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Matthew N. McCall, PhD

Matthew McCall, PhDAssociate Professor of Biostatistics
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

  • Lowery RL, Latchneya SE, Peera RP, Lamantiaa CE, Lordya KA, Opanashukb LA, McCall MN, Majewskaa AK (2022). Gestational and lactational exposure to 2,3,7,8- tetrachlorodibenzo-p-dioxin primes cortical microglia to tissue injury. Brain, Behavior, and Immunity. 

  • McCall MN, Chu C, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Grier A, Gill S, Falsey AR, Topham DJ, Caserta M, Wash E, Qiu X, Mariani TJ (2021). A systems genomics approach uncovers molecular associates of RSV severity. PLoS Computational Biology, 17(12):e1009617.

  • McMurray HR, Ambeskovic A, Newman LA, Aldersley J, Balakrishnan V, Smith B, Stern HA, Land H, McCall MN (2021). Gene network modeling via TopNet reveals robust epistatic interactions between functionally diverse tumor critical mediator genes. Cell Reports, 37(12):110136.

  • Nieuwenhuis TO, Rosenberg AZ, McCall MN, Halushka MK (2021). Sex, age, tissue, and disease patterns of matrisome expression in GTEx transcriptome data. Scientific Reports, 11:21549.

  • Croft D, Burton D, Nagel D, Bhattacharya S, Falsey A, Georas S, Hopke PK, Johnston CJ, Kottmann RM, Litonjua AA, Mariani TJ, Rich DQ, Thevenet-Morrison K, Thurston SW, Utell MJ, McCall MN (2021). The effect of air pollution on the transcriptomics of the immune response to respiratory infection. Scientific Reports, 11:19436.

  • Mendes MS, Le L, Atlas J, Brehm Z, Ladron-de-Guevara A, Matei E, Lamantia C, McCall MN, Majewska AK  (2021). The role of P2Y12 in the kinetics of microglial self-renewal and maturation in the adult visual cortex in vivo. Elife, 10:e61173.

  • Zhang Y, Cuerdo J, Halushka Mk, McCall MN (2021). The effect of tissue composition on gene co-expression. Briefings in Bioinformatics, 22(1):127-139.

  • Hsu b, Sherina V, McCall MN (2020). Autoregressive modeling and diagnostic for qPCR amplification. Bioinformatics, 36(22-23):5386-5391

  • Sherina V, McMurray HR, Powers W, Land H, Love TMT, and McCall MN (202). Multiple imputation and direct estimation for qPCR data with non-detects. BMC Bioinformatics, 21:545.

  • Lowery RL, Latchney SE, Peer RP, Lamantia CE, Opanashuk L, McCall MN, and Majewska Ak (2020). Acute 2, 3, 7, 8-Tetrachlorodibenzo-p-dioxin exposure in adult mice does not alter the morphology or inflammatory response of cortical microglia. Neuroscience Letter, 135516.

  • Nieuwenhuis To, Yang S, Verma RX, Pillalamarri V, Arking D, Rosenberg AZ, McCall MN, Halushka MK (2020). Consistent RNA sequencing contamination in GTEx and other data sets. Nat Communications, 11:1933.

  • Nassiri I and McCall MN (2018). Systematic exploration of cell morphological phenotypes associated with transcriptomic query. Nucleic Acids Research, 46(19):e116. 

  • 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.

Last updated: March 17, 2022