Schnable Lab@UNL
PrePrints

Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. "Differentially regulated orthologs in sorghum and the subgenomes of maize." bioRxiv doi: 10.1101/120303

Ott A,* Liu S,* Schnable JC, Yeh CT, Wang C, Schnable PS. "Tunable Genotyping-By-Sequencing (tGBS®) enables reliable genotyping of heterozygous loci." bioRxiv doi: 10.1101/100461

Mei W, Boatwright L, Feng G, Schnable JC, Barbazuk WB. "Evolutionarily conserved alternative splicing across monocots." bioRxiv doi: 10.1101/120469

2017

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 (Accepted pending minor revisions) bioRxiv preprint doi: 10.1101/120428

Lai X, Schnable JC. (2017) "Harnessing the potential of the tea tree genome." Molecular Plant (Accepted)

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

Joyce BL, Huag-Baltzell A, Davey S, Bomhoff M, Schnable JC, Lyons E. (2016) "FractBias: a graphical tool for assessing fractionation bias after whole genome duplications." Bioinformatics doi: 10.1093/bioinformatics/btw666

Studer AJ,* Schnable JC,* Weissmann S, Kolbe AR, McKain MR, Shao Y, Cousins AB, Kellogg EA, Brutnell TP. (2016) "The draft genome of Dichanthelium oligosanthes: A C3 panicoid grass species." Genome Biology doi: 10.1186/s13059-016-1080-3

Walley JW,* Sartor RC,* Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP. (2016) "Integration of omic networks in a developmental atlas of maize." Science doi: 10.1126/science.aag1125

Chaudhury SD, Steorger V, Samal A, Schnable JC, Liang Z, Yu J. (2016) "Automated vegetative stage phenotyping analysis of maize plants using visible light images." KDD: Data Science for Food, Energy, and Water (Conference Proceedings)

Ge Y, Bai G, Stoerger V, Schnable JC. (2016) "Temporal dynamics of maize plant growth, water use, and plant water content using automated high throughput RGB and hyperspectral imaging." Computers and Electronics in Agriculture doi: 10.1016/j.compag.2016.07.028

Huang P, Studer AJ, Schnable JC, Kellog EA, Brutnell TP. (2016) "Cross species selection scans identify components of C4 photosynthesis in the grasses." Journal of Experimental Botany doi: 10.1093/jxb/erw256

Liang Z, Schnable JC. "RNA-seq based analysis of population structure within the maize inbred B73." PLoS One doi: 10.1371/journal.pone.0157942 bioRxiv preprint doi: 10.1101/043513

Liu X, Tang S, Jia G, Schnable JC, Su X, Tang C, Zhi H, Diao X. (2016) "The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet [Setaria italica (L.) P. Beauv]" Journal of Experimental Botany doi: 10.1093/jxb/erw135

Rajput SG, Santra DK, Schnable JC. (2016) "Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.)." Molecular Breeding doi: 10.1007/s11032-016-0460-4

Cheng F, Sun C, Wu J, Schnable JC, Woodhouse MR, Liang J, Cai C, Freeling M, Wang X. (2016) "Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa." New Phytologist doi: 10.1111/nph.13884

2015

Chao S, Wu J, Schnable JC, Yang W, Cheng F, Wang X. (2015) "Impacts of Whole Genome Triplication on MIRNA Evolution in Brassica rapa." Genome Biology and Evolution doi: 10.1093/gbe/evv206

Tang H, Bamhoff MD, Briones E, Schnable JC, Lyons E. (2015) "SynFind: compiling syntenic regions across any set of genomes on demand." Genome Biology and Evolution doi: 10.1093/gbe/evv219

Washburn JD, Schnable JC, Davidse G, Pires JC. (2015) "Phylogeny and photosynthesis of the grass tribe Paniceae." American Journal of Botany doi: 10.3732/ajb.1500222

Jia G, Liu X, Schnable JC, Niu Z, Wang C, Li Y, Wang Sh, Wang Su, Liu J, Gou E, Diao X. (2015) "Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China." PLoS One doi:10.1371/journal.pone.0125688

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu Jianguo. (2015) "ALLMAPS: robust scaffold ordering based on multiple maps." Genome Biology doi:10.1186/s13059-014-0573-1

Schnable JC. (2015) "Genome evolution in maize: from genomes back to genes." Annual Review of Plant Biology doi:10.1146/annurev-arplant-043014-115604

2014

Paschold A, Larson NB, Marcon C, Schnable JC, Yeh C, Lanz C, Nettleton D, Piepho H, Schnable PS, Hochholdinger F. (2014) "Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids" Plant Cell doi:10.1105/tpc.114.130948

Almeida AMR, Yockteng R, Schnable JC, Alvarez-Buylla ER, Freeling M, Specht CD. (2014) "Co-option of the polarity gene network shapes filament morphology in angiosperms" Scientific Reports doi: 10.1038/srep06194

Qie L, Jia G, Zhang W, Schnable JC, Shang Z, Li W, Liu B, Li M, Chai, Y, Zhi H, Diao X. (2014) "Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica x Setaria viridis." PLoS One doi: 10.1371/journal.pone.0101868

Diao X, Schnable JC, Bennetzen JL, Li J. (2014) "Initiation of Setaria as a model plant." Frontiers of Agricultural Science and Engineering doi: 10.15302/J-FASE-2014011

Martin JA, Johnson NV, Gross SM, Schnable JC, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei C, Kaeppler S, Chen F, Wang Z. (2014) "A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing." Scientific Reports doi: 10.1038/srep04519

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

2011

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 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