My research interests are in statistical genomics, bioinformatics, systems biology, and biomedical data science. Currently, I am focusing on developing methods to: (1) preprocess and analyze miRNA-seq data, (2) estimate gene regulatory networks involved in cancer from Perturb-seq data, (3) adjust for the effect of cellular composition on tissue-level gene expression, and (4) process and analyze microglia imaging data.
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Patil AH, McCall MN, Halushka MK (2024). Brooklyn plots to identify co-expression dysregulation in single cell sequencing. NAR Genomics and Bioinformatics, 6(1):lqad112
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Patil AH, Baran A, Brehm ZP, McCall MN, Halushka MK (2022). A curated human cellular microRNAome based on 196 primary cell types. GigaScience, 11.
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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.
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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.
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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.
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Hsu B, Sherina V, McCall MN (2020). Autoregressive modeling and diagnostics for qPCR amplification. Bioinformatics, 36(22-23):5386-5391.
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Sherina V, McMurray HR, Powers W, Land H, Love TMT, and McCall MN (2020). Multiple imputation and direct estimation for qPCR data with non-detects. BMC Bioinformatics, 21:545.
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Nassiri I and McCall MN (2018). Systematic exploration of cell morphological phenotypes associated with a transcriptomic query. Nucleic Acids Research, 46(19):e116.
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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.