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Matthew N. McCall, Ph.D., M.H.S.


Showing all 53 journal articles & 0 books available

Journal Articles

McMurray HR, Stern HA, Ambeskovic A, Land H, McCall MN. "Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments." STAR protocols.. 2022 Sep 30; 3(4):101737. Epub 2022 Sep 30.

Patil AH, Baran A, Brehm ZP, McCall MN, Halushka MK. "A curated human cellular microRNAome based on 196 primary cell types." GigaScience.. 2022 Aug 25; 11

Lowery RL, Latchney SE, Peer RP, Lamantia CE, Lordy KA, Opanashuk LA, McCall M, Majewska AK. "Gestational and lactational exposure to 2,3,7,8-tetrachlorodibenzo-p-dioxin primes cortical microglia to tissue injury." Brain, behavior, and immunity.. 2022 Jan 19; Epub 2022 Jan 19.

McCall MN, Chu CY, Wang L, Benoodt L, Thakar J, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Qiu X, Mariani TJ. "A systems genomics approach uncovers molecular associates of RSV severity." PLoS computational biology.. 2021 Dec 28; 17(12):e1009617. Epub 2021 Dec 28.

McMurray HR, Ambeskovic A, Newman LA, Aldersley J, Balakrishnan V, Smith B, Stern HA, Land H, McCall MN. "Gene network modeling via TopNet reveals functional dependencies between diverse tumor-critical mediator genes." Cell reports.. 2021 Dec 21; 37(12):110136.

Nieuwenhuis TO, Rosenberg AZ, McCall MN, Halushka MK. "Tissue, age, sex, and disease patterns of matrisome expression in GTEx transcriptome data." Scientific reports.. 2021 Nov 3; 11(1):21549. Epub 2021 Nov 03.

Croft DP, Burton DS, Nagel DJ, Bhattacharya S, Falsey AR, Georas SN, Hopke PK, Johnston CJ, Kottmann RM, Litonjua AA, Mariani TJ, Rich DQ, Thevenet-Morrison K, Thurston SW, Utell MJ, McCall MN. "The effect of air pollution on the transcriptomics of the immune response to respiratory infection." Scientific reports.. 2021 Sep 30; 11(1):19436. Epub 2021 Sep 30.

Mendes M, Le L, Atlas J, Brehm Z, Ladron-de-Guevara A, Matei E, Lamantia C, McCall M, Majewska AK. "The role of P2Y12 in the kinetics of microglial self-renewal and maturation in the adult visual cortex ." eLife.. 2021 Jul 12; 10Epub 2021 Jul 12.

Verma RX, Kannan S, Lin BL, Fomchenko KM, Nieuwenhuis TO, Patil AH, Lukban C, Yang X, Fox-Talbot K, McCall MN, Kwon C, Kass DA, Rosenberg AZ, Halushka MK. "Single cell RNA-seq analysis of the flexor digitorum brevis mouse myofibers." Skeletal muscle. 2021 May 17; 11(1):13. Epub 2021 May 17.

Wang L, Chu CY, McCall MN, Slaunwhite C, Holden-Wiltse J, Corbett A, Falsey AR, Topham DJ, Caserta MT, Mariani TJ, Walsh EE, Qiu X. "Airway gene-expression classifiers for respiratory syncytial virus (RSV) disease severity in infants." BMC medical genomics.. 2021 Feb 25; 14(1):57. Epub 2021 Feb 25.

Lim Y, Berry B, Viteri S, McCall M, Park EC, Rongo C, Brookes PS, Nehrke K. "FNDC-1-Mediated Mitophagy and ATFS-1 Coordinate to Protect Against Hypoxia-Reoxygenation." Autophagy.. 2021 Jan 8; Epub 2021 Jan 08.

Fomchenko KM, Walsh EM, Yang X, Verma RX, Lin BL, Nieuwenhuis TO, Patil AH, Fox-Talbot K, McCall MN, Kass DA, Rosenberg AZ, Halushka MK. "Spatial Proteomic Approach to Characterize Skeletal Muscle Myofibers." Journal of proteome research.. 2020 Nov 30; Epub 2020 Nov 30.

Hsu B, Sherina V, McCall MN. "Auto-regressive modeling and diagnostics for qPCR amplification." Bioinformatics.. 2020 Nov 27; Epub 2020 Nov 27.

Sherina V, McMurray HR, Powers W, Land H, Love TMT, McCall MN. "Multiple imputation and direct estimation for qPCR data with non-detects." BMC bioinformatics.. 2020 Nov 26; 21(1):545. Epub 2020 Nov 26.

