Staff Directory

Matthew W. Vaughn, Ph.D

Matthew W. Vaughn, Ph.D

Manager, Life Sciences Computing Group
Research Associate, Computational Biology
Area: Scientific Applications
(512) 232-7124
ROC 1.447
vaughn@tacc.utexas.edu

Matthew received classical training in plant molecular biology and biochemistry in the University of Illinois at Urbana-Champaign's Photosynthesis Research Unit. From there, he moved on to Cold Spring Harbor Laboratory where he specialized in computational biology and bioinformatics pertaining to epigenetic gene regulation and genome organization. A long-time participant in the iPlant Collaborative, an NSF-funded project to build a cyberinfrastructure for the Plant Sciences, Matthew joined TACC in September of 2010 to help advance biologist's access to high-performance computational systems and to advanced information visualization technologies.

Areas of Research

  • Epigenetics, Genome Wide Association Mapping, Bioinformatics

Current Projects

  • The iPlant Collaborative
  • Maize epigenomic variation
  • Epigenome dynamics during DNA replication
  • Methods in next-generation genome assembly

Selected Publications

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.

Organization Membership/Professional Affiliations

  • American Society of Plant Biologists

Education

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