Revision as of 11:33, 21 March 2012

James Schnable

I'm a graduate student in the department of Plant and Microbial Biology at UC-Berkeley and a member of the Freeling lab. My research focuses on comparative grass genomics and the fate of genes following whole genome duplications.

Here at CoGePedia I maintain the Sequenced plant genomes and Classical Maize Genes resources. It's always a struggle to keep them up to date, so please don't hesitate to let me know if you find omissions in either list. I also created [qteller.com qTeller], the program to harvest information on all genes in an interval or check the expression values of your favorite gene in different people's RNA-seq data.

Complete online CV

Contact info

email:
jschnable (@) berkeley.edu

Physical Address:
434 Koshland Hall (Mail: 111 Koshland Hall)
University of California-Berkeley
Berkeley, CA 94720

Publications

An automatically updated list of James Schnable's publications (Google Scholar profile).

• Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC. 2012. "Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants." Current Opinion in Plant Biology DOI: 10.1016/j.pbi.2012.01.015
• Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant GC, Wang X, Freeling M, Pires JC. 2012. Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics DOI: 10.1534/genetics.111.137349
• Schnable JC, Freeling M, Lyons E. 2012. "Genome-wide analysis of syntenic gene deletion in the grasses." Genome Biology and Evolution DOI: 10.1093/gbe/evs009
• Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, and Jiang J. 2011. "High-resolution mapping of open chromatin in the rice genome." Genome Research DOI: 10.1101/gr.131342.111
• Eichten SR,* Swanson-Wagner RA,* Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh C, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. 2011. "Heritable epigenetic variation among maize inbreds". PLoS Genetics DOI: 10.1371/journal.pgen.1002372
• Schnable JC, Lyons E. 2011. "Comparative genomics with maize and other grass: from genes to genomes. "Maydica 56(2) 183-200
• Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. 2011. "Screening synteny blocks in pairwise genome comparisons through integer programming." BMC Bioinformatics DOI: 10.1186/1471-2105-12-102
• Schnable JC, Pedersen BS, Subramaniam S, Freeling M. 2011. "Dose-sensitivity, conserved noncoding sequences and duplicate gene retention through multiple tetraploidies in the grasses." Frontiers in Plant Science DOI: 10.3389/fpls.2011.00002
• Schnable JC, Freeling M. 2011. "Genes identifed by visible mutant phenotypes show increased bias towards one of two maize subgenomes." PLoS One DOI: 10.1371/journal.pone.0017855
• Schnable JC, Springer NM, Freeling M. 2011. "Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.". PNAS DOI: 10.1073/pnas.1101368108
• Woodhouse MR*, Schnable JC*, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. 2010. "Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs." PLoS Biology DOI:10.1371/journal.pbio.1000409
• The International Brachypodium Initiative. 2010. "Genome sequencing and analysis of the model grass Brachypodium distachyon." Nature DOI: 10.1038/nature08747

(*) Authors Contributed Equally

Education

• 2004-2008 B.A. Cornell University. Major: Biology with focuses in Genetics and Plant Biology.
• 2008-present PhD (in progress) University of California-Berkeley. Department of Plant and Microbial Biology.