Matthew N. McCall, Ph.D. - Publications

Affiliations: 
2010 Johns Hopkins University, Baltimore, MD 
Area:
Biostatistics Biology, Bioinformatics Biology, Statistics

20/64 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
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. 9: 18. PMID 27059462 DOI: 10.1186/S12920-016-0179-4  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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. 4: 263. PMID 24376454 DOI: 10.3389/Fgene.2013.00263  0.8
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  0.8
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  0.8
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  0.8
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  0.8
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  0.8
2011 McCall MN, Kent OA, Yu J, Fox-Talbot K, Zaiman AL, Halushka MK. MicroRNA profiling of diverse endothelial cell types. Bmc Medical Genomics. 4: 78. PMID 22047531 DOI: 10.1186/1755-8794-4-78  0.8
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  0.8
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  0.8
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  0.8
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, ... ... 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  0.8
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  0.8
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  0.8
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  0.8
Low-probability matches
2021 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. 11: 13. PMID 34001262 DOI: 10.1186/s13395-021-00269-2  0.01
2021 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. 14: 57. PMID 33632195 DOI: 10.1186/s12920-021-00913-2  0.01
2020 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. PMID 33251806 DOI: 10.1021/acs.jproteome.0c00673  0.01
2020 Hsu B, Sherina V, McCall MN. Auto-regressive modeling and diagnostics for qPCR amplification. Bioinformatics (Oxford, England). PMID 33244594 DOI: 10.1093/bioinformatics/btaa1000  0.01
2020 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. 21: 545. PMID 33243147 DOI: 10.1186/s12859-020-03807-9  0.01
2020 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. PMID 32926149 DOI: 10.1093/Infdis/Jiaa576  0.01
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  0.01
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  0.01
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  0.01
2019 Kreidenweiss A, Trauner F, Rodi M, Koehne E, Held J, Wyndorps L, Manouana GP, McCall M, Adegnika AA, Lalremruata A, Kremsner PG, Fendel R, Sandri TL. Monitoring the threatened utility of malaria rapid diagnostic tests by novel high-throughput detection of Plasmodium falciparum hrp2 and hrp3 deletions: A cross-sectional, diagnostic accuracy study. Ebiomedicine. PMID 31761619 DOI: 10.1016/J.Ebiom.2019.10.048  0.01
2019 Koehne E, Kreidenweiss A, Zoleko Manego R, McCall M, Mombo-Ngoma G, Mackwitz MKW, Hansen FK, Held J. Histone deacetylase inhibitors with high in vitro activities against Plasmodium falciparum isolates collected from Gabonese children and adults. Scientific Reports. 9: 17336. PMID 31758015 DOI: 10.1038/S41598-019-53912-W  0.01
2019 Wang YT, Lim Y, McCall MN, Huang KT, Haynes CM, Nehrke K, Brookes PS. Cardioprotection by the mitochondrial unfolded protein response (UPR) requires ATF5. American Journal of Physiology. Heart and Circulatory Physiology. PMID 31274354 DOI: 10.1152/Ajpheart.00244.2019  0.01
2019 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. 8: e12907. PMID 31199303 DOI: 10.2196/12907  0.01
2018 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. PMID 30403776 DOI: 10.1093/Hmg/Ddy383  0.01
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  0.01
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  0.01
2018 Hill MA, Alexander WB, Guo B, Kato Y, Patra KC, O'Dell MR, McCall MN, Whitney-Miller CL, Bardeesy N, Hezel AF. Kras and Tp53 mutations cause cholangiocyte- and hepatocyte-derived cholangiocarcinoma. Cancer Research. PMID 29871934 DOI: 10.1158/0008-5472.Can-17-1123  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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  0.01
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. 99: 624-35. PMID 27588449 DOI: 10.1016/J.Ajhg.2016.07.007  0.01
2015 Lee EM, Yee D, Busfield SJ, McManus JF, Cummings N, Vairo G, Wei A, Ramshaw HS, Powell JA, Lopez AF, Lewis ID, McCall MN, Lock RB. Efficacy of an Fc-modified anti-CD123 antibody (CSL362) combined with chemotherapy in xenograft models of acute myelogenous leukemia in immunodeficient mice. Haematologica. 100: 914-26. PMID 26130514 DOI: 10.3324/haematol.2014.113092  0.01