Lowery RL, Latchney SE, Peer RP, Lamantia CE, Opanashuk L, McCall M, Majewska AK. "Acute 2,3,7,8-Tetrachlorodibenzo-p-dioxin exposure in adult mice does not alter the morphology or inflammatory response of cortical microglia." Neuroscience letters.. 2020 Nov 20; :135516. Epub 2020 Nov 20.

Chu CY, Qiu X, McCall MN, Wang L, Corbett A, Holden-Wiltse J, Slaunwhite C, Grier A, Gill SR, Pryhuber GS, Falsey AR, Topham DJ, Caserta MT, Walsh EE, Mariani TJ. "Airway gene expression correlates of RSV disease severity and microbiome composition in infants." The Journal of infectious diseases.. 2020 Sep 14; Epub 2020 Sep 14.

Nieuwenhuis TO, Yang SY, Verma RX, Pillalamarri V, Arking DE, Rosenberg AZ, McCall MN, Halushka MK. "Consistent RNA sequencing contamination in GTEx and other data sets." Nature communications.. 2020 Apr 22; 11(1):1933. Epub 2020 Apr 22.

Zhang Y, Cuerdo J, Halushka MK, McCall MN. "The effect of tissue composition on gene co-expression." Briefings in bioinformatics. 2019 Dec 8; Epub 2019 Dec 08.

Wang YT, Lim Y, McCall MN, Huang KT, Haynes CM, Nehrke K, Brookes PS. "Cardioprotection by the mitochondrial unfolded protein response requires ATF5." American journal of physiology. Heart and circulatory physiology.. 2019 Aug 1; 317(2):H472-H478. Epub 2019 Jul 05.

Walsh EE, Mariani TJ, Chu C, Grier A, Gill SR, Qiu X, Wang L, Holden-Wiltse J, Corbett A, Thakar J, Benoodt L, McCall MN, Topham DJ, Falsey AR, Caserta MT. "Aims, Study Design, and Enrollment Results From the Assessing Predictors of Infant Respiratory Syncytial Virus Effects and Severity Study." JMIR research protocols.. 2019 Jun 6; 8(6):e12907. Epub 2019 Jun 06.

Spinelli P, Latchney SE, Reed JM, Fields A, Baier BS, Lu X, McCall MN, Murphy SP, Mak W, Susiarjo M. "Identification of the novel Ido1 imprinted locus and its potential epigenetic role in pregnancy loss." Human molecular genetics.. 2018 Nov 7; Epub 2018 Nov 07.

Nassiri I, McCall MN. "Systematic exploration of cell morphological phenotypes associated with a transcriptomic query." Nucleic acids research.. 2018 Nov 2; 46(19):e116.

Hill MA, Alexander WB, Guo B, Kato Y, Patra KC, O'Dell MR, McCall MN, Whitney-Miller CL, Bardeesy N, Hezel AF. "and Mutations Cause Cholangiocyte- and Hepatocyte-Derived Cholangiocarcinoma." Cancer research.. 2018 Aug 15; 78(16):4445-4451. Epub 2018 Jun 05.

Rosenberg AZ, Wright C, Fox-Talbot K, Rajpurohit A, Williams C, Porter C, Kovbasnjuk O, McCall MN, Shin JH, Halushka MK. "xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells." Scientific reports.. 2018 Jun 28; 8(1):9783. Epub 2018 Jun 28.

Halushka MK, Fromm B, Peterson KJ, McCall MN. "Big Strides in Cellular MicroRNA Expression." Trends in genetics : TIG.. 2018 Mar; 34(3):165-167. Epub 2018 Jan 18.

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. "Toward the human cellular microRNAome." Genome research.. 2017 Oct; 27(10):1769-1781. Epub 2017 Sep 06.

Komisarof J, McCall M, Newman L, Bshara W, Mohler JL, Morrison C, Land H. "A four gene signature predictive of recurrent prostate cancer." Oncotarget.. 2017 Jan 10; 8(2):3430-3440.

McCall MN, Illei PB, Halushka MK. "Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome." American journal of human genetics.. 2016 Sep 1; 99(3):624-635.

Xie QY, Almudevar A, Whitney-Miller CL, Barry CT, McCall MN. "A microRNA biomarker of hepatocellular carcinoma recurrence following liver transplantation accounting for within-patient heterogeneity." BMC medical genomics.. 2016 Apr 8; 9:18. Epub 2016 Apr 08.

