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Shared genetic control of root system architecture between Zea mays and Sorghum bicolor.

Zheng Z, Hey S, Jubery T, Liu H, Yang Y, Coffey L, Miao C, Sigmon B, Schnable J, Hochholdinger F, Ganapathysubramanian B, Schnable PS.

Plant Physiol. 2019 Nov 18. pii: pp.00752.2019. doi: 10.1104/pp.19.00752. [Epub ahead of print]


High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome.

Qi P, Eudy D, Schnable JC, Schmutz J, Raymer PL, Devos KM.

Sci Rep. 2019 Aug 21;9(1):12183. doi: 10.1038/s41598-019-48257-3.


High-throughput analysis of leaf physiological and chemical traits with VIS-NIR-SWIR spectroscopy: a case study with a maize diversity panel.

Ge Y, Atefi A, Zhang H, Miao C, Ramamurthy RK, Sigmon B, Yang J, Schnable JC.

Plant Methods. 2019 Jun 26;15:66. doi: 10.1186/s13007-019-0450-8. eCollection 2019.


Continuous Monitoring of Soil Nitrate Using a Miniature Sensor with Poly(3-octyl-thiophene) and Molybdenum Disulfide Nanocomposite.

Ali MA, Wang X, Chen Y, Jiao Y, Mahal NK, Moru S, Castellano MJ, Schnable JC, Schnable PS, Dong L.

ACS Appl Mater Interfaces. 2019 Aug 14;11(32):29195-29206. doi: 10.1021/acsami.9b07120. Epub 2019 Jul 31.


Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS.

Li YH, Li D, Jiao YQ, Schnable JC, Li YF, Li HH, Chen HZ, Hong HL, Zhang T, Liu B, Liu ZX, You QB, Tian Y, Guo Y, Guan RX, Zhang LJ, Chang RZ, Zhang Z, Reif J, Zhou XA, Schnable PS, Qiu LJ.

Plant Biotechnol J. 2019 Jul 6. doi: 10.1111/pbi.13206. [Epub ahead of print]


Genes and gene models, an important distinction.

Schnable JC.

New Phytol. 2019 Jun 26. doi: 10.1111/nph.16011. [Epub ahead of print] Review.


Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize.

Yan L, Kenchanmane Raju SK, Lai X, Zhang Y, Dai X, Rodriguez O, Mahboub S, Roston RL, Schnable JC.

Plant J. 2019 Sep;99(5):965-977. doi: 10.1111/tpj.14376. Epub 2019 Jun 26.


The genome of broomcorn millet.

Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H.

Nat Commun. 2019 Jan 25;10(1):436. doi: 10.1038/s41467-019-08409-5.


Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?

Kenchanmane Raju SK, Barnes AC, Schnable JC, Roston RL.

Plant Sci. 2018 Nov;276:73-86. doi: 10.1016/j.plantsci.2018.08.002. Epub 2018 Aug 7. Review.


Optimising the identification of causal variants across varying genetic architectures in crops.

Miao C, Yang J, Schnable JC.

Plant Biotechnol J. 2019 May;17(5):893-905. doi: 10.1111/pbi.13023. Epub 2018 Nov 9.


Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels.

Liu S, Schnable JC, Ott A, Yeh CE, Springer NM, Yu J, Muehlbauer G, Timmermans MCP, Scanlon MJ, Schnable PS.

Mol Biol Evol. 2018 Nov 1;35(11):2762-2772. doi: 10.1093/molbev/msy174.


Linked read technology for assembling large complex and polyploid genomes.

Ott A, Schnable JC, Yeh CT, Wu L, Liu C, Hu HC, Dalgard CL, Sarkar S, Schnable PS.

BMC Genomics. 2018 Sep 4;19(1):651. doi: 10.1186/s12864-018-5040-z.


Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets.

AlKhalifah N, Campbell DA, Falcon CM, Gardiner JM, Miller ND, Romay MC, Walls R, Walton R, Yeh CT, Bohn M, Bubert J, Buckler ES, Ciampitti I, Flint-Garcia S, Gore MA, Graham C, Hirsch C, Holland JB, Hooker D, Kaeppler S, Knoll J, Lauter N, Lee EC, Lorenz A, Lynch JP, Moose SP, Murray SC, Nelson R, Rocheford T, Rodriguez O, Schnable JC, Scully B, Smith M, Springer N, Thomison P, Tuinstra M, Wisser RJ, Xu W, Ertl D, Schnable PS, De Leon N, Spalding EP, Edwards J, Lawrence-Dill CJ.

BMC Res Notes. 2018 Jul 9;11(1):452. doi: 10.1186/s13104-018-3508-1.


Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations.

Miao C, Fang J, Li D, Liang P, Zhang X, Yang J, Schnable JC, Tang H.

Sci Rep. 2018 Jul 4;8(1):10088. doi: 10.1038/s41598-018-28294-0.


Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes.

Carvalho DS, Schnable JC, Almeida AMR.

Evol Bioinform Online. 2018 Apr 23;14:1176934318764683. doi: 10.1177/1176934318764683. eCollection 2018.


Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids.

Liang Z, Gupta SK, Yeh CT, Zhang Y, Ngu DW, Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupta R, Yang J, Varshney RK, Schnable PS, Schnable JC.

G3 (Bethesda). 2018 Jul 2;8(7):2513-2522. doi: 10.1534/g3.118.200242.


Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses.

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2018 May 2;8(1):7120. doi: 10.1038/s41598-018-25620-4.


Location of low copy genes in chromosomes of Brachiaria spp.

Nani TF, Schnable JC, Washburn JD, Albert P, Pereira WA, Sobrinho FS, Birchler JA, Techio VH.

Mol Biol Rep. 2018 Apr;45(2):109-118. doi: 10.1007/s11033-018-4144-5. Epub 2018 Jan 12.


Functional Divergence between Subgenomes and Gene Pairs after Whole Genome Duplications.

Liang Z, Schnable JC.

Mol Plant. 2018 Mar 5;11(3):388-397. doi: 10.1016/j.molp.2017.12.010. Epub 2017 Dec 22. Review.


Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum.

Lai X, Yan L, Lu Y, Schnable JC.

Plant J. 2018 Mar;93(5):843-855. doi: 10.1111/tpj.13806. Epub 2018 Jan 16.


Conventional and hyperspectral time-series imaging of maize lines widely used in field trials.

Liang Z, Pandey P, Stoerger V, Xu Y, Qiu Y, Ge Y, Schnable JC.

Gigascience. 2018 Feb 1;7(2):1-11. doi: 10.1093/gigascience/gix117.


The effect of artificial selection on phenotypic plasticity in maize.

Gage JL, Jarquin D, Romay C, Lorenz A, Buckler ES, Kaeppler S, Alkhalifah N, Bohn M, Campbell DA, Edwards J, Ertl D, Flint-Garcia S, Gardiner J, Good B, Hirsch CN, Holland J, Hooker DC, Knoll J, Kolkman J, Kruger G, Lauter N, Lawrence-Dill CJ, Lee E, Lynch J, Murray SC, Nelson R, Petzoldt J, Rocheford T, Schnable J, Schnable PS, Scully B, Smith M, Springer NM, Srinivasan S, Walton R, Weldekidan T, Wisser RJ, Xu W, Yu J, de Leon N.

Nat Commun. 2017 Nov 7;8(1):1348. doi: 10.1038/s41467-017-01450-2.


Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses.

Washburn JD, Schnable JC, Conant GC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC.

Sci Rep. 2017 Oct 19;7(1):13528. doi: 10.1038/s41598-017-13236-z. Erratum in: Sci Rep. 2018 May 2;8(1):7120.


tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci.

Ott A, Liu S, Schnable JC, Yeh C', Wang KS, Schnable PS.

Nucleic Acids Res. 2017 Dec 1;45(21):e178. doi: 10.1093/nar/gkx853.


Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize.

Lai X, Schnable JC, Liao Z, Xu J, Zhang G, Li C, Hu E, Rong T, Xu Y, Lu Y.

BMC Genomics. 2017 Sep 6;18(1):702. doi: 10.1186/s12864-017-4103-x.


Evolutionarily Conserved Alternative Splicing Across Monocots.

Mei W, Boatwright L, Feng G, Schnable JC, Barbazuk WB.

Genetics. 2017 Oct;207(2):465-480. doi: 10.1534/genetics.117.300189. Epub 2017 Aug 24.


High Throughput In vivo Analysis of Plant Leaf Chemical Properties Using Hyperspectral Imaging.

Pandey P, Ge Y, Stoerger V, Schnable JC.

Front Plant Sci. 2017 Aug 3;8:1348. doi: 10.3389/fpls.2017.01348. eCollection 2017.


Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize.

Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC.

Plant Cell. 2017 Aug;29(8):1938-1951. doi: 10.1105/tpc.17.00354. Epub 2017 Jul 21.


STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species.

Lai X, Behera S, Liang Z, Lu Y, Deogun JS, Schnable JC.

Mol Plant. 2017 Jul 5;10(7):990-999. doi: 10.1016/j.molp.2017.05.010. Epub 2017 Jun 6.


Harnessing the Potential of the Tea Tree Genome.

Lai X, Schnable JC.

Mol Plant. 2017 Jun 5;10(6):788-790. doi: 10.1016/j.molp.2017.05.009. Epub 2017 May 29. No abstract available.


A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize.

Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB.

Front Plant Sci. 2017 May 10;8:694. doi: 10.3389/fpls.2017.00694. eCollection 2017.


FractBias: a graphical tool for assessing fractionation bias following polyploidy.

