Matthew D. Wilkerson, Ph.D.
Research Summary      Publications      Software & Databases      Datasets
University of North Carolina at Chapel Hill
Lineberger Comprehensive Cancer Center
Department of Genetics
450 West Drive
Chapel Hill, North Carolina 27599
mwilkers - @ -

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 an Assistant Professor in the Department of Genetics and a 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.

(if you would like a reprint please email me)
  1. The Cancer Genome Atlas Network, Wilkerson MD - Virus, RNA, Mutation analysis. (2015) Comprehensive genomic characterization of head and neck squamous cell carcinomas. Nature 517, 576 - 582.

  2. Chandler RL, Damrauer JS, Raab JR, Schisler JC, Wilkerson MD, Didion JP, Starmer J, Serber D, Yee D, Xiong J, Darr DB, de Villena FP, Kim WY, Magnuson T. (2015) Coexistent ARID1A-PIK3CA mutations promote ovarian clear-cell tumorigenesis through pro-tumorigenic inflammatory cytokine signalling. Nature Communications . 6:6118

  3. The Cancer Genome Atlas Network, Wilkerson MD - Analysis Working Group. (2014) Integrated genomic characterization of papillary thyroid carcinoma. Cell 159(3):676-90.

  4. Parfenov M, Pedamallu CS, Gehlenborg N, Freeman SS, Danilova L, Bristow CA, Lee S, Hadjipanayis AG, Ivanova EV, Wilkerson MD, Protopopov A, Yang L, Seth S, Song X, Tang J, Ren X, Zhang J, Pantazi A, Santoso N, Xu AW, Mahadeshwar H, Wheeler DA, Haddad RI, Jung J, Ojesina AI, Issaeva N, Yarbrough WG, Hayes DN, Grandis JR, El-Naggar AK, Meyerson M, Park PJ, Chin L, Seidman JG, Hammerman PS, Kucherlapati R; Cancer Genome Atlas Network. (2014) Characterization of HPV and host genome interactions in primary head and neck cancers. Proc Natl Acad Sci. 2014 Oct 28;111(43):15544-9

  5. Ni Zhao, Matthew D. Wilkerson, Usman Shah, Xiaoying Yin, Anyou Wang, Michele C. Hayward, Patrick Roberts, Carrie B. Lee, Alden M. Parsons, Leigh B. Thorne, Benjamin E. Haithcock, Juneko E. Grilley-Olson, Thomas E. Stinchcombe, William K. Funkhouser, Kwok K. Wong, Norman E. Sharpless, D. Neil Hayes (2014) Alterations of LKB1 and KRAS and Risk of Brain Metastasis: Comprehensive Characterization by Mutation Analysis, Copy Number, and Gene Expression in Non-Small-Cell Lung Carcinoma . Lung Cancer 2014 Aug DOI: Publication stage: In Press Accepted Manuscript [Epub ahead of print]

  6. Davis et al. The Cancer Genome Atlas Research Network. (2014) The Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma . Cancer Cell 2014 Aug 20. pii: S1535-6108(14)00304-3. doi: 10.1016/j.ccr.2014.07.014. [Epub ahead of print] [Epub ahead of print]

  7. Hoadley KA, Yau C, Wolf DM, Cherniack AD, Tamborero D, Ng S, Leiserson MD, Niu B, McLellan MD, Uzunangelov V, Zhang J, Kandoth C, Akbani R, Shen H, Omberg L, Chu A, Margolin AA, Van't Veer LJ, Lopez-Bigas N, Laird PW, Raphael BJ, Ding L, Robertson AG, Byers LA, Mills GB, Weinstein JN, Van Waes C, Chen Z, Collisson EA; Cancer Genome Atlas Research Network (Wilkerson MD), Benz CC, Perou CM, Stuart JM., (2014) Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin. Cell 158(4):929-44.

