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

Publications

Showing all 28 journal articles & 0 books available

Journal Articles

10/2017
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 0; 27(10):1769-1781. Epub 2017 Sep 06.

1/10/2017
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.

9/1/2016
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.

4/8/2016
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.

3/22/2016
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.

10/19/2015
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.

5/2015
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 0; 20(5):505-13. Epub 2015 Jan 10.

1/2015
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 0; 11(1):86-96. Epub 2014 Sep 25.

8/15/2014
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.

7/2014
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 0; 42(12):7528-38. Epub 2014 May 29.

1/2014
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 0; 42(Database issue):D938-43. Epub 2013 Nov 22.

2014
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.

5/1/2013
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.

1/2013
McCall MN. "Estimation of Gene Regulatory Networks." Postdoc journal : a journal of postdoctoral research and postdoctoral affairs.. 2013 Jan 0; 1(1):60-69.

2013
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.

12/1/2012
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.

10/22/2012
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.

9/2012
McCall MN, Almudevar A. "Affymetrix GeneChip microarray preprocessing for multivariate analyses." Briefings in bioinformatics. 2012 Sep 0; 13(5):536-46. Epub 2011 Dec 30.

2/2012
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 0; 12(2):428-37. Epub 2011 Oct 18.

11/2/2011
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.

10/5/2011
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.

9/16/2011
McCall MN, Irizarry RA. "Thawing Frozen Robust Multi-array Analysis (fRMA)." BMC bioinformatics. 2011 Sep 16; 12:369. Epub 2011 Sep 16.

5/7/2011
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.

1/2011
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 0; 39(Database issue):D1011-5.

8/2010
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 0; 28(8):827-38. Epub 2010 Jul 30.

4/2010
McCall MN, Bolstad BM, Irizarry RA. "Frozen robust multiarray analysis (fRMA)." Biostatistics.. 2010 Apr 0; 11(2):242-53. Epub 2010 Jan 22.

3/18/2010
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.

10/2008
McCall MN, Irizarry RA. "Consolidated strategy for the analysis of microarray spike-in data." Nucleic acids research.. 2008 Oct 0; 36(17):e108. Epub 2008 Aug 01.