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Matthew N. McCall, Ph.D. - Publications

Affiliations: 
2010 Johns Hopkins University, Baltimore, MD 
Area:
Biostatistics Biology, Bioinformatics Biology, Statistics
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28 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 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. 11: 1933. PMID 32321923 DOI: 10.1038/S41467-020-15821-9  0.394
2020 Burton DS, McCall M. Mixture Modeling for Genetic Regulatory Networks from Single Perturbation Gene Expression Experiments F1000research. 9. DOI: 10.7490/F1000Research.1118158.1  0.336
2019 Zhang Y, Cuerdo J, Halushka MK, McCall MN. The effect of tissue composition on gene co-expression. Briefings in Bioinformatics. PMID 31813949 DOI: 10.1093/Bib/Bbz135  0.368
2018 Nassiri I, McCall MN. Systematic exploration of cell morphological phenotypes associated with a transcriptomic query. Nucleic Acids Research. PMID 30011038 DOI: 10.1093/Nar/Gky626  0.318
2018 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. 8: 9783. PMID 29955168 DOI: 10.1038/S41598-018-28198-Z  0.316
2018 Halushka MK, Fromm B, Peterson KJ, McCall MN. Big Strides in Cellular MicroRNA Expression. Trends in Genetics : Tig. PMID 29361313 DOI: 10.1016/J.Tig.2017.12.015  0.325
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, et al. Toward the human cellular microRNAome. Genome Research. PMID 28877962 DOI: 10.1101/Gr.222067.117  0.388
2017 Kemperman L, McCall MN. miRcomp-Shiny: Interactive assessment of qPCR-based microRNA quantification and quality control algorithms F1000research. 6: 2046. DOI: 10.12688/F1000Research.13098.1  0.39
2017 Li N, McCall MN, Wu Z. Establishing Informative Prior for Gene Expression Variance from Public Databases Statistics in Biosciences. 9: 160-177. DOI: 10.1007/S12561-016-9172-X  0.429
2016 Komisarof J, McCall M, Newman L, Bshara W, Mohler JL, Morrison C, Land H. A four gene signature predictive of recurrent prostate cancer. Oncotarget. PMID 27966447 DOI: 10.18632/Oncotarget.13837  0.305
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. 17: 138. PMID 27000067 DOI: 10.1186/S12859-016-0987-8  0.402
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. 42: 7528-38. PMID 24875473 DOI: 10.1093/Nar/Gku461  0.304
2014 McCall MN, McMurray HR, Land H, Almudevar A. On non-detects in qPCR data. Bioinformatics (Oxford, England). 30: 2310-6. PMID 24764462 DOI: 10.1093/Bioinformatics/Btu239  0.346
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. 9: e89565. PMID 24586876 DOI: 10.1371/Journal.Pone.0089565  0.343
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. 42: D938-43. PMID 24271388 DOI: 10.1093/Nar/Gkt1204  0.619
2013 McCall MN. Estimation of Gene Regulatory Networks. Postdoc Journal : a Journal of Postdoctoral Research and Postdoctoral Affairs. 1: 60-69. PMID 27595119 DOI: 10.14304/Surya.Jpr.V1N1.7  0.357
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 (Oxford, England). 29: 1182-1189. PMID 23457041 DOI: 10.1093/Bioinformatics/Btt108  0.584
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. 13: 272. PMID 23088656 DOI: 10.1186/1471-2105-13-272  0.518
2012 McCall MN, Jaffee HA, Irizarry RA. fRMA ST: frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays. Bioinformatics (Oxford, England). 28: 3153-4. PMID 23044545 DOI: 10.1093/Bioinformatics/Bts588  0.571
2012 McCall MN, Almudevar A. Affymetrix GeneChip microarray preprocessing for multivariate analyses. Briefings in Bioinformatics. 13: 536-46. PMID 22210854 DOI: 10.1093/Bib/Bbr072  0.428
2011 Almudevar A, McCall MN, McMurray H, Land H. Fitting Boolean networks from steady state perturbation data. Statistical Applications in Genetics and Molecular Biology. 10. PMID 23089817 DOI: 10.2202/1544-6115.1727  0.345
2011 McCall MN, Irizarry RA. Thawing Frozen Robust Multi-array Analysis (fRMA). Bmc Bioinformatics. 12: 369. PMID 21923903 DOI: 10.1186/1471-2105-12-369  0.558
2011 McCall MN, Murakami PN, Lukk M, Huber W, Irizarry RA. Assessing affymetrix GeneChip microarray quality. Bmc Bioinformatics. 12: 137. PMID 21548974 DOI: 10.1186/1471-2105-12-137  0.554
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. 39: D1011-5. PMID 21177656 DOI: 10.1093/Nar/Gkq1259  0.615
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, ... ... McCall MN, et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology. 28: 827-38. PMID 20676074 DOI: 10.1038/Nbt.1665  0.574
2010 Sah S, McCall MN, Eveleigh D, Wilson M, Irizarry RA. Performance evaluation of commercial miRNA expression array platforms. Bmc Research Notes. 3: 80. PMID 20298588 DOI: 10.1186/1756-0500-3-80  0.538
2010 McCall MN, Bolstad BM, Irizarry RA. Frozen robust multiarray analysis (fRMA). Biostatistics (Oxford, England). 11: 242-53. PMID 20097884 DOI: 10.1093/Biostatistics/Kxp059  0.609
2008 McCall MN, Irizarry RA. Consolidated strategy for the analysis of microarray spike-in data. Nucleic Acids Research. 36: e108. PMID 18676452 DOI: 10.1093/Nar/Gkn430  0.559
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