Publications

Selected publications, lab members underlined:

  • Min Pan, Yinwen Zhang, William C. Wright, Xueying Liu, Barbara Passaia, Duane Currier, Jonathan Low, Richard H. Chapple, Jacob A. Steele, Jon P. Connelly, Meifen Lu, Allister J. Loughran, Lei Yang, Brian J Abraham, Shondra M. Pruett-Miller, Burgess Freeman III, George E. Campbell, Michael A. Dyer, Taosheng Chen, Elizabeth Stewart, Selene Koo, Heather Sheppard, John Easton, Paul Geeleher : Bone morphogenetic protein (BMP) signaling determines neuroblastoma cell fate and sensitivity to retinoic acid, BioRxiv (2024).
  • Chapple RH, Liu X, Natarajan S, Alexander MIM, Kim Y, Patel AG, LaFlamme CW, Pan M, Wright WC, Lee HM, Zhang Y, Lu M, Koo SC, Long C, Harper J, Savage C, Johnson MD, Confer T, Akers WJ, Dyer MA, Sheppard H, Easton J, Geeleher P: An integrated single-cell RNA-seq map of human neuroblastoma tumors and preclinical models uncovers divergent mesenchymal-like gene expression programs, Genome Biology (2024).
  • Lee HM*, Wright WC*, Pan M, Low J, Currier D, Fang J, Singh S, Nance S, Delahunty I, Kim Y, Chapple RH, Zhang Y, Liu X, Steele JA, Qi J, Pruett-Miller SM, Easton J, Chen T, Yang J, Durbin AD, Geeleher P: A CRISPR-drug perturbational map for identifying compounds to combine with commonly used chemotherapeutics, Nature Communications (2023).
  • Zubair A, Chapple RH, Natarajan S, Wright WC, Pan M, Lee HM, Tillman H,Easton J, Geeleher P: Cell type identification in spatial transcriptomics data can be improved by leveraging cell-type-informative paired tissue images using a Bayesian probabilistic model, Nucleic Acids Research (2022)
  • Pan M, Wright M, Chapple R, Zubair A, Sandhu M, Batchelder J, Low J, Blankenship K, Wang Y, Gordon B, Archer P, Brady SW, Natarajan S, Posgai MJ, Schuetz J, Miller D, Kalathur R, Chen S, Connelly JP, Babu MM, Dyer MA, Pruett-Miller SM, Freeman B, Chen T, Godley LA, Blanchard S, Stewart E, Easton J, Geeleher P: The chemotherapeutic CX-5461 primarily targets TOP2B and exhibits selective activity in high-risk neuroblastoma, Nature Communications, 12:6468 (2021)
  • Nath A, Geeleher P, Huang RS: Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes, Briefings in Bioinformatics (2020).
  • Nath A, Lau EYT, Lee AM, Geeleher P, Cho WCS, Huang RS: Discovering novel long non-coding RNA predictors of anticancer drug sensitivity beyond protein-coding genes, in press PNAS (2019).
  • 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 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 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).