Joyce BL, Haug-Baltzell A, Davey S, Bomhoff M, Schnable JC, Lyons E.

Bioinformatics. 2017 Feb 15;33(4):552-554. doi: 10.1093/bioinformatics/btw666.


The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes.

Studer AJ, Schnable JC, Weissmann S, Kolbe AR, McKain MR, Shao Y, Cousins AB, Kellogg EA, Brutnell TP.

Genome Biol. 2016 Oct 28;17(1):223.


Integration of omic networks in a developmental atlas of maize.

Walley JW, Sartor RC, Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP.

Science. 2016 Aug 19;353(6301):814-8. doi: 10.1126/science.aag1125.


Cross species selection scans identify components of C4 photosynthesis in the grasses.

Huang P, Studer AJ, Schnable JC, Kellogg EA, Brutnell TP.

J Exp Bot. 2017 Jan;68(2):127-135. doi: 10.1093/jxb/erw256. Epub 2016 Jul 19.


RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

Liang Z, Schnable JC.

PLoS One. 2016 Jun 27;11(6):e0157942. doi: 10.1371/journal.pone.0157942. eCollection 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).

Liu X, Tang S, Jia G, Schnable JC, Su H, Tang C, Zhi H, Diao X.

J Exp Bot. 2016 May;67(11):3237-49. doi: 10.1093/jxb/erw135. Epub 2016 Apr 4.


Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

Cheng F, Sun C, Wu J, Schnable J, Woodhouse MR, Liang J, Cai C, Freeling M, Wang X.

New Phytol. 2016 Jul;211(1):288-99. doi: 10.1111/nph.13884. Epub 2016 Feb 12.


SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand.

Tang H, Bomhoff MD, Briones E, Zhang L, Schnable JC, Lyons E.

Genome Biol Evol. 2015 Nov 11;7(12):3286-98. doi: 10.1093/gbe/evv219.


Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.

Sun C, Wu J, Liang J, Schnable JC, Yang W, Cheng F, Wang X.

Genome Biol Evol. 2015 Nov 1;7(11):3085-96. doi: 10.1093/gbe/evv206.


Phylogeny and photosynthesis of the grass tribe Paniceae.

Washburn JD, Schnable JC, Davidse G, Pires JC.

Am J Bot. 2015 Sep;102(9):1493-505. doi: 10.3732/ajb.1500222. Epub 2015 Sep 15.


Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China.

Jia G, Liu X, Schnable JC, Niu Z, Wang C, Li Y, Wang S, Wang S, Liu J, Guo E, Zhi H, Diao X.

PLoS One. 2015 May 1;10(5):e0125688. doi: 10.1371/journal.pone.0125688. eCollection 2015.


ALLMAPS: robust scaffold ordering based on multiple maps.

Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J.

Genome Biol. 2015 Jan 13;16:3. doi: 10.1186/s13059-014-0573-1.


Genome evolution in maize: from genomes back to genes.

Schnable JC.

Annu Rev Plant Biol. 2015;66:329-43. doi: 10.1146/annurev-arplant-043014-115604. Epub 2014 Dec 1. Review.


Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.

Paschold A, Larson NB, Marcon C, Schnable JC, Yeh CT, Lanz C, Nettleton D, Piepho HP, Schnable PS, Hochholdinger F.

Plant Cell. 2014 Oct;26(10):3939-48. doi: 10.1105/tpc.114.130948. Epub 2014 Oct 14.


Co-option of the polarity gene network shapes filament morphology in angiosperms.

de Almeida AM, Yockteng R, Schnable J, Alvarez-Buylla ER, Freeling M, Specht CD.

Sci Rep. 2014 Aug 29;4:6194. doi: 10.1038/srep06194.


Mapping of quantitative trait locus (QTLs) that contribute to germination and early seedling drought tolerance in the interspecific cross Setaria italica×Setaria viridis.

Qie L, Jia G, Zhang W, Schnable J, Shang Z, Li W, Liu B, Li M, Chai Y, Zhi H, Diao X.

PLoS One. 2014 Jul 17;9(7):e101868. doi: 10.1371/journal.pone.0101868. eCollection 2014.


A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

Martin JA, Johnson NV, Gross SM, Schnable J, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei CL, Kaeppler S, Chen F, Wang Z.

Sci Rep. 2014 Mar 31;4:4519. doi: 10.1038/srep04519.


Two evolutionarily distinct classes of paleopolyploidy.

Garsmeur O, Schnable JC, Almeida A, Jourda C, D'Hont A, Freeling M.

Mol Biol Evol. 2014 Feb;31(2):448-54. doi: 10.1093/molbev/mst230. Epub 2013 Dec 1.


Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses.

Turco G, Schnable JC, Pedersen B, Freeling M.

Front Plant Sci. 2013 Jul 2;4:170. doi: 10.3389/fpls.2013.00170. eCollection 2013.

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