  8. Orvis T, Hepperla A, Walter V, Song S, Simon JM, Parker JS, Wilkerson MD, Desai N, Major MB, Hayes DN, Davis IJ, Weissman BE. (2014) BRG1/SMARCA4 inactivation promotes non-small cell lung cancer aggressiveness by altering chromatin organization. . Cancer Research 2014 Aug 12. pii: canres.0061.2014. [Epub ahead of print]

  9. Kimes PK, Cabanski CR , Wilkerson MD, Zhao N, Johnson AR, Perou CM, Makowski L, Maher CA, Liu Y, Marron JS, Hayes DN. (2014) SigFuge: single gene clustering of RNA-seq reveals differential isoform usage among cancer samples. Nucleic Acids Research (2014) 42 (14): e113. doi: 10.1093/nar/gku521 First published online: July 16, 2014

  10. The Cancer Genome Atlas Research Network, Wilkerson MD (mRNA analysis, Figure 2A, 5A, Disease Analysis Working Group). (2014) Comprehensive molecular profiling of lung adenocarcinoma Nature, doi:10.1038/nature13385, Online ahead of print, 09 July 2014
    Popular press coverage: Further characterizes subtypes described in [17]

  11. 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. doi: 10.1093/nar/gku489 first published online June 26, 2014
    Popular press coverage:

  12. Li R, Faden DL, Fakhry C, Langelier C, Jiao Y, Wang Y, Wilkerson MD, Pedamallu CS, Old M, Lang J, Loyo M, Ahn SM, Tan M, Gooi Z, Chan J, Richmon J, Wood LD, Hruban RH, Bishop J, Westra WH, Chung CH, Califano J, Gourin CG, Bettegowda C, Meyerson M, Papadopoulos N, Kinzler KW, Vogelstein B, DeRisi JL, Koch WM, Agrawal N. (2014) Clinical, Genomic and Metagenomic Characterization of Oral Tongue Squamous Cell Carcinoma in Patients Who Do Not Smoke.. Head & Neck. Jun 21. doi: 10.1002/hed.23807. [Epub ahead of print]

  13. Mose LE, Wilkerson MD, Hayes DN, Perou CM, Parker JS. (2014) ABRA: improved coding indel detection via assembly based re-alignment. Bioinformatics. 2014 Jun 6. pii: btu376. [Epub ahead of print]

  14. Wilkerson LM, Iwata II, Wilkerson MD, Heflin MT (2014) An Educational Intervention to Improve Internal Medicine Interns' Awareness of Hazards of Hospitalization in Acutely Ill Older Adults Journal of the American Geriatrics Society. Article first published online: 11 MAR 2014 DOI: 10.1111/jgs.12733 [Epub ahead of print]

  15. The Cancer Genome Atlas Research Network (2014) Comprehensive molecular characterization of urothelial bladder carcinoma Nature. 2014 Jan 29. doi: 10.1038/nature12965. [Epub ahead of print]

  16. Kim Y, Hammerman PS, Kim J, Yoon JA, Lee Y, Sun JM, Wilkerson MD, Pedamallu CS, Cibulskis K, Yoo YK, Lawrence MS, Stojanov P, Carter SL, McKenna A, Stewart C, Sivachenko AY, Oh IJ, Kim HK, Choi YS, Kim K, Shim YM, Kim KS, Song SY, Na KJ, Choi YL, Hayes DN, Kim J, Cho S, Kim YC, Ahn JS, Ahn MJ, Getz G, Meyerson M, Park K. (2013) Integrative and Comparative Genomic Analysis of Lung Squamous Cell Carcinomas in East Asian Patients. J Clin Oncol. 2013 Dec 9. [Epub ahead of print]

  17. Seidel D, Zander T, Peifer M, Cuesta LF, Leenders F, Ansen S, Lu X, Heukamp LC, Russell P, Wainer Z, Rogers TM, Gabler F, Wilkening I, Muller C, Nguyen C, Berg J, Dahmen I, Menon R, Petersen I, Chen Y, Soltermann A, Moch H, Solberg S, Iversen ML, Helland A, Muley T, Hoffmann H, Schnabel PA, Groen H, Timens W, Sietsma H, Stoelben E, Ludwig C, Brockmann M, Smit E, Heideman DA, Snijders PJ, Besse B, Brambilla C, Lantuejoul S, Sibilot DM, Clement JH, Weder W, Schildhaus HU, Querings S, Altmuller J, Baessmann I, Carter SL, Getz G, Meyerson M, Hayes DN, Wilkerson MD, Achter V, Lang U, Schneider PM, Bogus M, Cappuzzo F, Ligorio C, Damiani S, Field JK, Hyde R, Validire P, Girard P, Muscarella LA, Fazio VM, Sanger J, Hallek M, Solomon B, Soria JC, Pao W, Nurnberg P, Thunnissen E, Brustugun OT, Travis WD, Buttner R, Perner S, Wolf J, Wright G, Thomas RK. (2013) A Genomics-Based Classification of Human Lung Tumors. Science Translational Medicine. Vol. 5, Issue 209, p. 209ra153

