Matthew D. Wilkerson, Ph.D.
Research Summary      Publications      Software & Databases      Datasets
University of North Carolina at Chapel Hill
Lineberger Comprehensive Cancer Center
450 West Drive
Chapel Hill, North Carolina 27599
(919)-966-3864
mwilkers - @ - med.unc.edu

Research Summary

My general research aim is to answer cancer biology questions using computational methods for the purpose of improving patient-tailored therapies, prognosis and targetted basic research. More specifically, I seek to discover genetically-similar groups in heterogenous cancer types such as lung and head/neck and to characterize these groups in terms of their cancer-causing genetic mutations. Secondarily, I study genome evolution and annotation. My software is open source so that my tools are freely available to the research community.

I am a Research Staff member of the Lineberger Comprehensive Cancer Center of the University of North Carolina at Chapel Hill. I was a NIH Ruth L. Kirschstein NRSA Postdoctoral Fellow (1F32CA142039-01) at the University of North Carolina at Chapel Hill under the direction of Dr. D. Neil Hayes. My education includes a Ph.D. in Bioinformatics and Computational Biology from Iowa State University under the direction of Dr. Volker Brendel, and a B.S. in Biological Sciences from the University of Notre Dame.

Publications
(if you would like a reprint please email me)
  1. The Cancer Genome Atlas Research Network (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature. 2012 Sep 9. doi: 10.1038/nature11404. [Epub ahead of print]
    Popular press coverage:

  2. Cabanski CR, Cavin K, Bizon C, Wilkerson MD, Parker JS, Wilhelmsen KC, Perou CM, Marron JS, Hayes DN. (2012) ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data. BMC Bioinformatics. 2012 Sep 4;13(1):221. [Epub ahead of print]

  3. The Cancer Genome Atlas Research Network (2012) Comprehensive molecular characterization of human colon and rectal cancer. Nature. Jul 18;487(7407):330-7

  4. Zhao N, Ang MK, Yin XY, Patel MR, Fritchie K, Thorne L, Muldrew KL, Hayward MC, Sun W, Wilkerson MD, Chera BS, Hackman T, Zanation AM, Grilley-Olson JE, Couch ME, Shockley WW, Weissler MC, Shores CG, Funkhouser WK, Olshan AF, Hayes DN. (2012) Different cellular p16(INK4a) localisation may signal different survival outcomes in head and neck cancer. British Journal of Cancer . 2012 Jun 26. doi: 10.1038/bjc.2012.264. [Epub ahead of print]

  5. Wilkerson MD, Yin X, Walter V, Zhao N, Cabanski CR, Hayward MC, Miller CR, Socinski MA, Parsons, AM, Thorne, LB, Haithcock BE, Veeramachaneni NK, Funkhouser WK, Randell SH, Bernard PS, Perou CM, Hayes DN. (2012) Differential pathogenesis of lung adenocarcinoma subtypes involving sequence mutations, copy number, chromosomal instability and methylation. PLoS ONE 7(5): e36530. doi:10.1371/journal.pone.0036530
    Popular press coverage:

  6. Grilley-Olson JE, Hayes DN, Moore DT, Leslie KO, Wilkerson MD, Qaqish BF, Hayward MC, Cabanski CR, Yin X, Socinski MA, Stinchcombe TE, Thorne LB, Allen TC, Banks PM, Beasley MB, Borczuk AC, Cagle PT, Christensen R, Colby TV, Deblois GG, Elmberger G, Graziano P, Hart CF, Jones KD, Maia DM, Miller CR, Nance KV, Travis WD, Funkhouser WK. (2012) Validation of Interobserver Agreement in Lung Cancer Assessment Hematoxylin-Eosin Diagnostic Reproducibility for Non-Small Cell Lung Cancer-The 2004 World Health Organization Classification and Therapeutically Relevant Subsets The Archives of Pathology & Laboratory Medicine Early Online Release.

