Publications

  • Geeleher P, Wang F, Zhenyu Z, Fessler J, Grossman RL, Seoighe C, Huang RS: Cancer eQTLs can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. In press Genome Biology (preprint)
  • Geeleher P, Huang RS: Exploring the Link between the Germline and Somatic Genome in Cancer, Cancer discovery, 7(4); 354-5 (2017).
  • Geeleher P, Zhang Z, Wang F, Nath A, Bhutra S, Grossman R, Huang RS: Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies, Genome Research, 27:1743-1751 (2017).
  • Geeleher P, Gamazon E, Seoighe C, Cox NJ, Huang RS: Consistency in large pharmacogenomic studies, Nature, 540, E1-E2 (2016).
  • Geeleher P, Cox NJ, Huang RS: Cancer biomarker discovery is improved by accounting for variability in general levels of drug sensitivity in pre-clinical models, Genome Biology, 17:190 (2016).
  • Cannavo E, Khoueiry P, Garfield D, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel J and Furlong EEM: Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks, Current Biology, 26: 1-14 (2015).
  • Geeleher P, Loboda A, Lenkala D, Wang F, LaCroix B, Karovic S, Wang S, Nebozhyn M, Chisamore M, Hardwick J, Maitland M, Huang RS: Predicting response to histone deacetylase inhibitors using high-throughput genomics, Journal of the National Cancer Institute (JNCI), 107(11): djv247 (2015).
  • Korir P, Geeleher P, Seoighe C: Seq-ing improved gene expression estimates from microarrays using machine learning, BMC Bioinformatics, 16:286 (2015).
  • Geeleher P, Cox NJ, Huang RS: pRRophetic: An R package for prediction of clinical drug sensitivity from gene expression data, PLOS ONE, 9(9):e107468 (2014).
  • Wu K, Gamazon ER, Im HK, Geeleher P, White S, Solway J, Clemmer G, Weiss ST, Tantisira K, Cox NJ, Ratain MJ, Huang RS: Genome-wide interrogation of longitudinal FEV1 in asthmatic children, American Journal of Respiratory and Critical Care Medicine, 190(6):619-27 (2014).
  • Heitmann J, Geeleher P, Zuo Z, Weichselbaum RR, Vokes EE, Fetscher S, Seiwert TY: Poly (ADP-ribose) polymerase inhibitor efficacy in head and neck cancer, Oral Oncology, 50: 825-831 (2014).
  • Geeleher P, Cox NJ, Huang RS: Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. Genome Biology 15:R47 (2014).
  • Weng L, Ziliak D, LaCroix B, Geeleher P, Huang RS: Integrative omic analysis for tamoxifen sensitivity through cell based models. PLOS ONE 9(4): e93420 (2014)
  • LaCroix B, Gamazon ER, Lenkala D, Hae Kyung Im, Geeleher P, Ziliak D, Dolan EM, Cox NJ, and Huang RS: Integrative analyses of genetic, epigenetic and transcriptome reveal the biology of platinum sensitivity, BMC Genomics 15:292 (2014).
  • Lenkala D, LaCroix B, Geeleher P, Gamazon ER, Hae Kyung Im, Huang RS: The impact of microRNA expression on cellular proliferation, Human Genetics 1-8 (2014).
  • Geeleher P, Hartnett L, Affendi RRA, Egan LJ, Golden A, Seoighe C: Gene-Set Analysis is Severely Biased When Applied to Genome-wide Methylation Data, Bioinformatics 29 (15): 1851-1857 (2013).
  • Geeleher P, Huang RS, Gamazon ER, Golden A and Seoighe C: The regulatory effect of miRNAs is a heritable genetic trait in humans, BMC Genomics 13:383 (2012).
  • Geeleher P, Morris D, Hinde JP, Golden A: BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server, Bioinformatics 25(11):1438-9 (2009).