Selected Publications

miRglmm: a generalized linear mixed model of isomiR-level counts improves estimation of miRNA-level differential expression and uncovers variable differential expression between isomiRs
Andrea M. Baran, Arun H. Patil, Ernesto Aparicio-Puerta, Seong-Hwan Jun, Marc K. Halushka, Matthew N. McCall
Genome Biology, 26, 102 (2025)
Apr 22, 2025

journal URL

Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human Tissues

Patterns of Unwanted Biological and Technical Expression Variation Among 49 Human Tissues
Tim O. Nieuwenhuis, Hunter H. Giles, Jeremy V.A. Arking, Arun H. Patil, Wen Shi, Matthew N. McCall, Marc K. Halushka
Laboratory Investigation, 104, 6 (2024)
May 15, 2024

journal URL

A model-based hierarchical Bayesian approach to Sholl analysis

A model-based hierarchical Bayesian approach to Sholl analysis
Erik VonKaenel, Alexis Feidler, Rebecca Lowery, Katherine Andersh, Tanzy Love, Ania Majewska, Matthew N McCall
Bioinformatics, 40, 4 (2024)
Apr 2, 2024

journal URL

Protocol to use TopNet for gene regulatory network modeling using gene expression data from perturbation experiments
Helene R. McMurray, Harry A. Stern, Aslihan Ambeskovic, Hartmut Land, Matthew N. McCall
STAR Protocols, 3(4), 101737 (2022)
Dec 16, 2022

journal URL

A curated human cellular microRNAome based on 196 primary cell types

A curated human cellular microRNAome based on 196 primary cell types
Arun H Patil, Andrea Baran, Zachary P Brehm, Matthew N McCall, Marc K Halushka
GigaScience, 11, giac083 (2022)
Aug 25, 2022

journal URL

A systems genomics approach uncovers molecular associates of RSV severity

A systems genomics approach uncovers molecular associates of RSV severity
Matthew N. McCall, Chin-Yi Chu, Lu Wang, Lauren Benoodt, Juilee Thakar, Anthony Corbett, Jeanne Holden-Wiltse, Christopher Slaunwhite, Alex Grier, Steven R. Gill, Ann R. Falsey, David J. Topham, Mary T. Caserta, Edward E. Walsh, Xing Qiu, Thomas J. Mariani
PLoS Computational Biology, 17(12), e1009617 (2021)
Dec 28, 2021

journal URL

Gene network modeling via TopNet reveals functional dependencies between diverse tumor-critical mediator genes

Gene network modeling via TopNet reveals functional dependencies between diverse tumor-critical mediator genes
Helene R. McMurray, Aslihan Ambeskovic, Laurel A. Newman, Jordan Aldersley, Vijaya Balakrishnan, Bradley Smith, Harry A. Stern, Hartmut Land, Matthew N. McCall
Cell Reports, 37(12), 110136 (2021)
Dec 21, 2021

journal URL

The role of P2Y12 in the kinetics of microglial self-renewal and maturation in the adult visual cortex in vivo
Monique S Mendes, Linh Le, Jason Atlas, Zachary Brehm, Antonio Ladron-de-Guevara, Evelyn Matei, Cassandra Lamantia, Matthew N McCall, Ania K Majewska
eLife, 10, e61173 (2021)
Jul 12, 2021

journal URL

Autoregressive modeling and diagnostics for qPCR amplification

Autoregressive modeling and diagnostics for qPCR amplification
Benjamin Hsu, Valeriia Sherina, Matthew N McCall
Bioinformatics, 36(22-23), 5386–5391 (2020)
Dec 11, 2020

journal URL

Multiple imputation and direct estimation for qPCR data with non-detects
Valeriia Sherina, Helene R. McMurray, Winslow Powers, Harmut Land, Tanzy M. T. Love, Matthew N. McCall
BMC Bioinformatics, 21, 545 (2020)
Nov 26, 2020

journal URL

Consistent RNA sequencing contamination in GTEx and other data sets
Tim O. Nieuwenhuis, Stephanie Y. Yang, Rohan X. Verma, Vamsee Pillalamarri, Dan E. Arking, Avi Z. Rosenberg, Matthew N. McCall, Marc K. Halushka
Nature Communications, 11, 1933 (2020)
Apr 22, 2020

journal URL

The effect of tissue composition on gene co-expression

The effect of tissue composition on gene co-expression
Yun Zhang, Jonavelle Cuerdo, Marc K Halushka, Matthew N McCall
Briefings in Bioinformatics, 22(1), 127-139 (2021)
Dec 8, 2019

