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Items: 1 to 50 of 158

1.

Quantitative Trait Locus Mapping for Flowering Time in a Lowland × Upland Switchgrass Pseudo-F2 Population.

Tornqvist CE, Taylor M, Jiang Y, Evans J, Buell CR, Kaeppler SM, Casler MD.

Plant Genome. 2018 Jul;11(2). doi: 10.3835/plantgenome2017.10.0093.

2.

Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits.

Manrique-Carpintero NC, Coombs JJ, Pham GM, Laimbeer FPE, Braz GT, Jiang J, Veilleux RE, Buell CR, Douches DS.

Front Plant Sci. 2018 Jul 3;9:944. doi: 10.3389/fpls.2018.00944. eCollection 2018.

3.

Reply to Huang et al.: Avoiding "one-size-fits-all" approaches to variant discovery.

Hardigan MA, Laimbeer FPE, Hamilton JP, Vaillancourt B, Douches DS, Farré EM, Veilleux RE, Buell CR.

Proc Natl Acad Sci U S A. 2018 Jul 10;115(28):E6394-E6395. doi: 10.1073/pnas.1807622115. Epub 2018 Jun 22. No abstract available.

PMID:
29934402
4.

Trust but Verify: A Lesson in Technology Limitations and Error Propagation.

Buell CR.

Plant Cell. 2018 Mar;30(3):515-516. doi: 10.1105/tpc.18.00202. Epub 2018 Mar 8. No abstract available.

5.

Extensive Genetic Diversity is Present within North American Switchgrass Germplasm.

Evans J, Sanciangco MD, Lau KH, Crisovan E, Barry K, Daum C, Hundley H, Jenkins J, Kennedy M, Kunde-Ramamoorthy G, Vaillancourt B, Acharya A, Schmutz J, Saha M, Kaeppler SM, Brummer EC, Casler MD, Buell CR.

Plant Genome. 2018 Mar;11(1). doi: 10.3835/plantgenome2017.06.0055.

6.

The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.

Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N.

Nucleic Acids Res. 2018 Mar 16;46(5):2700. doi: 10.1093/nar/gky091. No abstract available.

7.

Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

Leisner CP, Hamilton JP, Crisovan E, Manrique-Carpintero NC, Marand AP, Newton L, Pham GM, Jiang J, Douches DS, Jansky SH, Buell CR.

Plant J. 2018 May;94(3):562-570. doi: 10.1111/tpj.13857. Epub 2018 Mar 22.

PMID:
29405524
8.

The unique epigenetic features of Pack-MULEs and their impact on chromosomal base composition and expression spectrum.

Zhao D, Hamilton JP, Vaillancourt B, Zhang W, Eizenga GC, Cui Y, Jiang J, Buell CR, Jiang N.

Nucleic Acids Res. 2018 Mar 16;46(5):2380-2397. doi: 10.1093/nar/gky025.

9.

Genome Assembly and Annotation of the Medicinal Plant Calotropis gigantea, a Producer of Anticancer and Antimalarial Cardenolides.

Hoopes GM, Hamilton JP, Kim J, Zhao D, Wiegert-Rininger K, Crisovan E, Buell CR.

G3 (Bethesda). 2018 Feb 2;8(2):385-391. doi: 10.1534/g3.117.300331.

10.

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.

PMID:
29208732
11.

Identification of iridoid synthases from Nepeta species: Iridoid cyclization does not determine nepetalactone stereochemistry.

Sherden NH, Lichman B, Caputi L, Zhao D, Kamileen MO, Buell CR, O'Connor SE.

Phytochemistry. 2018 Jan;145:48-56. doi: 10.1016/j.phytochem.2017.10.004. Epub 2017 Nov 5.

12.

Genome diversity of tuber-bearing Solanum uncovers complex evolutionary history and targets of domestication in the cultivated potato.

Hardigan MA, Laimbeer FPE, Newton L, Crisovan E, Hamilton JP, Vaillancourt B, Wiegert-Rininger K, Wood JC, Douches DS, Farré EM, Veilleux RE, Buell CR.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):E9999-E10008. doi: 10.1073/pnas.1714380114. Epub 2017 Oct 30.

13.

Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato.

Marand AP, Jansky SH, Zhao H, Leisner CP, Zhu X, Zeng Z, Crisovan E, Newton L, Hamernik AJ, Veilleux RE, Buell CR, Jiang J.

Genome Biol. 2017 Oct 30;18(1):203. doi: 10.1186/s13059-017-1326-8.

14.

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain.

Diepenbrock CH, Kandianis CB, Lipka AE, Magallanes-Lundback M, Vaillancourt B, Góngora-Castillo E, Wallace JG, Cepela J, Mesberg A, Bradbury PJ, Ilut DC, Mateos-Hernandez M, Hamilton J, Owens BF, Tiede T, Buckler ES, Rocheford T, Buell CR, Gore MA, DellaPenna D.

