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Software

Please see lab’s github page also.

  • 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.
  • Local_ancestry
    1. Zhong Y, Perera M, Gamazon ER. On using local ancestry to characterize the genetic architecture of human phenotypes: Genetic regulation of gene expression in a multiethnic or admixed populations as a model. In revision.
  • 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.
  • 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.