  18. Akbay EA, Koyama S, Carretero J, Altabef A, Tchaicha JH, Christensen CL, Mikse OR, Cherniack AD, Beauchamp EM, Pugh TJ, Wilkerson MD, Fecci PE, Butaney M, Reibel JB, Soucheray M, Cohoon TJ, Janne PA, Meyerson M, Hayes DN, Shapiro GI, Shimamura T, Sholl LM, Rodig SJ, Freeman GJ, Hammerman PS, Dranoff G, Wong KK. (2013) Activation of the PD-1 pathway contributes to immune escape in EGFR-driven lung tumors. Cancer Discovery. Epub ahead of print.

  19. The Cancer Genome Atlas Research Network (2013) The Cancer Genome Atlas Pan-Cancer analysis project . Nature Genetics. Epub ahead of print.

  20. Wu D, Pang Y, Wilkerson MD, Wang D, Hammerman PS, Liu JS.(2013) Gene-expression data integration to squamous cell lung cancer subtypes reveals drug sensitivity. . British Journal of Cancer Epub ahead of print.

  21. Cabanski CR, Wilkerson MD, Soloway M, Parker JS, Liu J, Prins JF, Marron JS, Perou CM, Hayes DN. (2013) BlackOPs: increasing confidence in variant detection through mappability filtering. Nucleic Acids Research Epub ahead of print.

  22. Liao RG, Jung J, Tchaicha JH, Wilkerson MD, Sivachenko A, Beauchamp EM, Liu Q, Pugh TJ, Pedamallu CS, Hayes DN, Gray NS, Getz G, Wong KK, Haddad RI, Meyerson M, Hammerman PS. (2013) Inhibitor-sensitive FGFR2 and FGFR3 mutations in lung squamous cell carcinoma. Cancer Research. Aug 15;73(16):5195-205.

  23. Wilkerson MD, Schallheim JM, Hayes DN, Roberts PJ, Bastien RR, Mullins M, Yin X, Miller CR, Thorne LB, Geiersbach KB, Muldrew K, Funkhouser WK, Fan C, Hayward MC, Bayer S, Perou CM, Bernard PS. (2013) Prediction of Lung Cancer Histological Types by RT-qPCR Gene Expression in FFPE Specimens. The Journal of Molecular Diagnostics. Jul;15(4):485-97.
    Popular press coverage:

  24. Walter V, Yin X, Wilkerson MD, Cabanski CR, Zhao N, Du Y, Ang MK, Hayward MC, Salazar AH, Hoadley KA, Fritchie K, Sailey CG, Weissler MC, Shockley WW, Zanation AM, Hackman T, Thorne LB, Funkhouser WD, Muldrew KL, Olshan AF, Randell SH, Wright FA, Shores CG, Hayes DN. (2013) Molecular Subtypes in Head and Neck Cancer Exhibit Distinct Patterns of Chromosomal Gain and Loss of Canonical Cancer Genes. PLoS One. 2013;8(2):e56823. doi: 10.1371/journal.pone.0056823.

  25. The Cancer Genome Atlas Research Network, Wilkerson MD (Data Coordinator, Writing commitee, RNA-seq analysis, Disease working group, Fig 3) (2012) Comprehensive genomic characterization of squamous cell lung cancers. Nature. Sep 27;489(7417):519-25.
    Popular press coverage:

  26. 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.

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

  28. 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 . Jul 24;107(3):482-90.

  29. 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:

  30. 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. (2013) 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 Jan;137(1):32-40.

  31. 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.

  32. 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.

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

  34. 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.

  35. 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.

  36. 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.

  37. 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.

  38. 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:

  39. 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.

  40. 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.

  41. 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

  42. 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.

  43. 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.

  44. 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.

  45. 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