Plant Cell. 2017 Oct;29(10):2374-2392. doi: 10.1105/tpc.17.00475. Epub 2017 Oct 2.

15.

De novo genome assembly of Camptotheca acuminata, a natural source of the anti-cancer compound camptothecin.

Zhao D, Hamilton JP, Pham GM, Crisovan E, Wiegert-Rininger K, Vaillancourt B, DellaPenna D, Buell CR.

Gigascience. 2017 Sep 1;6(9):1-7. doi: 10.1093/gigascience/gix065.

16.

Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato.

Pham GM, Newton L, Wiegert-Rininger K, Vaillancourt B, Douches DS, Buell CR.

Plant J. 2017 Nov;92(4):624-637. doi: 10.1111/tpj.13706. Epub 2017 Oct 16.

PMID:
28869794
17.

Differential iridoid production as revealed by a diversity panel of 84 cultivated and wild blueberry species.

Leisner CP, Kamileen MO, Conway ME, O'Connor SE, Buell CR.

PLoS One. 2017 Jun 13;12(6):e0179417. doi: 10.1371/journal.pone.0179417. eCollection 2017.

18.

Technology Turbocharges Functional Genomics.

Buell CR, Voytas D.

Plant Cell. 2017 Jun;29(6):1179-1180. doi: 10.1105/tpc.17.00443. Epub 2017 Jun 5. No abstract available.

19.

Elevating the conversation about GE crops.

Gould F, Amasino RM, Brossard D, Buell CR, Dixon RA, Falck-Zepeda JB, Gallo MA, Giller KE, Glenna LL, Griffin T, Hamaker BR, Kareiva PM, Magraw D, Mallory-Smith C, Pixley KV, Ransom EP, Rodemeyer M, Stelly DM, Stewart CN Jr, Whitaker RJ.

Nat Biotechnol. 2017 Apr 11;35(4):302-304. doi: 10.1038/nbt.3841. No abstract available.

PMID:
28398318
20.

Self-Fertility in a Cultivated Diploid Potato Population Examined with the Infinium 8303 Potato Single-Nucleotide Polymorphism Array.

Peterson BA, Holt SH, Laimbeer FP, Doulis AG, Coombs J, Douches DS, Hardigan MA, Buell CR, Veilleux RE.

Plant Genome. 2016 Nov;9(3). doi: 10.3835/plantgenome2016.01.0003.

21.

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development.

Stelpflug SC, Sekhon RS, Vaillancourt B, Hirsch CN, Buell CR, de Leon N, Kaeppler SM.

Plant Genome. 2016 Mar;9(1). doi: 10.3835/plantgenome2015.04.0025.

22.

Analysis of Ribosome-Associated mRNAs in Rice Reveals the Importance of Transcript Size and GC Content in Translation.

Zhao D, Hamilton JP, Hardigan M, Yin D, He T, Vaillancourt B, Reynoso M, Pauluzzi G, Funkhouser S, Cui Y, Bailey-Serres J, Jiang J, Buell CR, Jiang N.

G3 (Bethesda). 2017 Jan 5;7(1):203-219. doi: 10.1534/g3.116.036020.

23.

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize.

Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA.

Plant Cell. 2016 Nov;28(11):2700-2714. Epub 2016 Nov 1.

24.

Integrating metabolomics and transcriptomics data to discover a biocatalyst that can generate the amine precursors for alkamide biosynthesis.

Rizhsky L, Jin H, Shepard MR, Scott HW, Teitgen AM, Perera MA, Mhaske V, Jose A, Zheng X, Crispin M, Wurtele ES, Jones D, Hur M, Góngora-Castillo E, Buell CR, Minto RE, Nikolau BJ.

Plant J. 2016 Dec;88(5):775-793. doi: 10.1111/tpj.13295. Epub 2016 Sep 27.

25.

Genome-wide associations with flowering time in switchgrass using exome-capture sequencing data.

Grabowski PP, Evans J, Daum C, Deshpande S, Barry KW, Kennedy M, Ramstein G, Kaeppler SM, Buell CR, Jiang Y, Casler MD.

New Phytol. 2017 Jan;213(1):154-169. doi: 10.1111/nph.14101. Epub 2016 Jul 22.

26.

Comparative Analysis of Regions with Distorted Segregation in Three Diploid Populations of Potato.

Manrique-Carpintero NC, Coombs JJ, Veilleux RE, Buell CR, Douches DS.

G3 (Bethesda). 2016 Aug 9;6(8):2617-28. doi: 10.1534/g3.116.030031.

