Publications

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



Selected Publications

Statistical Genomics Methodology:

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]
Highly Accessed.

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

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]



Systems Biology Methodology:

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 microRNA expression:

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]
Highly Accessed.

* corresponding author(s)