Publications 1992 2018

2018

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

Sherden, N. H., Lichman, B., Caputi, L., Zhao, D., Kamileen, M. O., Buell, C. R. & O'Connor, S. E. Jan 1 2018 In : Phytochemistry. 145, p. 48-56 9 p.

Research output: Research - peer-reviewArticle

Stereochemistry
Cyclization
nepetalactone
Nepeta
stereochemistry
2017
3 Citations

Analysis of ribosome-associated mRNAs in rice reveals the importance of transcript size and GC content in translation

Zhao, D., Hamilton, J. P., Hardigan, M., Yin, D., He, T., Vaillancourt, B., Reynoso, M., Pauluzzi, G., Funkhouser, S., Cui, Y., Bailey-Serres, J., Jiang, J., Buell, C. R. & Jiang, N. 2017 In : G3: Genes, Genomes, Genetics. 7, 1, p. 203-219 17 p.

Research output: Research - peer-reviewArticle

Base Composition
Ribosomes
Messenger RNA
Oryza
Genes

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

Zhao, D., Hamilton, J. P., Pham, G. M., Crisovan, E., Wiegert-Rininger, K., Vaillancourt, B., DellaPenna, D. & Robin Buell, C. Sep 1 2017 In : GigaScience. 6, 9, gix065

Research output: Research - peer-reviewArticle

Camptotheca
Camptothecin
Genome
Neoplasms
Genes
1 Citations

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

Leisner, C. P., Kamileen, M. O., Conway, M. E., O'Connor, S. E. & Buell, C. R. Jun 1 2017 In : PLoS ONE. 12, 6, 0179417

Research output: Research - peer-reviewArticle

blueberries
Iridoids
Fruits
Blueberry Plants
Tissue
1 Citations

Elevating the conversation about GE crops

Gould, F., Amasino, R. M., Brossard, D., Buell, C. R., DIxon, R. A., Falck-Zepeda, J. B., Gallo, M. A., Giller, K. E., Glenna, L. L., Griffin, T., Hamaker, B. R., Kareiva, P. M., Magraw, D., Mallory-Smith, C., Pixley, K. V., Ransom, E. P., Rodemeyer, M., Stelly, D. M., Stewart, C. N. & Whitaker, R. J. Apr 11 2017 In : Nature Biotechnology. 35, 4, p. 302-304 3 p.

Research output: Research - peer-reviewLetter

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

Pham, G. M., Newton, L., Wiegert-Rininger, K., Vaillancourt, B., Douches, D. S. & Buell, C. R. Nov 1 2017 In : Plant Journal. 92, 4, p. 624-637 14 p.

Research output: Research - peer-reviewArticle

potatoes
alleles
genome
genes
Solanum tuberosum

Novel loci underlie natural variation in vitamin E levels in maize grain

Diepenbrock, C. H., Kandianis, C. B., Lipka, A. E., Magallanes-Lundback, M., Vaillancourt, B., Góngora-Castillo, E., Wallace, J. G., Cepela, J., Mesberg, A., Bradbury, P. J., Ilut, D. C., Mateos-Hernandez, M., Hamilton, J., Owens, B. F., Tiede, T., Buckler, E. S., Rocheford, T., Buell, C. R., Gore, M. A. & DellaPenna, D. Oct 1 2017 In : Plant Cell. 29, 10, p. 2374-2392 19 p.

Research output: Research - peer-reviewArticle

vitamin E
loci
corn
Vitamin E
Zea mays

Protoplast isolation prior to flow cytometry reveals clear patterns of endoreduplication in potato tubers, related species, and some starchy root crops

Laimbeer, F. P. E., Holt, S. H., Makris, M., Hardigan, M. A., Robin Buell, C. & Veilleux, R. E. Apr 14 2017 In : Plant Methods. 13, 1, 27

Research output: Research - peer-reviewArticle

endopolyploidy
protoplasts
flow cytometry
tubers
potatoes

Technology turbocharges functional genomics

Buell, C. R. & Voytas, D. Jun 1 2017 In : Plant Cell. 29, 6, p. 1179-1180 2 p.