27.

Susceptibility of Maize to Stalk Rot Caused by Fusarium graminearum Deoxynivalenol and Zearalenone Mutants.

Quesada-Ocampo LM, Al-Haddad J, Scruggs AC, Buell CR, Trail F.

Phytopathology. 2016 Aug;106(8):920-7. doi: 10.1094/PHYTO-09-15-0199-R. Epub 2016 May 17.

28.

Accuracy of Genomic Prediction in Switchgrass (Panicum virgatum L.) Improved by Accounting for Linkage Disequilibrium.

Ramstein GP, Evans J, Kaeppler SM, Mitchell RB, Vogel KP, Buell CR, Casler MD.

G3 (Bethesda). 2016 Apr 7;6(4):1049-62. doi: 10.1534/g3.115.024950.

29.

Haplotype-Phased Synthetic Long Reads from Short-Read Sequencing.

Stapleton JA, Kim J, Hamilton JP, Wu M, Irber LC, Maddamsetti R, Briney B, Newton L, Burton DR, Brown CT, Chan C, Buell CR, Whitehead TA.

PLoS One. 2016 Jan 20;11(1):e0147229. doi: 10.1371/journal.pone.0147229. eCollection 2016.

30.

Genome Reduction Uncovers a Large Dispensable Genome and Adaptive Role for Copy Number Variation in Asexually Propagated Solanum tuberosum.

Hardigan MA, Crisovan E, Hamilton JP, Kim J, Laimbeer P, Leisner CP, Manrique-Carpintero NC, Newton L, Pham GM, Vaillancourt B, Yang X, Zeng Z, Douches DS, Jiang J, Veilleux RE, Buell CR.

Plant Cell. 2016 Feb;28(2):388-405. doi: 10.1105/tpc.15.00538. Epub 2016 Jan 15.

31.

Diversity and population structure of northern switchgrass as revealed through exome capture sequencing.

Evans J, Crisovan E, Barry K, Daum C, Jenkins J, Kunde-Ramamoorthy G, Nandety A, Ngan CY, Vaillancourt B, Wei CL, Schmutz J, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2015 Nov;84(4):800-15. doi: 10.1111/tpj.13041.

32.

A Revolution in Plant Metabolism: Genome-Enabled Pathway Discovery.

Kim J, Buell CR.

Plant Physiol. 2015 Nov;169(3):1532-9. doi: 10.1104/pp.15.00976. Epub 2015 Jul 29.

33.

Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis.

Haase NJ, Beissinger T, Hirsch CN, Vaillancourt B, Deshpande S, Barry K, Buell CR, Kaeppler SM, de Leon N.

G3 (Bethesda). 2015 Jun 1;5(8):1593-602. doi: 10.1534/g3.115.017665.

34.

Transcriptome responses to Ralstonia solanacearum infection in the roots of the wild potato Solanum commersonii.

Zuluaga AP, Solé M, Lu H, Góngora-Castillo E, Vaillancourt B, Coll N, Buell CR, Valls M.

BMC Genomics. 2015 Mar 26;16:246. doi: 10.1186/s12864-015-1460-1.

35.

Genome-guided investigation of plant natural product biosynthesis.

Kellner F, Kim J, Clavijo BJ, Hamilton JP, Childs KL, Vaillancourt B, Cepela J, Habermann M, Steuernagel B, Clissold L, McLay K, Buell CR, O'Connor SE.

Plant J. 2015 May;82(4):680-92. doi: 10.1111/tpj.12827. Epub 2015 Apr 11.

36.

Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes.

Salvo SA, Hirsch CN, Buell CR, Kaeppler SM, Kaeppler HF.

PLoS One. 2014 Oct 30;9(10):e111407. doi: 10.1371/journal.pone.0111407. eCollection 2014.

37.

Treatment of potato tubers with the synthetic cytokinin 1-(α-ethylbenzyl)-3-nitroguanidine results in rapid termination of endodormancy and induction of transcripts associated with cell proliferation and growth.

Campbell M, Suttle J, Douches DS, Buell CR.

Funct Integr Genomics. 2014 Dec;14(4):789-99. doi: 10.1007/s10142-014-0404-1. Epub 2014 Oct 1.

PMID:
25270889
38.

A foundation for provitamin A biofortification of maize: genome-wide association and genomic prediction models of carotenoid levels.

Owens BF, Lipka AE, Magallanes-Lundback M, Tiede T, Diepenbrock CH, Kandianis CB, Kim E, Cepela J, Mateos-Hernandez M, Buell CR, Buckler ES, DellaPenna D, Gore MA, Rocheford T.

Genetics. 2014 Dec;198(4):1699-716. doi: 10.1534/genetics.114.169979. Epub 2014 Sep 25.

