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Matthew N. McCall, PhD

Matthew McCall, PhDAssociate Professor of Biostatistics
Associate Director, Statistics PhD Program
PhD, Johns Hopkins University

Contact Information

University of Rochester
Dept of Biostatistics and Computational Biology
265 Crittenden Boulevard, CU 420630
Rochester, New York 14642-0630
Office: Saunders Research Building 4143
Phone: (585) 273-3177
Fax: (585) 273-1031

Research Interests

My research interests are in statistical genomics, systems biology, and bioinformatics. Currently, I am focusing on: (1) developing methods to estimate gene regulatory networks involved in cancer from perturbation experiments, (2) tackling within-subject genomic heterogeneity, focusing on predicting recurrence of hepatocellular carcinoma after liver transplantation, (3) developing methods for preprocessing and analysis of genomic data, and (4) examining the effect of cellular composition on tissue-level gene expression.

Matthew McCall's Personal Website

Selected Publications

  • Halushka MK, Fromm B, Peterson KJ, McCall MN (2018). Big Strides in Cellular MicroRNA Expression. Trends in Genetics. 34(3):165-167.
  • McCall MN, Kim MS, Adil M, Patil AH, Lu Y, Mitchell CJ, Leal-Rojas P, Xu J, Kumar M, Dawson VL, Dawson TM, Baras AS, Rosenberg AZ, Arking DE, Burns KH, Pandey A, Halushka MK (2017). Toward the human cellular microRNAome. Genome Research. 27(10):1769-1781.​
  • McCall MN, Illei PB, Halushka MK (2016). Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome. The American Journal of Human Genetics. 99(3):624-635.
  • McCall MN, Baras AS, Crits-Christoph A, Ingersoll R, McAlexander MA, Witwer KW, Halushka MK (2016). A benchmark for microRNA quantification algorithms using the OpenArray platform, BMC Bioinformatics, 17:138.
  • Xie QY, Almudevar A, Whitney-Miller CL, Barry CT, and McCall MN (2016). A microRNA biomarker of hepatocellular carcinoma recurrence following liver transplantation accounting for within-patient heterogeneity, BMC Medical Genomics, 9:18.
  • McCall MN, McMurray H, Land H, Almudevar A (2014). On Non-Detects in qPCR Data, Bioinformatics, 30(16):2310-2316.
  • McCall MN, Jaffee HA, Zelisko SJ, Sinha N, Hooiveld G, Irizarry RA, Zilliox MJ (2014). The Gene Expression Barcode 3.0: improved data processing and mining tools, Nucleic Acids Research, 42(D1):D938-D943.
  • Tran V, McCall MN, McMurray H, Almudevar A (2013). On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior, Frontiers in Genetics, 4:263. doi: 10.3389/fgene.2013.00263.
  • McCall MN, Jaffee HA, Irizarry RA (2012). fRMA ST: Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays, Bioinformatics, 28(23):3153-3154.
  • McCall MN and Almudevar A (2012). Affymetrix GeneChip microarray preprocessing for multivariate analyses, Briefings in Bioinformatics, 13(5):536-546.
  • McCall MN, Kent OA, Yu J, Fox-Talbot K, Zaiman AL, Halushka MK (2011). MicroRNA profiling of diverse endothelial cell types, BMC Medical Genomics, 4:78.
  • Almudevar A, McCall MN, McMurray H, Land H (2011). Fitting Boolean Networks from Steady State Perturbation Data, Statistical Applications in Genetics and Molecular Biology, 10(1):Article 47.
  • McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA (2011). Assessing Affymetrix GeneChip Microarray Quality, BMC Bioinformatics, 12:137.
  • McCall MN, Uppal K, Jaffee HA, Zilliox MJ, and Irizarry RA (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes, Nucleic Acids Research, 39:D1011-D1015.
  • McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253.

Last updated: April 13, 2018