James Schnable

James Schnable

Website:

·Schnable Lab

James Schnable

Assistant Professor

B.A., Biology, Cornell University, 2008

Ph.D., Plant Biology, University of California-Berkeley, 2012.

Area of Focus

Computational Biology

Research Interests

  • Cross-species functional genomics
  • High throughput phenotyping

Publications

2016

2015

2014

2013

  • Garsmeur O,* Schnable JC,* Almeida A, Jourda C, D'Hont A, Freeling M (2013) "Two Evolutionarily Distinct Classes of Paleopolyploidy." Molecular Biology and Evolution DOI: 10.1093/molbev/mst230
  • Turco G, Schnable JC, Bedersen B, Freeling M. (2013) "Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among the grasses." Frontiers in Plant Sciences DOI: 10.3389/fpls.2013.00170

2012

  • Schnable JC, Wang X, Pires JC, Freeling M. (2012) "Escape from preferential retention following repeated whole genome duplication in plants." Frontiers in Plant Science DOI: 10.3389/fpls.2012.00094
  • 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. (2012) "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

2011

  • Schnable JC, Lyons E. (2011) "Comparative genomics with maize and other grasses: from genes to genomes" Maydica (Link is directly to PDF).
  • 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  (Commentary on this article by Birchler and Veitia, also published in Frontiers in Plant Science).
  • 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 Read for free at PubMed Central  (Selected as an Editor's Choice by MaizeGDB May 2011).

2010

  • 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 (Selected as an Editor's Choice by MaizeGDB August 2010; an image related to this manuscript was used for the journal cover; "recommended" by Faculty of 1000).
  • The International Brachypodium Initiative. (2010) "Genome sequencing and analysis of the model grass Brachypodium distachyon." Nature DOI: 10.1038/nature08747

*Authors contributed equally