Paul Geeleher

Learn More
We demonstrate a method for the prediction of chemotherapeutic response in patients using only before-treatment baseline tumor gene expression data. First, we fitted models for whole-genome gene expression against drug sensitivity in a large panel of cell lines, using a method that allows every gene to influence the prediction. Following data homogenization(More)
SUMMARY BioconductorBuntu is a custom distribution of Ubuntu Linux that automatically installs a server-side microarray processing environment, providing a user-friendly web-based GUI to many of the tools developed by the Bioconductor Project, accessible locally or across a network. System installation is via booting off a CD image or by using a Debian(More)
We recently described a methodology that reliably predicted chemotherapeutic response in multiple independent clinical trials. The method worked by building statistical models from gene expression and drug sensitivity data in a very large panel of cancer cell lines, then applying these models to gene expression data from primary tumor biopsies. Here, to(More)
BACKGROUND Many disparate biomarkers have been proposed as predictors of response to histone deacetylase inhibitors (HDI); however, all have failed when applied clinically. Rather than this being entirely an issue of reproducibility, response to the HDI vorinostat may be determined by the additive effect of multiple molecular factors, many of which have(More)
OBJECTIVES Poly (ADP-ribose) polymerase inhibitors (PARPi) have shown single agent activity against tumors with deficiencies in the DNA repair mechanism homologous recombination including, but not limited to those harboring BRCA mutations. We hypothesized that, in the context of homologous recombination deficiency (HRD), PARPi could have an effect in head(More)
Using genome-wide genetic, gene expression, and microRNA expression (miRNA) data, we developed an integrative approach to investigate the genetic and epigenetic basis of chemotherapeutic sensitivity. Through a sequential multi-stage framework, we identified genes and miRNAs whose expression correlated with platinum sensitivity, mapped these to genomic loci(More)
<b/> Carter and colleagues propose a systematic analysis of the germline and somatic genome in cancer. They identify interactions that occur between germline and somatic variants. This elucidates the function of the germline genome in the context of cancer risk and development. Cancer Discov; 7(4); 354-5. ©2017 AACRSee related article by Carter et al., p.(More)
It has long been observed that tamoxifen sensitivity varies among breast cancer patients. Further, ethnic differences of tamoxifen therapy between Caucasian and African American have also been reported. Since most studies have been focused on Caucasian people, we sought to comprehensively evaluate genetic variants related to tamoxifen therapy in(More)
Haibe-Kains et al.1 reported inconsistency between two large-scale pharmacogenomic studies—the Cancer Cell Line Encyclopedia (CCLE)2 and the Cancer Genome Project (CGP)3. Upon careful analysis of the same data, we have come to quite different and much more positive conclusions. Here we highlight the most important reasons for this. There is a Reply to this(More)
The Huang Lab was established in 2009 at the University of Chicago and has since been active in conducting pharmacogenomic research. Our laboratory's main research focus is translational pharmacogenomics with a particular interest in the pharmacogenomics of anticancer agents. By systematically evaluating the human genome and its relationships to drug(More)