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  0.01
2013 Leuschen JN, Schuman SG, Winter KP, McCall MN, Wong WT, Chew EY, Hwang T, Srivastava S, Sarin N, Clemons T, Harrington M, Toth CA. Spectral-domain optical coherence tomography characteristics of intermediate age-related macular degeneration. Ophthalmology. 120: 140-50. PMID 22968145 DOI: 10.1016/J.Ophtha.2012.07.004  0.01
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. 12: 428-437. PMID 22008552 DOI: 10.1111/J.1600-6143.2011.03788.X  0.01
2008 Sleiman RJ, Gray PP, McCall MN, Codamo J, Sunstrom NAS. Accelerated cell line development using two-color fluorescence activated cell sorting to select highly expressing antibody-producing clones Biotechnology and Bioengineering. 99: 578-587. DOI: 10.1002/bit.21612  0.01
2006 Bigelow CE, Hammer DX, Ferguson RD, Iftimia NV, Ustun TE, Rockwell BA, Toth CA. Precision targeting with a tracking adaptive optics scanning laser ophthalmoscope Optics Infobase Conference Papers. DOI: 10.1117/12.647477  0.01
2005 Lee WJ, Robinson JA, Holman NA, McCall MN, Roberts-Thomson SJ, Monteith GR. Antisense-mediated inhibition of the plasma membrane calcium-ATPase suppresses proliferation of MCF-7 cells Journal of Biological Chemistry. 280: 27076-27084. PMID 15911623 DOI: 10.1074/jbc.M414142200  0.01
2001 Quan A, McCall MN, Sewell WA. Rapid publication: Dexamethasone inhibits the binding of nuclear factors to the IL-5 promoter in human CD4 +T cells Journal of Allergy and Clinical Immunology. 108: 340-348. PMID 11544451 DOI: 10.1067/mai.2001.118512  0.01
2001 Toth CA, Chiu EK, Winter KP, McCall MN, Bailey SF, Harkrider CJ, Hauger S. In-vivo response to free electron laser incision of the rabbit cornea. Lasers in Surgery and Medicine. 29: 44-52. PMID 11500862 DOI: 10.1002/lsm.1085  0.01
2001 McCall MN, Harkrider CJ, Deramo V, Bailey SF, Winter KP, Rockwell BA, Stolarski D, Toth CA. Using optical coherence tomography to elucidate the impact of fixation on retinal laser pathology Proceedings of Spie - the International Society For Optical Engineering. 4257: 142-148. DOI: 10.1117/12.434698  0.01
1999 McCall MN, Hodgkin PD. Switch recombination and germ-line transcription are division-regulated events in B lymphocytes Biochimica Et Biophysica Acta - Gene Structure and Expression. 1447: 43-50. PMID 10500242 DOI: 10.1016/S0167-4781(99)00131-1  0.01
1998 McCall MN. Repressible antisense inhibition in B lymphocytes Biochimica Et Biophysica Acta - Gene Structure and Expression. 1397: 65-72. PMID 9545537 DOI: 10.1016/S0167-4781(98)00003-7  0.01
1997 McCall MN, Kuchel MG, Basten A. Evaluation of antisense inhibition in a B cell model Biochemistry and Molecular Biology International. 42: 45-56. PMID 9192084 DOI: 10.1080/15216549700202421  0.01
1996 Bradbury RA, McCall MN, Brown MJ, Conigrave AD. Functional heterogeneity of human term cytotrophoblasts revealed by differential sensitivity to extracellular Ca2+ and nucleotides Journal of Endocrinology. 149: 135-144. PMID 8676046  0.01
1992 McCall MN, Shotton DM, Barclay AN. Expression of soluble isoforms of rat CD45. Analysis by electron microscopy and use in epitope mapping of anti-CD45R monoclonal antibodies Immunology. 76: 310-317. PMID 1378817  0.01
1992 Barclay AN, McCall MN. CD45; from alloantigen to mapping of restricted epitopes using recombinant soluble CD45 isoforms. Biochemical Society Transactions. 20: 161-4. PMID 1378795  0.01
1989 Mendz GL, McCall MN, Kuchel PW. Identification of methyl resonances in the 1H NMR spectrum of incubated blood cell lysates Journal of Biological Chemistry. 264: 2100-2107. PMID 2914895  0.01
1989 McCall MN, Easterbrook-Smith SB. Comparison of the role of tyrosine residues in human IgG and rabbit IgG in binding of complement subcomponent C1q Biochemical Journal. 257: 845-851. PMID 2784672  0.01
1989 Mendz GL, McCall MN, Kuchel PW. Characterization of leukocyte enzymes involved in the release of amino acids in incubated blood cell lysates Journal of Biological Chemistry. 264: 2108-2117. PMID 2644254  0.01
1987 McCall MN, Easterbrook-Smith SB. The presence of histidine residues at or near the C1q binding site of rabbit immunoglobulin G Biochimica Et Biophysica Acta (Bba)/Protein Structure and Molecular. 912: 9-15. PMID 3493808 DOI: 10.1016/0167-4838(87)90241-X  0.01
1987 McCall MN, Easterbrook-Smith SB. High-performance liquid chromatography-based assay for the quantitation of protein maleylation at the picomole level Analytical Biochemistry. 166: 440-445. PMID 3434785 DOI: 10.1016/0003-2697(87)90597-5  0.01
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