Lab Members

Qingyan (Lilly) Xie

Postdoctoral Associate

Isar Nassiri

Postdoctoral Associate

Yun Zhang

Statistics PhD Student

Valeriia Sherina

Statistics PhD Student

David Burton

Statistics PhD Student

Zachary Brehm

Statistics PhD Student

Jeremiah Jones

Statistics PhD Student

Jonavelle Cuerdo

Data Science Undergraduate

Lauren Kemperman

Data Science Undergraduate

Benjamin Hsu

Statistics Undergraduate

Kailey Ferger

Comp Bio Undergraduate

Oleg Demus

Comp Bio Undergraduate

Winslow Powers

BME Undergraduate

Qidi Yang

Biochemistry Undergraduate

Jeffrey Hrebenach

Data Science Undergraduate

Alida Mooney

Mathematics Undergraduate

Allison Maier

Biology Undergraduate

Lindsey Barden

Biostatistics Undergraduate

Scott Onestak

Data Science Undergraduate

Fatimar Umar

High School Student

Raymond Feng

High School Student

Selected Publications

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

Preprint Dataset Paper Research@URMC

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


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

Code Paper GenomeWeb

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

Code Paper

Recent Publications

More Publications

(2018). Identification of the novel Ido1 imprinted locus and its potential epigenetic role in pregnancy loss. Human Molecular Genetics.


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


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


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


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

Preprint Code



Preprocessing and analysis for single microarrays and microarray batches.


Tools for advanced use of the frma package.


Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.


Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves.


This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines.


Methods to model and impute non-detects in the results of qPCR experiments.


The package contains functions that can be used to compare expression measures on different array platforms.


A computational Bayesian approach to ternary gene regulatory network estimation from gene perturbation experiments.

Valeriia Sherina is presenting at Rocky 2018. Title: Fully Bayesian model for non-random missing data in qPCR. Abstract: We propose a new statistical approach to obtain differential gene expression of non-detects in quantitative real-time PCR (qPCR) experiments through Bayesian hierarchical modeling. We propose to treat non-detects as non-random missing data, model the missing data mechanism, and use this model to impute Ct values or obtain direct estimates of relevant model parameters.


Congratulations to Valeriia Sherina on starting a new job at GlaxoSmithKline! She’ll be back in early 2019 to defend her thesis.


Kailey Ferger, a senior Computational Biology major, has joined the lab where she will be working on analysis of microRNA expression data.


Oleg Demus, a senior Computational Biology major, has joined the lab where he will be working to combine multiple publicly available RNA-seq data sets to address questions of tissue composition in atherosclerosis.