James Schnable

James Schnable

Website:

·Schnable Lab
·Nebraska Food for Health Center

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

2018

(N=11)

  • Zou C, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable P, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H (2018) The genome of broomcorn millet (Panicum miliaceum L.) NATURE COMMUNICATIONS (Accepted)
  • Miao C, Yang, J, Schnable JC (2018) Optimizing the identification of causal variants across varying genetic architectures in crops. PLANT BIOTECHNOLOGY JOURNAL doi: 10.1111/pbi.13023 BIORXIV doi: 10.1101/310391
  • Liang Z, Gupta SK, Yeh CT, Zhang Y, Ngu DW, Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupkta R, Yang J, Varshney RK, Schnable PS, Schnable JC (2018) Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids. G3: GENES GENOMES GENETICS doi: 10.1534/g3.118.200242
  • Miao C, Fang J, Li D, Liang P, Zhang X, Yang J, Schnable JC, Tang H (2018) Genotype-Corrector: improved genotype calls for genetic mapping. SCIENTIFIC REPORTS doi: 10.1038/s41598-018-28294-0 20.
  • Raju SKK, Barnes A, Schnable JC, Roston RL (2018) Low-temperature tolerance in land plants: Are transcript and membrane responses conserved? PLANTSCIENCE doi: 10.1016/j.plantsci.2018.08.002 19.
  • Carvalho DS, Schnable JC, Almeida AMR (2018) Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes. EVOLUTIONARY BIOINFORMATICS doi: 10.1177/1176934318764683 BIORXIV doi: 10.1101/195669
  • Xu Y, Qiu Y, Schnable JC (2018) Functional modeling of plant growth dynamics. THE PLANT PHENOME doi: 10.2135/tppj2017.09.0007 BIORXIV doi: 10.1101/190967
  • Ott A, Schnable JC, Yeh CT, Wu L, Liu C, Hu HC, Dolgard CL, Sarkar S, Schnable PS. (2018) Linked read technology for assembling large complex and polyploid genomes. BMC GENOMICS doi: 10.1186/s12864-018-5040-z
  • Liu S, Schnable JC, Ott A, Yeh CT, Springer NM, Yu J, Meuhbauer G, Timmermans MCP, Scanlon MJ, Schnable PS (2018) Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels. MOLECULAR BIOLOGY AND EVOLUTION doi: 10.1093/molbev/msy174
  • Alkhalifah N, Campbell DA, Falcon CM, ... Schnable JC (31 of 44 authors) ... Spalding EP, Edwards J, Lawrence-Dill CJ (2018) Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC RESEARCH NOTES doi: 10.1186/s13104-018-3508-1
  • Nani TF, Schnable JC, Washburn JD, Albert P, Pereira WA, Sobrinho FS, Birchler JA, Techia VH (2018) Location of low copy genes in chromosomes of Brachiaria spp. MOLECULAR BIOLOGY REPORTS doi: 10.1007/s11033-018-4144-5

2017

(N=13)

  • Liang Z, Schnable JC (2017) Functional divergence between subgenomes and gene pairs after whole genome duplications. MOLECULAR PLANT doi: 10.1016/j.molp.2017.12.010
  • Lai X, Yan L, Lu Y, Schnable JC (2018) Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. THE PLANT JOURNAL doi: 10.1111/tpj.13806 BIORXIV doi: 10.1101/184424
  • Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC (2017) Differentially regulated orthologs in sorghum and the subgenomes of maize. THE PLANT CELL doi: 10.1105/tpc.17.00354
  • Lai X, Behera S, Liang Z, Lu Y, Deogun JS, Schnable JC (2017) STAG-CNS: An order-aware conserved noncoding sequence discovery tool for arbitrary numbers of species. MOLECULAR PLANT. doi: 10.1016/j.molp.2017.05.010
  • Liang Z, Pandey P, Stoerger V, Xu Y, Qiu Y, Ge Y, Schnable JC (2017) Conventional and hyperspectral time-series imaging of maize lines widely used in field trials. GIGASCIENCE 10.1093/gigascience/gix117 BIORXIV doi: 10.1101/169045
  • Gage J, Jarquin D, Romay M, ... Schnable JC (29th of 40 authors) .. Yu J, de Leon N (2017) The effect of artificial selection on phenotypic plasticity in maize. NATURE COMMUNICATIONS doi: 10.1038/s41467-017-01450-2
  • Washburn JD, Schnable JC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC (2017) Genome-guided phylo-transcriptomics. SCIENTIFIC REPORTS doi: 10.1038/s41598-017-13236-z
  • Ott A, Liu S, Schnable JC, Yeh CT, Wang C, Schnable PS (2017) Tunable Genotyping-By-Sequencing (tGBS®;) enables reliable genotyping of heterozygous loci. NUCLEIC ACIDS RESEARCH doi:10.1093/nar/gkx853
  • Lai X, Schnable JC, Liao Z, Xu J, Zhang G, Li C, Hu E, Rong T, Xu Y, Lu Y (2017) Genome-wide characterization of non-reference transposable elements insertion polymorphisms reveals genetic diversity in tropical and temperate maize. BMC GENOMICS doi: 10.1186/s12864-017-4103-x
  • Mei W, Boatwright L, Feng G, Schnable JC, Barbazuk WB (2017) Evolutionarily conserved alternative splicing across monocots. GENETICS doi: 10.1534/genetics.117.300189
  • Pandey P, Ge Y, Stoerger V, Schnable JC (2017) High throughput in vivo analysis of plant leaf chemical properties using hyperspectral imaging. FRONTIERS IN PLANT SCIENCE doi 10.3389/fpls.2017.01348
  • Lai X, Schnable JC (2017) Harnessing the potential of the tea tree genome. MOLECULAR PLANT. doi:10.1016/j.molp.2017.05.009
  • Mei W, Liu S, Schnable JC, Yeh C, Springer NM, Schnable PS, Barbazuk WB. (2017) A comprehensive analysis of alternative splicing in paleopolyploid maize. FRONTIERS IN PLANT SCIENCE doi: 10.3389/fpls.2017.00694

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; ‡Undergraduate