Matthew D Wilkerson

Ph.D.

Department of Primary Appointment:
School of Medicine
Anatomy, Physiology and Genetics
Title
Associate Professor, Director of Data Science Division, Center for Military Precision Health
Location: Uniformed Services University of the Health Sciences, Bethesda, MD
Research Interests:
Computational Biology, Bioinformatics, Data Science
Lung Cancer, Cancer Biology, Psychiatric Genomics.
Office Phone

Education

Postdoctoral Fellowship
Lineberger Comprehensive Cancer Center
University of North Carolina at Chapel Hill, Chapel Hill, NC

Ph.D. in Bioinformatics and Computational Biology
Iowa State University, Ames, IA

B.S. in Biological Sciences
University of Notre Dame, Notre Dame, IN

Biography

Dr. Wilkerson is Associate Professor of Anatomy, Physiology and Genetics at Uniformed Services University and serves as Director of the Data Science Division in the Center for Military Precision Health (CMPH). Under Dr. Wilkerson’s leadership, the Data Science Division analyzes sequencing data produced by CMPH through applying and developing computational tools for genome data analysis, phenotype analysis, hypothesis evaluation, and data management. Through this infrastructure, the Data Science Division has analyzed over one hundred thousand samples across all studies, since the origination of the Collaborative Health Initiative Research Program through the present in CMPH. These research efforts are focused on characterizing the molecular profiles of cancer, inherited diseases, and environmental exposures.

The Wilkerson laboratory’s overall research aim is to identify and characterize molecular subtypes of disease and their underlying molecular etiology. Dr. Wilkerson discovered new molecular classifications of lung adenocarcinoma and squamous cell carcinoma using gene expression profiling, which have been utilized by the lung cancer research community. He contributed to the National Cancer Institute’s The Cancer Genome Atlas research program, including leading the pheochromocytoma and paraganglioma study, which reported the first fusion gene in the disease defining a new prognostic subtype. The Wilkerson laboratory also develops novel computational methods for genome analysis, which are published as open source software. Dr. Wilkerson currently leads the Data Analysis Working Group for the Applied Proteogenomics OrganizationaL Learning and Outcomes (APOLLO) network. APOLLO is a DoD, NCI and VA collaborative cancer research study and is described in this paper (PubMed ID: 30838639)

Representative publications, projects, and/or deployments

Data Science Core Director, Center for Military Precision Health, 2021-present

Member, John P. Murtha Cancer Center. Walter Reed National Military Medical Center, 2017-present

Bioinformatics Core Director, Collaborative Health Initiative Research Program, The American Genome Center, 2015-2020

Superior Performance Award, Henry M. Jackson Foundation for the Advancement of Military Medicine, 2016,2018-2020

AACR Team Science Award, The American Association for Cancer Research 2020

Research Associate Professor of Genetics, University of North Carolina, Chapel Hill, NC 2013-2015

The Cancer Genome Atlas Research Network, 2008-2017

Ruth L. Kirschstein National Research Service Award Fellowship (F32 NRSA), National Cancer Institute, 2009-2012

Bibliography

Soltis AR, Bateman NW, Liu J, Nguyen T, Franks TJ, Zhang X, Dalgard CL, Viollet C, Somiari S, Yan C, Zeman K, Skinner WJ, Lee JSH, Pollard HB, Turner C, Petricoin EF, Meerzaman D, Conrads TP, Hu H; APOLLO Research Network, Shriver CD, Moskaluk CA, Browning RF Jr, Wilkerson MD. (2022) Proteogenomic analysis of lung adenocarcinoma reveals tumor heterogeneity, survival determinants, and therapeutically relevant pathways. Cell Reports Medicine. 2022 Nov 15;3(11):100819. doi: 10.1016/j.xcrm.2022.100819.

Kohaar I, Zhang X, Tan SH, Nousome D, Babcock K, Ravindranath L, Sukumar G, Mcgrath-Martinez E, Rosenberger J, Alba C, Ali A, Young D, Chen Y, Cullen J, Rosner IL, Sesterhenn IA, Dobi A, Chesnut G, Turner C, Dalgard C, Wilkerson MD, Pollard HB, Srivastava S, Petrovics G. (2022) Germline mutation landscape of DNA damage repair genes in African Americans with prostate cancer highlights potentially targetable RAD genes.Nature Communications. 2022 Mar 15;13(1):1361. doi: 10.1038/s41467-022-28945-x.

Hupalo D, Forsberg CW, Goldberg J, Kremen WS, Lyons MJ, Soltis AR, Viollet C, Ursano RJ, Stein MB, Franz CE, Sun YV, Vaccarino V, Smith NL, Dalgard CL, Wilkerson MD*, Pollard HB*. (2021) Rare variant association study of veteran twin whole-genomes links severe depression with a nonsynonymous change in the neuronal gene BHLHE22. World Journal Biological Psychiatry. 2021 Nov 29:1-12. doi: 10.1080/15622975.2021.1980316 *contributed equally

Zhang Q, et al. including Wilkerson MD in NIAID-USUHS/TAGC COVID Immunity Group. (2020). Inborn errors of type I IFN immunity in patients with life-threatening COVID-19. Science. 2020 Oct 23;370(6515):eabd4570

Soltis AR, Dalgard CL, Pollard HB, Wilkerson MD. (2020). MutEnricher: a flexible toolset for somatic mutation enrichment analysis of tumor whole genomes. BMC Bioinformatics. Jul 31;21(1):338. doi: 10.1186/s12859-020-03695-z.

Fishbein L, Leshchiner I, Walter V, Danilova L, Robertson AG, Johnson AR, Lichtenberg TM, Murray BA, Ghayee HK, Else T, Ling S, Jefferys SR, de Cubas AA, Wenz B, Korpershoek E, Amelio AL, Makowski L, Rathmell WK, Gimenez-Roqueplo AP, Giordano TJ, Asa SL, Tischler AS; Cancer Genome Atlas Research Network, Pacak K, Nathanson KL, Wilkerson MD. (2017) Comprehensive Molecular Characterization of Pheochromocytoma and Paraganglioma. Cancer Cell. 2017 Feb 13;31(2):181-193

The Cancer Genome Atlas Research Network (including Wilkerson MD). (2014) Comprehensive molecular profiling of lung adenocarcinoma. Nature, 511(7511):543-50.

Wilkerson MD, Cabanski CR, Sun W, Hoadley KA, Walter V, Mose LE, Troester MA, Hammerman PS, Parker JS, Perou CM, Hayes DN. (2014) Integrated RNA and DNA sequencing improves mutation detection in low purity tumors. Nucleic Acids Research. 42 (13): e107.

Wilkerson MD, Yin X, Hoadley KA, Liu Y, Hayward MC, Cabanski CR, Muldrew KL, Miller CR, Randell SH, Socinski MA, Parsons AM, Funkhouser WK, Lee CB, Robert PJ, Thorne L, Bernard PS, Perou CM, Hayes DN. (2010). Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types. Clinical Cancer Research. 16(19):4864-75.

Wilkerson MD, Hayes DN. (2010). ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking. Bioinformatics, Jun 15;26(12):1572-3.