Selected publications are listed below. A complete list of all publications is available at:

Selected Publications

Statistical Genomics:

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. [link] 

McCall MN*McMurray H, Land H, Almudevar A (2014). On Non-Detects in qPCR Data, Bioinformatics, 30(16):2310-2316. [link]
Coverage in GenomeWeb [link] [pdf]

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. [link] 

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. [link]

McCall MN* and Almudevar A (2012). Affymetrix GeneChip microarray preprocessing for multivariate analyses, Briefings in Bioinformatics, 13(5):536-546. [link]

McCall MN* and Irizarry RA (2011). Thawing Frozen Robust Multi-array Analysis (fRMA), BMC Bioinformatics, 12:369. [link]

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA* (2011). Assessing Affymetrix GeneChip Microarray Quality, BMC Bioinformatics, 12:137. [link]

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. [link]

McCall MN, Bolstad BM, and Irizarry RA* (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253. [link]

McCall MN and Irizarry RA* (2008). Consolidated strategy for the analysis of microarray spike-in data, Nucleic Acids Research, 36(17):e108. [link]

Translational Genomics:

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. [link]

Barry CT*, D'Souza M, McCall MN, Safadjou S, Ryan C, Kashyap R, Marroquin C, Orloff M, Almudevar A, Godfrey TE (2012). Micro RNA Expression Profiles as Adjunctive Data to Assess the Risk of Hepatocellular Carcinoma Recurrence After Liver Transplantation, American Journal of Transplantation, 12(2):428-437. [link]

Systems Biology:

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. [link]

McCall MN* (2013). Estimation of Gene Regulatory Networks, Journal of Postdoctoral Research, 1(1):60-69. [link]

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. [link]

Cell-type specific expression:

Halushka MK*, Fromm B, Peterson KJ, McCall MN (2018). Big Strides in Cellular MicroRNA Expression, Trends in Genetics. [link]

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[link]
Coverage in Research@URMC [link]

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. [link]

Kent O, McCall MN, Cornish T, Halushka MK* (2014). Lessons from miR-143/145: The importance of cell-type localization of miRNAs, Nucleic Acids Research, 42(12):7528-7538. [link]

Haider BA, Baras AS, McCall MN, Hertel JA, Cornish TC, Halushka MK* (2014). A Critical Evaluation of microRNA Biomarkers in Non-Neoplastic Disease, PLoS ONE 9(2): e89565. [link]

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. [link]

* corresponding author(s)