McCall MN, Baras AS, Crits-Christoph A, Ingersoll R, McAlexander MA, Witwer KW, Halushka MK. "A benchmark for microRNA quantification algorithms using the OpenArray platform." BMC bioinformatics.. 2016 Mar 22; 17:138. Epub 2016 Mar 22.

Verbist BM, Verheyen GR, Vervoort L, Crabbe M, Beerens D, Bosmans C, Jaensch S, Osselaer S, Talloen W, Van den Wyngaert I, Van Hecke G, Wuyts D, , Van Goethem F, Göhlmann HW. "Integrating High-Dimensional Transcriptomics and Image Analysis Tools into Early Safety Screening: Proof of Concept for a New Early Drug Development Strategy." Chemical research in toxicology.. 2015 Oct 19; 28(10):1914-25. Epub 2015 Sep 15.

Verbist B, Klambauer G, Vervoort L, Talloen W, , Shkedy Z, Thas O, Bender A, Göhlmann HW, Hochreiter S. "Using transcriptomics to guide lead optimization in drug discovery projects: Lessons learned from the QSTAR project." Drug discovery today.. 2015 May; 20(5):505-13. Epub 2015 Jan 10.

Ravindranath AC, Perualila-Tan N, Kasim A, Drakakis G, Liggi S, Brewerton SC, Mason D, Bodkin MJ, Evans DA, Bhagwat A, Talloen W, Göhlmann HW, Qstar Consortium , Shkedy Z, Bender A. "Connecting gene expression data from connectivity map and in silico target predictions for small molecule mechanism-of-action analysis." Molecular bioSystems.. 2015 Jan; 11(1):86-96. Epub 2014 Sep 25.

McCall MN, McMurray H, Land H, Almudevar A. "On non-detects in qPCR data." Bioinformatics.. 2014 Aug 15; 30(16):2310-6. Epub 2014 Apr 23.

Kent OA, McCall MN, Cornish TC, Halushka MK. "Lessons from miR-143/145: the importance of cell-type localization of miRNAs." Nucleic acids research.. 2014 Jul; 42(12):7528-38. Epub 2014 May 29.

McCall MN, Jaffee HA, Zelisko SJ, Sinha N, Hooiveld G, Irizarry RA, Zilliox MJ. "The Gene Expression Barcode 3.0: improved data processing and mining tools." Nucleic acids research.. 2014 Jan; 42(Database issue):D938-43. Epub 2013 Nov 22.

Haider BA, Baras AS, McCall MN, Hertel JA, Cornish TC, Halushka MK. "A critical evaluation of microRNA biomarkers in non-neoplastic disease." PloS one.. 2014 9(2):e89565. Epub 2014 Feb 26.

Wu G, Yustein JT, McCall MN, Zilliox M, Irizarry RA, Zeller K, Dang CV, Ji H. "ChIP-PED enhances the analysis of ChIP-seq and ChIP-chip data." Bioinformatics.. 2013 May 1; 29(9):1182-9. Epub 2013 Mar 01.

McCall MN. "Estimation of Gene Regulatory Networks." Postdoc journal : a journal of postdoctoral research and postdoctoral affairs.. 2013 Jan; 1(1):60-69.

Tran V, McCall MN, McMurray HR, Almudevar A. "On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior." Frontiers in genetics.. 2013 4:263. Epub 2013 Dec 11.

McCall MN, Jaffee HA, Irizarry RA. "fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays." Bioinformatics.. 2012 Dec 1; 28(23):3153-4. Epub 2012 Oct 07.

Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT. "Gene expression anti-profiles as a basis for accurate universal cancer signatures." BMC bioinformatics.. 2012 Oct 22; 13:272. Epub 2012 Oct 22.

McCall MN, Almudevar A. "Affymetrix GeneChip microarray preprocessing for multivariate analyses." Briefings in bioinformatics. 2012 Sep; 13(5):536-46. Epub 2011 Dec 30.

Barry CT, D'Souza M, McCall M, Safadjou S, Ryan C, Kashyap R, Marroquin C, Orloff M, Almudevar A, Godfrey TE. "Micro RNA expression profiles as adjunctive data to assess the risk of hepatocellular carcinoma recurrence after liver transplantation." American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons.. 2012 Feb; 12(2):428-37. Epub 2011 Oct 18.

McCall MN, Kent OA, Yu J, Fox-Talbot K, Zaiman AL, Halushka MK. "MicroRNA profiling of diverse endothelial cell types." BMC medical genomics.. 2011 Nov 2; 4:78. Epub 2011 Nov 02.

