I'm a Research Assistant Professor here at Cold Spring Harbor Laboratory, where I work on a variety of exciting projects in yeast and plant epigenomics. I'm also Scientific Lead for the iPlant Collaborative Genotype to Phenotype cyberinfrastructure development project.

Contact Information(Edit)

Matthew W. Vaughn
Research Assistant Professor
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724

tel: 516-367-8808
fax: 516-367-8369
aim: matthewwvaughn
skype: matt.vaughn



  • 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.
  • 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.
  • Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA. Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol. 2008 Dec 9;6(12):2880-95. PubMed PMID: 19071958; PubMed Central PMCID: PMC2596858.
  • Li F, Huarte M, Zaratiegui M, Vaughn MW, Shi Y, Martienssen R, Cande WZ. Lid2 is required for coordinating H3K4 and H3K9 methylation of heterochromatin and euchromatin. Cell. 2008 Oct 17;135(2):272-83. PubMed PMID: 18957202; PubMed Central PMCID: PMC2614271.
  • 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)
  • Huarte, M., Lan, F., Kim, T., Vaughn, M.W., Zaratiegui,M., Martienssen, R.A., Buratowski, S., and Y. Shi (2007) The fission yeast JMJ2 reverses histone H3 lysine trimethylation. Journal of Biological Chemistry (in press)
  • Lan F., Zaratiegui M., Villen J., Vaughn M.W., Verdel A., Huarte M., Gygi S.P., Moazed D., Martienssen R.A., Shi Y. (2007) S. pombe LSD1 homologs regulate heterochromatin propagation and euchromatic gene transcription. Molecular Cell 26:89-101
  • Irvine, D.V., Zaratiegui, M., Tolia, N. H., Goto, D. B., Chitwood, D. H., Vaughn, M. W., Joshua-Tor, L., and R. A. Martienssen (2006) Argonaute slicing is required for heterochromatic silencing and spreading. Science 313(5790):1134-7
  • 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
  • Vaughn, M.W., Tanurdzic, M., and R. A. Martienssen (2005) Replication, Repair, and Reactivation. Developmental Cell 9(6): 724-725
  • Vaughn, M.W. and R. A. Martienssen (2005) It’s a Small RNA World, After All. Science 309(5740): 1525-1526
  • Vaughn, M.W. and R. M. Martienssen (2005) Finding the Right Template: RNA Pol IV, a Plant-Specific RNA Polymerase. Molecular Cell 18: 754-756
  • Martienssen, R.A., Lippman Z., May, B., Ronemus, M., and M.W. Vaughn (2005) Transposons, Tandem Repeats, and the Silencing of Imprinted Genes. Cold Spring Harbor Symposia on Quantitative Biology 2004, Symposium 69, Pages 1-10, Posted online on January 5, 2005. (doi:10.1101/sqb.2004.69.051)
  • 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
  • Chen, Z. J., Wang, J., Tian, L., Lee, H. S., Wang, J. J., Chen, M., Lee, J. J., Josefsson, C., Madlung, A., Watson, B., Pires, J. C., Lippman, Z., Vaughn, M. W., Colot, V., Birchler, J. A., Doerge, R. W., Martienssen, R., Comai, L., & Osborn, T. (2004). The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biological Journal of the Linnean Society. 82,: 689-700
  • Ransom-Hodgkins, W.D., Vaughn, M.W., Bush, D.R. (2003) Protein phosphorylation plays a key role in sucrose-mediated transcriptional regulation of a phloem-specific proton-sucrose symporter. Planta 217: 483-48
  • Vaughn, M. W., Harrington, G.N, Bush, D. R. (2002) Sucrose-mediated transcriptional regulation of sucrose symporter activity in the phloem. Proceedings of the National Academy of Sciences (USA) 99: 10876-10880


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