Publications

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
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A curated human cellular microRNAome based on 196 primary cell types
Arun H. Patil, Andrea Baran, Zachary Brehm, Matthew N. McCall, Marc K. Halushka
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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 Gill, Ann R. Falsey, David J Topham, Mary Caserta, Edward Walsh, Xing Qiu, Thomas J. Mariani
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Gene network modeling via TopNet reveals functional dependencies between diverse tumorcritical mediator genes.
Helene R. McMurray, Aslihan Ambeskovic, Laurel A. Newman, Jordan Aldersley, Vijaya Balakrishnan, Bradley Smith, Harry A. Stern, Hartmut Land, Matthew N. McCall
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The effect of tissue composition on gene co-expression
Yun Zhang, Jonavelle Cuerdo, Marc K. Halushka, Matthew N. McCall
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Multiple imputation and direct estimation for qPCR data with non-detects
Valeriia Sherina, Helene R. McMurray, Winslow Powers, Hartmut Land, Tanzy M.T. Love, Matthew N. McCall
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Auto-regressive modeling and diagnostics for qPCR amplification
Benjamin Hsu, Valeriia Sherina, Matthew N. McCall
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Fully Bayesian imputation model for non-random missing data in qPCR
Valeriia Sherina, Matthew N. McCall, Tanzy M.T. Love
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Systematic exploration of cell morphological phenotypes associated with a transcriptomic query
Isar Nassiri, Matthew N. McCall
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Big Strides in Cellular MicroRNA Expression
Marc K. Halushka, Bastian Fromm, Kevin J. Peterson, Matthew N. McCall
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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
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Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome
Matthew N. McCall, Peter B. Illei, Marc K. Halushka
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A microRNA biomarker of hepatocellular carcinoma recurrence following liver transplantation accounting for within-patient heterogeneity
Qingyan Lilly Xie, Anthony Almudevar, Christa L. Whitney-Miller, Christopher T. Barry, Matthew N. McCall
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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
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Lessons from miR-143/145: The importance of cell-type localization of miRNAs
Oliver A. Kent, Matthew N. McCall, Toby C. Cornish, Marc K. Halushka
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On Non-Detects in qPCR Data
Matthew N. McCall, Helene R. McMurray, Hartmut Land, Anthony Almudevar
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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
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