  1. Mitigating pathogenesis for target discovery and disease subtyping. Eric V. Strobl, Thomas A. Lasko, Eric R. Gamazon. medRxiv. 2023. doi: 10.1101/2023.08.12.23294026. 
• HYFA
  1.  Hypergraph factorisation for multi-tissue gene expression imputation. Viñas R, Joshi CK, Georgiev D, Lin P, Dumitrascu B*, Gamazon ER*, and Liò P*. doi: 10.1038/s42256-023-00684-8. *Co-corresponding authors.
• MR-JTI
  1.  A unified framework for joint-tissue transcriptome-wide association and Mendelian randomization analysis. Zhou D, Jiang Y, Zhong X, Cox NJ, Liu C, Gamazon ER. Nature Genetics. 2020. doi: 10.1038/s41588-020-0706-2
• PrediXcan
  1.  A gene-based association method for mapping traits using reference transcriptome data. 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.
• Local_ancestry
  1.  On using local ancestry to characterize the genetic architecture of human phenotypes: Genetic regulation of gene expression in multiethnic or admixed populations as a model. Zhong Y, Perera M, Gamazon ER. American Journal of Human Genetics. 2019. 104(6):1097-1115. doi: 10.1016/j.ajhg.2019.04.009.
• neanderthal_predixcan_manuscript
  1.  Inferred divergent gene regulation in archaic hominins reveals potential phenotypic differences. Colbran LL, Gamazon ER, Zhou D, et al. Nature Ecology & Evolution. 2019 Oct 7. doi: 10.1038/s41559-019-0996-x. PMID: 31591491.
• SCAN: SNP and CNV annotation database (GEO: GSE9703, GSE39672)
  1.  SCAN: 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.
  2.  Trait-associated SNPs are more likely to be eQTLs: annotation to enhance discovery from GWAS. Nicolae DL, Gamazon E, Zhang W, Duan S, Dolan ME, et al. PLoS Genetics. 2010 Apr 1;6(4):e1000888. PMID: 20369019.
  3.  SCAN database: facilitating integrative analyses of cytosine modification and expression QTL. Zhang W*, Gamazon ER*, Zhang X*, Konkashbaev A, Liu C, Szilágyi KL, Dolan ME, Cox NJ. Database (Oxford). 2015 Mar 27;2015. pii: bav025. doi: 10.1093/database/bav025. Print 2015. PMID: 25818895. *Contributed equally.
• PACdb: a pharmacogenetics-cell line database
  1.  PACdb: 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.
  2.  Chemotherapeutic 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.
• ExprTargetDB: An expression-corroborated catalogue of human microRNA targets (GEO: GSE34406)
  1.  Exprtarget: 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.
• OmicKriging R package
  1.  Poly-Omic Prediction of Complex Traits: OmicKriging. 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.
• eFDR
  1.  Integrative 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.
• GxTheta
  1.  An ancestry based approach for detecting interactions. Park DS, Eskin I, Kang EY, Gamazon ER, Eng C, Gignoux CR, Galanter JM, Burchard E, et al.
• MixRF
  1.  Imputing Gene Expression in Uncollected Tissues Within and Beyond GTEx. 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.