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Items: 21

1.

Discovering long noncoding RNA predictors of anticancer drug sensitivity beyond protein-coding genes.

Nath A, Lau EYT, Lee AM, Geeleher P, Cho WCS, Huang RS.

Proc Natl Acad Sci U S A. 2019 Oct 29;116(44):22020-22029. doi: 10.1073/pnas.1909998116. Epub 2019 Sep 23.

2.

Long non-coding RNA transcriptome of uncharacterized samples can be accurately imputed using protein-coding genes.

Nath A, Geeleher P, Huang RS.

Brief Bioinform. 2019 Jan 17. doi: 10.1093/bib/bby129. [Epub ahead of print]

PMID:
30657858
3.

Cancer expression quantitative trait loci (eQTLs) can be determined from heterogeneous tumor gene expression data by modeling variation in tumor purity.

Geeleher P, Nath A, Wang F, Zhang Z, Barbeira AN, Fessler J, Grossman RL, Seoighe C, Stephanie Huang R.

Genome Biol. 2018 Sep 11;19(1):130. doi: 10.1186/s13059-018-1507-0.

4.

Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies.

Geeleher P, Zhang Z, Wang F, Gruener RF, Nath A, Morrison G, Bhutra S, Grossman RL, Huang RS.

Genome Res. 2017 Oct;27(10):1743-1751. doi: 10.1101/gr.221077.117. Epub 2017 Aug 28.

5.

Exploring the Link between the Germline and Somatic Genome in Cancer.

Geeleher P, Huang RS.

Cancer Discov. 2017 Apr;7(4):354-355. doi: 10.1158/2159-8290.CD-17-0192.

6.

Institutional Profile: Pharmacogenomic research in R Stephanie Huang Laboratory.

Geeleher P, Nath A, Huang RS.

Pharmacogenomics. 2017 Apr;18(6):519-522. doi: 10.2217/pgs-2017-0031. Epub 2017 Mar 14.

PMID:
28290771
7.

Consistency in large pharmacogenomic studies.

Geeleher P, Gamazon ER, Seoighe C, Cox NJ, Huang RS.

Nature. 2016 Nov 30;540(7631):E1-E2. doi: 10.1038/nature19838. No abstract available.

9.

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks.

Cannavò E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, Furlong EE.

Curr Biol. 2016 Jan 11;26(1):38-51. doi: 10.1016/j.cub.2015.11.034. Epub 2015 Dec 10.

10.

Seq-ing improved gene expression estimates from microarrays using machine learning.

Korir PK, Geeleher P, Seoighe C.

BMC Bioinformatics. 2015 Sep 4;16:286. doi: 10.1186/s12859-015-0712-z.

11.

Predicting Response to Histone Deacetylase Inhibitors Using High-Throughput Genomics.

Geeleher P, Loboda A, Lenkala D, Wang F, LaCroix B, Karovic S, Wang J, Nebozhyn M, Chisamore M, Hardwick J, Maitland ML, Huang RS.

J Natl Cancer Inst. 2015 Aug 21;107(11). pii: djv247. doi: 10.1093/jnci/djv247. Print 2015 Nov.

12.

pRRophetic: an R package for prediction of clinical chemotherapeutic response from tumor gene expression levels.

Geeleher P, Cox N, Huang RS.

PLoS One. 2014 Sep 17;9(9):e107468. doi: 10.1371/journal.pone.0107468. eCollection 2014.

13.

Genome-wide interrogation of longitudinal FEV1 in children with asthma.

Wu K, Gamazon ER, Im HK, Geeleher P, White SR, Solway J, Clemmer GL, Weiss ST, Tantisira KG, Cox NJ, Ratain MJ, Huang RS.

Am J Respir Crit Care Med. 2014 Sep 15;190(6):619-27. doi: 10.1164/rccm.201403-0460OC.

14.

Poly (ADP-ribose) polymerase inhibitor efficacy in head and neck cancer.

Heitmann J, Geeleher P, Zuo Z, Weichselbaum RR, Vokes EE, Fetscher S, Seiwert TY.

Oral Oncol. 2014 Sep;50(9):825-31. doi: 10.1016/j.oraloncology.2014.06.004. Epub 2014 Jul 10.

PMID:
25017803
15.

Integrative analyses of genetic variation, epigenetic regulation, and the transcriptome to elucidate the biology of platinum sensitivity.

LaCroix B, Gamazon ER, Lenkala D, Im HK, Geeleher P, Ziliak D, Cox NJ, Huang RS.

BMC Genomics. 2014 Apr 16;15:292. doi: 10.1186/1471-2164-15-292.

16.

Integrative "omic" analysis for tamoxifen sensitivity through cell based models.

Weng L, Ziliak D, Lacroix B, Geeleher P, Huang RS.

PLoS One. 2014 Apr 3;9(4):e93420. doi: 10.1371/journal.pone.0093420. eCollection 2014.

17.

The impact of microRNA expression on cellular proliferation.

Lenkala D, LaCroix B, Gamazon ER, Geeleher P, Im HK, Huang RS.

Hum Genet. 2014 Jul;133(7):931-8. doi: 10.1007/s00439-014-1434-4. Epub 2014 Mar 8.

18.

Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines.

Geeleher P, Cox NJ, Huang RS.

Genome Biol. 2014 Mar 3;15(3):R47. doi: 10.1186/gb-2014-15-3-r47.

19.

Gene-set analysis is severely biased when applied to genome-wide methylation data.

Geeleher P, Hartnett L, Egan LJ, Golden A, Raja Ali RA, Seoighe C.

Bioinformatics. 2013 Aug 1;29(15):1851-7. doi: 10.1093/bioinformatics/btt311. Epub 2013 Jun 3.

PMID:
23732277
20.

The regulatory effect of miRNAs is a heritable genetic trait in humans.

Geeleher P, Huang SR, Gamazon ER, Golden A, Seoighe C.

BMC Genomics. 2012 Aug 10;13:383. doi: 10.1186/1471-2164-13-383.

21.

BioconductorBuntu: a Linux distribution that implements a web-based DNA microarray analysis server.

Geeleher P, Morris D, Hinde JP, Golden A.

Bioinformatics. 2009 Jun 1;25(11):1438-9. doi: 10.1093/bioinformatics/btp165. Epub 2009 Mar 23.

PMID:
19307241

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