Paul Geeleher, PhD
Paul Geeleher, PhD

Paul Geeleher, PhD

Assistant Member, St. Jude Faculty

Departments

Education

Postdoc and K99 Fellowship – Department of Medicine (Sections of Genetic Medicine and Hematology/Oncology), The University of Chicago
PhD – Department of Mathematics, Statistics and Applied Mathematics, National University of Ireland (NUI), Galway

Research Interests

  • Computational genomics
  • Drug repurposing and Pharmacogenomics
  • Bioinformatics

Selected Publications

Geeleher P, Nath A, Wang F, Zhenyu Z, Fessler J, Grossman RL, Seoighe C, Huang RS. Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity. Genome Biology 19:130, 2018.

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, 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, 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, Seoighe C. The regulatory effect of miRNAs is a heritable genetic trait in humans. BMC Genomics 13:383, 2012.

Affendi RRA, Harnett L, Newell J, Golden A, Geeleher P, Seoighe C, Egan LJ. Analysis of the interleukin 6/STAT3 signaling pathway and DNA methylation patterns in patients with short or longstanding inflammatory bowel disease. Gastroenterology and Hepatology 27, 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.

Last update: April 2019