Matthew Vaughn

Matthew Vaughn, Ph.D.

Director of Life Sciences Computing


Matt Vaughn earned a Bachelor of Science in Cellular and Molecular Biology In 1994 and a PhD in Physiological and Molecular Plant Biology in 2001 from the University of Illinois at Urbana-Champaign, where he worked on evolution and regulation of photosynthetic carbon metabolism. After a postdoctoral fellowship in the Plant Genetics group at Cold Spring Harbor Laboratory, where he researched genome architecture, genetic regulation, and small RNA biology, Matt joined the research faculty of Cold Spring Harbor Laboratory in 2007 to conduct a program of research in epigenetics and life sciences cyberinfrastructure. In 2010, he joined the Texas Advanced Computing Center and today serves as the Manager of its Life Sciences Computing Program where he leads efforts to advance biologists' access to and utilization of advanced scientific computing technologies.

Areas of Research

Epigenetic natural diversity

Cell cycle regulation

Scalable and reproducible computational biology

Information visualization

Current Projects

The Arabidopsis Information Portal (Co-Director)

Development of Systems Informatics Tools to Accelerate Livestock Genomics (co-PI)

Causes and Consequences of Epigenetic Variation in Maize (co-PI)

Epigenome Dynamics During DNA Replication

CyVerse (Senior Personnel)

The Agave API (Chief Evangelist)

Selected Publications/Conferences

Leduc R, Vaughn M, Fonner JM, Sullivan M, Williams JG, Blood PD, Taylor J, Barnett W. Leveraging the national cyberinfrastructure for biomedical research. J Am Med Inform Assoc. 2013 Aug 20. doi: 10.1136/amiajnl-2013-002059

Eichten SR, Briskine R, Song J, Li Q, Swanson-Wagner R, Hermanson PJ, Waters AJ, Starr E, West PT, Tiffin P, Myers CL, Vaughn MW, Springer NM. Epigenetic and genetic influences on DNA methylation variation in maize populations. Plant Cell. 2013 Aug;25(8):2783-97. doi: 10.1105/tpc.113.114793. Epub 2013 Aug 6

Makarevitch I, Eichten SR, Briskine R, Waters AJ, Danilevskaya ON, Meeley RB, Myers CL, Vaughn MW, Springer NM. Genomic distribution of maize facultative heterochromatin marked by trimethylation of H3K27. Plant Cell. 2013 Mar;25(3):780-93. doi: 10.1105/tpc.112.106427. Epub 2013 Mar 5

International Arabidopsis Informatics Consortium. Taking the next step: building an Arabidopsis information portal. Plant Cell. 2012 Jun;24(6):2248-56. Epub 2012 Jun 29

Waters AJ, Makarevitch I, Eichten SR, Swanson-Wagner RA, Yeh CT, Xu W, Schnable PS, Vaughn MW, Gehring M, Springer NM. Parent-of-origin effects on gene expression and DNA methylation in the maize endosperm. Plant Cell. 2011 Dec;23(12):4221-33. Epub 2011 Dec 23.

Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. Heritable epigenetic variation among maize inbreds. PLoS Genet. 2011 Nov;7(11):e1002372. Epub 2011 Nov 17.

Zaratiegui MB, Vaughn MW, Irvine, DV, Goto DB, Watt, W, Bahler J, Arcangioli B, Martienssen RA. CENP-B preserves genome integrity at replication forks paused by Retrotransposon LTR. Nature 2010 in press.

Lee TJ, Pascuzzi PE, Settlage, SB, Schultz RW, Tanurdzic M, Rabinowicz PD, Menges M, Zheng P, Main D, Murray JAH, Sosinski B, Allen GC, Martienssen RA, Hanley-Bowdoin L, Vaughn MW, Thompson WF. Arabidopsis thaliana Chromosome 4 Replicates in Two Phases That Correlate with Chromatin State. PLOS Genetics 2010 Jun 10; 6(6):e1000982. PubMed PMID: 20548960.

The Maize Sequencing Consortium. The B73 maize genome: complexity, diversity and dynamics. Science 2009 Nov 20:326(5956):1112-1115. PubMed PMID: 19965430.

Irvine DV, Goto DB, Vaughn MW, Nakaseko Y, McCombie WR, Yanagida M, Martienssen R. Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing. Genome Res. 2009 Jun;19(6):1077-83. Epub 2009 May 7. PubMed PMID: 19423874; PubMed Central PMCID: PMC2694473.

Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA. 2009. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 2009 Feb 6;136(3):461-72. PubMed PMID: 19203581; PubMed Central PMCID: PMC2661848.

Vaughn, M.W., Tanurdzic, M., Lippman, Z., Jiang, H., Carasqiullo, R., Rabinowicz, P.D., Dedhia, N., McCombie, W.R., Agier, N., Bulski, A., Colot, V., Doerge, R.W., and R.A. Martienssen (2007) Epigenetic natural variation in Arabidopsis thaliana. PLOS Biology (Vol. 5, No. 7, e174 doi:10.1371/journal.pbio.0050174).

Ronemus, M., Vaughn, M. W., and R. A. Martienssen (2006) miRNA-Targeted and siRNA- Mediated mRNA Degradation Is Regulated by Argonaute, Dicer and RdRP In Arabidopsis. Plant Cell 18(7):1559-74.

Lippman, Z., Gendrel, A.V., Black, M., Vaughn, M.W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K., Carrington, J.C., Doerge, R.W., Colot, V., and Martienssen, R.A. (2004) Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471-476.


Ph.D, Biology
University of Illinois at Urbana-Champaign

B.S., Biology
University of Illinois at Urbana-Champaign

Memberships/Professional Affiliations

American Society of Plant Biologists