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Items: 44

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

PMID:
29330722
7.

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.

PMID:
29275166
8.

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.

PMID:
29265526
9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

PMID:
28839042
14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

PMID:
27794557
20.

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.

21.

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.

22.

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.

23.

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.

24.

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.

25.

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.

26.

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.

27.

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.

28.

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.

29.

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.

30.

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.

PMID:
25494463
31.

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.

32.

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.

PMID:
24296661
33.

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.

34.

Escape from preferential retention following repeated whole genome duplications in plants.

Schnable JC, Wang X, Pires JC, Freeling M.

Front Plant Sci. 2012 May 15;3:94. doi: 10.3389/fpls.2012.00094. eCollection 2012.

35.

Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants.

Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC.

Curr Opin Plant Biol. 2012 Apr;15(2):131-9. doi: 10.1016/j.pbi.2012.01.015. Epub 2012 Feb 14. Review.

PMID:
22341793
36.

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy.

Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant G, Wang X, Freeling M, Pires JC.

Genetics. 2012 Apr;190(4):1563-74. doi: 10.1534/genetics.111.137349. Epub 2012 Feb 2.

37.

Genome-wide analysis of syntenic gene deletion in the grasses.

Schnable JC, Freeling M, Lyons E.

Genome Biol Evol. 2012;4(3):265-77. doi: 10.1093/gbe/evs009. Epub 2012 Jan 23.

38.

Heritable epigenetic variation among maize inbreds.

Eichten SR, Swanson-Wagner RA, Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh CT, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM.

PLoS Genet. 2011 Nov;7(11):e1002372. doi: 10.1371/journal.pgen.1002372. Epub 2011 Nov 17.

39.

High-resolution mapping of open chromatin in the rice genome.

Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, Jiang J.

Genome Res. 2012 Jan;22(1):151-62. doi: 10.1101/gr.131342.111. Epub 2011 Nov 22.

40.

Screening synteny blocks in pairwise genome comparisons through integer programming.

Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M.

BMC Bioinformatics. 2011 Apr 18;12:102. doi: 10.1186/1471-2105-12-102.

41.

Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize.

Schnable JC, Freeling M.

PLoS One. 2011 Mar 10;6(3):e17855. doi: 10.1371/journal.pone.0017855.

42.

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.

Schnable JC, Springer NM, Freeling M.

Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4069-74. doi: 10.1073/pnas.1101368108. Epub 2011 Feb 22.

43.

Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses.

Schnable JC, Pedersen BS, Subramaniam S, Freeling M.

Front Plant Sci. 2011 Mar 10;2:2. doi: 10.3389/fpls.2011.00002. eCollection 2011.

44.

Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.

Woodhouse MR, Schnable JC, Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M.

PLoS Biol. 2010 Jun 29;8(6):e1000409. doi: 10.1371/journal.pbio.1000409.

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