Almudevar A, McCall MN, McMurray H, Land H. "Fitting Boolean networks from steady state perturbation data." Statistical applications in genetics and molecular biology. 2011 Oct 5; 10(1)Epub 2011 Oct 05.

McCall MN, Irizarry RA. "Thawing Frozen Robust Multi-array Analysis (fRMA)." BMC bioinformatics.. 2011 Sep 16; 12:369. Epub 2011 Sep 16.

McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. "Assessing affymetrix GeneChip microarray quality." BMC bioinformatics.. 2011 May 7; 12:137. Epub 2011 May 07.

McCall MN, Uppal K, Jaffee HA, Zilliox MJ, Irizarry RA. "The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes." Nucleic acids research.. 2011 Jan; 39(Database issue):D1011-5.

Shi L, Campbell G, Jones WD, Campagne F, Wen Z, Walker SJ, Su Z, Chu TM, Goodsaid FM, Pusztai L, Shaughnessy JD, Oberthuer A, Thomas RS, Paules RS, Fielden M, Barlogie B, Chen W, Du P, Fischer M, Furlanello C, Gallas BD, Ge X, Megherbi DB, Symmans WF, Wang MD, Zhang J, Bitter H, Brors B, Bushel PR, Bylesjo M, Chen M, Cheng J, Cheng J, Chou J, Davison TS, Delorenzi M, Deng Y, Devanarayan V, Dix DJ, Dopazo J, Dorff KC, Elloumi F, Fan J, Fan S, Fan X, Fang H, Gonzaludo N, Hess KR, Hong H, Huan J, Irizarry RA, Judson R, Juraeva D, Lababidi S, Lambert CG, Li L, Li Y, Li Z, Lin SM, Liu G, Lobenhofer EK, Luo J, Luo W, McCall MN, Nikolsky Y, Pennello GA, Perkins RG, Philip R, Popovici V, Price ND, Qian F, Scherer A, Shi T, Shi W, Sung J, Thierry-Mieg D, Thierry-Mieg J, Thodima V, Trygg J, Vishnuvajjala L, Wang SJ, Wu J, Wu Y, Xie Q, Yousef WA, Zhang L, Zhang X, Zhong S, Zhou Y, Zhu S, Arasappan D, Bao W, Lucas AB, Berthold F, Brennan RJ, Buness A, Catalano JG, Chang C, Chen R, Cheng Y, Cui J, Czika W, Demichelis F, Deng X, Dosymbekov D, Eils R, Feng Y, Fostel J, Fulmer-Smentek S, Fuscoe JC, Gatto L, Ge W, Goldstein DR, Guo L, Halbert DN, Han J, Harris SC, Hatzis C, Herman D, Huang J, Jensen RV, Jiang R, Johnson CD, Jurman G, Kahlert Y, Khuder SA, Kohl M, Li J, Li L, Li M, Li QZ, Li S, Li Z, Liu J, Liu Y, Liu Z, Meng L, Madera M, Martinez-Murillo F, Medina I, Meehan J, Miclaus K, Moffitt RA, Montaner D, Mukherjee P, Mulligan GJ, Neville P, Nikolskaya T, Ning B, Page GP, Parker J, Parry RM, Peng X, Peterson RL, Phan JH, Quanz B, Ren Y, Riccadonna S, Roter AH, Samuelson FW, Schumacher MM, Shambaugh JD, Shi Q, Shippy R, Si S, Smalter A, Sotiriou C, Soukup M, Staedtler F, Steiner G, Stokes TH, Sun Q, Tan PY, Tang R, Tezak Z, Thorn B, Tsyganova M, Turpaz Y, Vega SC, Visintainer R, von Frese J, Wang C, Wang E, Wang J, Wang W, Westermann F, Willey JC, Woods M, Wu S, Xiao N, Xu J, Xu L, Yang L, Zeng X, Zhang J, Zhang L, Zhang M, Zhao C, Puri RK, Scherf U, Tong W, Wolfinger RD, . "The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models." Nature biotechnology.. 2010 Aug; 28(8):827-38. Epub 2010 Jul 30.

McCall MN, Bolstad BM, Irizarry RA. "Frozen robust multiarray analysis (fRMA)." Biostatistics.. 2010 Apr; 11(2):242-53. Epub 2010 Jan 22.

Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA. "Performance evaluation of commercial miRNA expression array platforms." BMC research notes.. 2010 Mar 18; 3:80. Epub 2010 Mar 18.

McCall MN, Irizarry RA. "Consolidated strategy for the analysis of microarray spike-in data." Nucleic acids research.. 2008 Oct; 36(17):e108. Epub 2008 Aug 01.