Publications

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(2018). Kras and Tp53 mutations cause cholangiocyte- and hepatocyte-derived cholangiocarcinoma. Cancer Research.

Paper

(2018). xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells. Scientific Reports.

Paper

(2018). Big Strides in Cellular MicroRNA Expression. Trends in Genetics.

Paper

(2017). Statistical Approches to Decreasing the Discrepancy of Non-detects in qPCR Data. BioRxiv.

Preprint Code

(2017). Toward the human cellular microRNAome. Genome Research.

Preprint Dataset Paper Research@URMC

(2017). Establishing Informative Prior for Gene Expression Variance from Public Databases. Statistics in Biosciences.

Paper

(2017). A Four Gene Signature Predictive of Recurrent Prostate Cancer. Oncotarget.

Paper

(2016). Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome. The American Journal of Human Genetics.

Paper

(2016). A benchmark for microRNA quantification algorithms using the OpenArray platform. BMC Bioinformatics.

Code Dataset Paper

(2015). Integrating High-Dimensional Transcriptomics and Image Analysis Tools into Early Safety Screening: Proof of Concept for a New Early Drug Development Strategy. Chemical Research in Toxicology.

Paper

(2015). Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project. Drug Discovery Today.

Paper

(2015). Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis. Molecular Biosystems.

Paper

(2014). Lessons from miR-143/145: The importance of cell-type localization of miRNAs. Nucleic Acids Research.

Paper

(2014). On Non-Detects in qPCR Data. Bioinformatics.

Code Paper GenomeWeb

(2014). A critical evaluation of microRNA biomarkers in non-neoplastic disease. PLoS ONE.

Paper

(2014). The Gene Expression Barcode 3.0: improved data processing and mining tools. Nucleic Acids Research.

Code Paper Website

(2013). ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data. Bioinformatics.

Paper

(2013). Estimation of Gene Regulatory Networks. Journal of Postdoctoral Research.

PDF Paper

(2012). Gene expression anti-profiles as a basis for accurate universal cancer signatures. BMC Bioinformatics.

Paper

(2012). Affymetrix GeneChip microarray preprocessing for multivariate analyses. Briefings in Bioinformatics.

Paper

(2012). Micro RNA expression profiles as adjunctive data to assess the risk of hepatocellular carcinoma recurrence after liver transplantation. American Journal of Transplantation.

Paper

(2011). Fitting Boolean Networks from Steady State Perturbation Data. Statistical Applications in Genetics and Molecular Biology.

Paper

(2011). Thawing Frozen Robust Multi-array Analysis (fRMA). BMC Bioinformatics.

Code Paper

(2011). MicroRNA profiling of diverse endothelial cell types. BMC Medical Genomics.

Paper

(2011). Assessing Affymetrix GeneChip Microarray Quality. BMC Bioinformatics.

Code Paper

(2010). Performance Evaluation of Commercial miRNA Expression Array Platforms. BMC Research Notes.

Paper

(2010). Frozen Robust Multi-Array Analysis (fRMA). Biostatistics.

Code Paper

(2008). Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Research.

Code Paper