  7. Chen Z, Cheng K, Walton Z, Wang Y, Ebi H, Shimamura T, Liu Y, Tupper T, Ouyang J, Li J, Gao P, Woo MS, Xu C, Yanagita M, Altabef A, Wang S, Lee C, Nakada Y, Pena CG, Sun Y, Franchetti Y, Yao C, Saur A, Cameron MD, Nishino M, Hayes DN, Wilkerson MD, Roberts PJ, Lee CB, Bardeesy N, Butaney M, Chirieac LR, Costa DB, Jackman D, Sharpless NE, Castrillon DH, Demetri GD, Janne PA, Pandolfi PP, Cantley LC, Kung AL, Engelman JA, Wong KK. (2012) A murine lung cancer co-clinical trial identifies genetic modifiers of therapeutic response. Nature. Mar 18;483(7391):613-7.

  8. Ang MK, Patel MR, Yin X, Sundaram S, Fritchie K, Zhao N, Liu Y, Freemerman AJ, Wilkerson MD, Walter V, Weissler MC, Shockley WW, Couch ME, Zanation AM, Hackman TG, Chera BS, Harris SL, Miller CR, Thorne L, Hayward MC, Funkhouser W, Olshan AF, Shores CG, Makowski L, Hayes DN. (2011) High XRCC1-protein expression is associated with poorer survival in patients with head and neck squamous cell carcinoma. Clinical Cancer Research Oct 15;17(20):6542-52.

  9. The Cancer Genome Atlas Research Network (2011) Integrated genomic analyses of ovarian carcinoma. Nature. 2011 Jun 29;474(7353):609-15

  10. 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. Oct 1;16(19):4864-75.

  11. Carretero, J., Shimamura, T., Rikova, K., Jackson, A.L., Wilkerson, M.D., et al (2010) Integrative Genomic and Proteomic Analyses Identify Targets for Lkb1-Deficient Metastatic Lung Tumors. Cancer Cell. Volume 17, Issue 6, 547-559.

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

  13. Cabanski C.R., Qi Y., Yin X., Bair E., Hayward M.C., Fan C., Li J., Wilkerson M.D., Marron JS, Perou CM, Hayes DN. (2010) SWISS MADE: Standardized WithIn Class Sum of Squares to evaluate methodologies and dataset elements. PLoS One. 5(3):e9905.

  14. Verhaak, R.G.W., Hoadely, K.A., Purdom, E., Wang. V., Qi. Y., Wilkerson, M.D., Miller, C.R., Ding, L., Golub, T., Mesirov, J.P., Alexe, G., Lawrence, M., O'Kelly, M., Tamayo, P., Weir, B.A., Gabriel, S., Winckler, S., Gupta, S., Jakkula, L., Feiler, H.S., Hodgson, J.G., James, C.D., Sarkaria, J.N., Brennan, C., Kahn, A., Spellman, P.T., Wilson, R.K., Speed, T.P., Gray, J.W., Meyerson, M., Getz, G., Perou, C.M., & Hayes, D.N. (2010) Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. Volume 17, Issue 1, 98-110.
    Covered in popular press:

  15. Wilkerson, M.D., Bru, Y., & Brendel, V.P. (2009). Common introns within orthologous genes: software and application to plants. Briefings in Bioinformatics 10(6):631-644.

  16. Duvick, J., Fu, A., Muppirala, U., Sabharval, M., Wilkerson, M.D., Lawrence, C.J., Lushbough, C. & Brendel, V. (2008 ) PlantGDB: a resource for comparative plant genomics. Nucl. Acids Res. 36, D959-D965.

  17. Dong, Q.*, Wilkerson, M.D.* & Brendel, V. (2007) Tracembler - software for in silico chromosome walking in unassembled genomes. BMC Bioinformatics 8, 151.
    * denotes equal contribution

  18. Schlueter, S.D., Wilkerson, M.D., Dong, Q. & Brendel, V. (2006) xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features. Genome Biology 7, R111.

  19. Wilkerson, M.D., Schlueter, S.D. & Brendel, V. (2006) yrGATE: a web-based gene-structure annotation tool for the identification and dissemination of eukaryotic genes. Genome Biology 7, R58.

  20. Dong, Q., Lawrence, C.J., Schlueter, S.D., Wilkerson, M.D., Kurtz, S., Lushbough, C. & Brendel, V. (2005) Comparative plant genomics resources at PlantGDB. Plant Physiology 139, 610-618.

  21. Schlueter, S.D., Wilkerson, M.D., Huala, E., Rhee, S.Y. & Brendel, V. (2005) Community-based gene structure annotation for the Arabidopsis thaliana genome. Trends in Plant Science 10, 9-14.
Software and Databases

Datasets