Difference between revisions from 2009/09/09 07:48 and 2009/09/09 07:47.!!Research
Keywords: Bioinformatics, Computational Genomics, Regulation of gene expression, Genome structure and evolution, DNA methylation, Genetic Redundancy, RNA interference, Quantitative Sequencing, Assembler Design and Optimization, Biological networks
!!Personnel
* [Matthew Vaughn, PhD|MWVaughn]
* Vishal Thapar, PhD
* Phil Tully
* Shabari Das
!!Projects
* [Global Analysis of Functional Domains of Plant Chromosomes|http://www.plantreplication.org/] - Understand how chromosome functions are spatially organized and coordinated in structural and functional domains
* [Functional Genomics of Plant Polyploids|http://abc.polyploidy.org/index.php/Main_Page] - Determine mechanisms governing fate of duplicated genes and genomes and understand basis of non-additive gene regulation
* [Next-generation sequencing of Maize Targeted Mutagenesis Transposon Insertion Sites|MTM2009] - Determine insertion sites for Mu transposons in MTM collection to build a maize functional genomics resource
* [Extending Epigenomic Profiling via Usage of Next-Generation Sequencing Technology|NSG2009] - Develop tools and methods to replace microarrays for epigenomic profiling
* [Sequencing and Assembly of Arabidopsis arenosa (CARE-1)|http://hispaniola.cshl.edu/sequencing/aarenosa/] - Develop methods for de novo assembly of polyploid, heterogeneous relative to A. thaliana
* [The iPlant Collaborative|http://www.iplantcollaborative.org/] - Initiative to build national cyberinfrastructure for the plant sciences
!!Recruitment
* [Postdoctoral Researcher|Postdoctoral Positions] (1)
* Scientific Developer (1)
*[About The Lab]
!!Collaborator Resources
*[Galaxy Server|http://hispaniola.cshl.edu/galaxy/]
*[Generic Genome Browsers|http://hispaniola.cshl.edu/gbrowse2/]
*MySQL server
*Expression Viewer
*Linux command line tools
*Request Single Sign-on Account
!!Recent Publications
*The Maize Sequencing Consortium (2009) The B73 maize genome: complexity, diversity and dynamics. Science (submitted).
*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.
* 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)
!!Support
*National Science Foundation
*National Institutes of Health
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