39.

QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.).

Burton AL, Johnson JM, Foerster JM, Hirsch CN, Buell CR, Hanlon MT, Kaeppler SM, Brown KM, Lynch JP.

Theor Appl Genet. 2014 Nov;127(11):2293-311. doi: 10.1007/s00122-014-2353-4. Epub 2014 Sep 18.

PMID:
25230896
40.

A root-expressed L-phenylalanine:4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in Atropa belladonna.

Bedewitz MA, Góngora-Castillo E, Uebler JB, Gonzales-Vigil E, Wiegert-Rininger KE, Childs KL, Hamilton JP, Vaillancourt B, Yeo YS, Chappell J, DellaPenna D, Jones AD, Buell CR, Barry CS.

Plant Cell. 2014 Sep;26(9):3745-62. doi: 10.1105/tpc.114.130534. Epub 2014 Sep 16.

41.

Comparative transcriptome atlases reveal altered gene expression modules between two Cleomaceae C3 and C4 plant species.

Külahoglu C, Denton AK, Sommer M, Maß J, Schliesky S, Wrobel TJ, Berckmans B, Gongora-Castillo E, Buell CR, Simon R, De Veylder L, Bräutigam A, Weber AP.

Plant Cell. 2014 Aug;26(8):3243-60. doi: 10.1105/tpc.114.123752. Epub 2014 Aug 8.

42.

Insights into the effects of long-term artificial selection on seed size in maize.

Hirsch CN, Flint-Garcia SA, Beissinger TM, Eichten SR, Deshpande S, Barry K, McMullen MD, Holland JB, Buckler ES, Springer N, Buell CR, de Leon N, Kaeppler SM.

Genetics. 2014 Sep;198(1):409-21. doi: 10.1534/genetics.114.167155. Epub 2014 Jul 17.

43.

Timber! Felling the loblolly pine genome.

Hamilton JP, Buell CR.

Genome Biol. 2014 Mar 31;15(3):111. doi: 10.1186/gb4170.

44.

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum.

Evans J, Kim J, Childs KL, Vaillancourt B, Crisovan E, Nandety A, Gerhardt DJ, Richmond TA, Jeddeloh JA, Kaeppler SM, Casler MD, Buell CR.

Plant J. 2014 Sep;79(6):993-1008. doi: 10.1111/tpj.12601. Epub 2014 Aug 11.

45.

Boom-Bust Turnovers of Megabase-Sized Centromeric DNA in Solanum Species: Rapid Evolution of DNA Sequences Associated with Centromeres.

Zhang H, Koblížková A, Wang K, Gong Z, Oliveira L, Torres GA, Wu Y, Zhang W, Novák P, Buell CR, Macas J, Jiang J.

Plant Cell. 2014 Apr;26(4):1436-1447. Epub 2014 Apr 11.

46.

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination.

Sekhon RS, Hirsch CN, Childs KL, Breitzman MW, Kell P, Duvick S, Spalding EP, Buell CR, de Leon N, Kaeppler SM.

Plant Physiol. 2014 Jun;165(2):658-669. Epub 2014 Apr 7.

47.

Insights into the maize pan-genome and pan-transcriptome.

Hirsch CN, Foerster JM, Johnson JM, Sekhon RS, Muttoni G, Vaillancourt B, Peñagaricano F, Lindquist E, Pedraza MA, Barry K, de Leon N, Kaeppler SM, Buell CR.

Plant Cell. 2014 Jan;26(1):121-35. doi: 10.1105/tpc.113.119982. Epub 2014 Jan 31.

48.

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

Hirsch CD, Evans J, Buell CR, Hirsch CN.

Brief Funct Genomics. 2014 Jul;13(4):257-67. doi: 10.1093/bfgp/elt051. Epub 2014 Jan 6.

PMID:
24395692
49.

A genome-wide scan for evidence of selection in a maize population under long-term artificial selection for ear number.

Beissinger TM, Hirsch CN, Vaillancourt B, Deshpande S, Barry K, Buell CR, Kaeppler SM, Gianola D, de Leon N.

Genetics. 2014 Mar;196(3):829-40. doi: 10.1534/genetics.113.160655. Epub 2013 Dec 30.

50.

Carotenoid cleavage dioxygenase4 is a negative regulator of β-carotene content in Arabidopsis seeds.

Gonzalez-Jorge S, Ha SH, Magallanes-Lundback M, Gilliland LU, Zhou A, Lipka AE, Nguyen YN, Angelovici R, Lin H, Cepela J, Little H, Buell CR, Gore MA, Dellapenna D.

Plant Cell. 2013 Dec;25(12):4812-26. doi: 10.1105/tpc.113.119677. Epub 2013 Dec 24.

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