journal URL

Systematic exploration of cell morphological phenotypes associated with a transcriptomic query
Isar Nassiri, Matthew N. McCall
Nucleic Acids Research, 46(19), e116 (2018)
Jul 16, 2018

journal URL

Big Strides in Cellular MicroRNA Expression
Marc K. Halushka, Bastian Fromm, Kevin J. Peterson, Matthew N. McCall
Trends in Genetics, 34(3), 165-167 (2018)
Jan 17, 2018

journal URL

Toward the human cellular microRNAome

Toward the human cellular microRNAome
Matthew N. McCall, Min-Sik Kim, Mohammed Adil, Arun H. Patil, Yin Lu, Christopher J. Mitchell, Pamela Leal-Rojas, Jinchong Xu, Manoj Kumar, Valina L. Dawson, Ted M. Dawson, Alexander S. Baras, Avi Z. Rosenberg, Dan E. Arking, Kathleen H. Burns, Akhilesh Pandey, Marc K. Halushka
Genome Research, 27, 1769-1781 (2017)
Sep 6, 2017

journal URL

Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome
Matthew N. McCall, Peter B. Illei, Marc K. Halushka
American Journal of Human Genetics, 99(3), 624-635 (2016)
Sep 1, 2016

journal URL

A microRNA biomarker of hepatocellular carcinoma recurrence following liver transplantation accounting for within-patient heterogeneity
Qing Yan Xie, Anthony Almudevar, Christa L. Whitney-Miller, Christopher T. Barry, Matthew N. McCall
BMC Medical Genomics, 9, 18 (2016)
Apr 8, 2016

journal URL

A benchmark for microRNA quantification algorithms using the OpenArray platform
Matthew N. McCall, Alexander S. Baras, Alexander Crits-Christoph, Roxann Ingersoll, Melissa A. McAlexander, Kenneth W. Witwer, Marc K. Halushka
BMC Bioinformatics, 17, 138 (2016)
Mar 22, 2016

journal URL

On Non-Detects in qPCR Data
Matthew N. McCall, Helene R. McMurray, Hartmut Land, Anthony Almudevar
Bioinformatics, 30(16), 2310-2316 (2014)
Apr 23, 2014

journal URL

On the underlying assumptions of threshold Boolean networks as a model for genetic regulatory network behavior
Van Tran, Matthew N. McCall, Helene R. McMurray, Anthony Almudevar
Frontiers in Genetics, 4, 263 (2013)
Dec 10, 2013

journal URL

The Gene Expression Barcode 3.0: improved data processing and mining tools
Matthew N. McCall, Harris A. Jaffee, Susan J. Zelisko, Neeraj Sinha, Guido Hooiveld, Rafael A. Irizarry, Michael J. Zilliox
Nucleic Acids Research, 42(D1), D938–D943 (2014)
Nov 22, 2013

journal URL

fRMA ST: Frozen robust multiarray analysis for Affymetrix Exon and Gene ST arrays
Matthew N. McCall, Harris A. Jaffee, Rafael A. Irizarry
Bioinformatics, 28(23), 3153–3154 (2012)
Oct 7, 2012

journal URL

Affymetrix GeneChip microarray preprocessing for multivariate analyses
Matthew N. McCall, Anthony Almudevar
Briefings in Bioinformatics, 13(5), 536–546 (2012)
Dec 31, 2011

journal URL

Thawing Frozen Robust Multi-array Analysis
Matthew N. McCall, Rafael A. Irizarry
BMC Bioinformatics, 12, 369 (2011)
Sep 16, 2011

journal URL

Assessing Affymetrix GeneChip Microarray Quality
Matthew N. McCall, Peter N Murakami, Margus Lukk, Wolfgang Huber, Rafael A. Irizarry
BMC Bioinformatics, 12, 137 (2011)
May 7, 2011

journal URL

The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes
Matthew N. McCall, Karan Uppal, Harris A. Jaffee, Michael J. Zilliox, Rafael A. Irizarry
Nucleic Acids Research, 38, D1011–D1015 (2011)
Dec 16, 2010

journal URL

Frozen Robust Multi-Array Analysis (fRMA)
Matthew N. McCall, Benjamin M. Bolstad, Rafael A. Irizarry
Biostatistics, 11(2), 242–253 (2010)
Jan 22, 2010

journal URL

Consolidated strategy for the analysis of microarray spike-in data
Matthew N. McCall, Rafael A. Irizarry
Nucleic Acids Research, 16(17), e108 (2008)
Aug 1, 2008

journal URL

No matching items