Research output: Research - peer-reviewComment/debate

Transcriptional Analysis of Flowering Time in Switchgrass

Tornqvist, C. E., Vaillancourt, B., Kim, J., Buell, C. R., Kaeppler, S. M. & Casler, M. D. Apr 27 2017 (Accepted/In press) In : Bioenergy Research. p. 1-14 14 p.

Research output: Research - peer-reviewArticle

Panicum virgatum
flowering
Genes
RNA
genes
2016

Accuracy of genomic prediction in switchgrass (Panicum virgatum L.) improved by accounting for linkage disequilibrium

Ramstein, G. P., Evans, J., Kaeppler, S. M., Mitchell, R. B., Vogel, K. P., Buell, C. R. & Casler, M. D. 2016 In : G3: Genes, Genomes, Genetics. 6, 4, p. 1049-1062 14 p.

Research output: Research - peer-reviewArticle

Panicum
Linkage Disequilibrium
Biomass
Exome
Biofuels
15 Citations

An expanded maize gene expression atlas based on RNA sequencing and its use to explore root development

Stelpflug, S. C., Sekhon, R. S., Vaillancourt, B., Hirsch, C. N., Buell, C. R., de Leon, N. & Kaeppler, S. M. Mar 1 2016 In : Plant Genome. 9, 1

Research output: Research - peer-reviewArticle

sequence analysis
gene expression
corn
genes
RNA Sequence Analysis
2 Citations

A Toolbox of Potato Genetic and Genomic Resources

Hirsch, C. D., Buell, C. R. & Hirsch, C. N. Feb 1 2016 In : American Journal of Potato Research. 93, 1, p. 21-32 12 p.

Research output: Research - peer-reviewArticle

potatoes
genomics
crops
cultivars
genome assembly
3 Citations

Comparative analysis of regions with distorted segregation in three diploid populations of potato

Manrique-Carpintero, N. C., Coombs, J. J., Veilleux, R. E., Buell, C. R. & Douches, D. S. 2016 In : G3: Genes, Genomes, Genetics. 6, 8, p. 2617-2628 12 p.

Research output: Research - peer-reviewArticle

Solanum tuberosum
Diploidy
Population
Chromosomes, Human, Pair 2
Chromosomes, Human, Pair 12
12 Citations

Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A. G., Fields, C. J., Wright, C. L., Koehler, K., Springer, N. M., Buckler, E., Buell, C. R., de Leon, N., Kaeppler, S. M., Childs, K. L. & Mikel, M. A. Nov 1 2016 In : Plant Cell. 28, 11, p. 2700-2714 15 p.

Research output: Research - peer-reviewArticle

transcriptome
inbred lines
genomics
corn
Transcriptome
2 Citations

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

Grabowski, P. P., Evans, J., Daum, C., Deshpande, S., Barry, K. W., Kennedy, M., Ramstein, G., Kaeppler, S. M., Buell, C. R., Jiang, Y. & Casler, M. D. 2016 (Accepted/In press) In : New Phytologist.

Research output: Research - peer-reviewArticle

Panicum virgatum
flowering
genome
Exome
Panicum
2 Citations

Haplotype-phased synthetic long reads from short-read sequencing

Stapleton, J. A., Kim, J., Hamilton, J. P., Wu, M., Irber, L. C., Maddamsetti, R., Briney, B., Newton, L., Burton, D. R., Brown, C. T., Chan, C., Buell, C. R. & Whitehead, T. A. Jan 1 2016 In : PLoS One. 11, 1, e0147229

Research output: Research - peer-reviewArticle

Haplotypes
haplotypes
Genes
DNA
sampling

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

Rizhsky, L., Jin, H., Shepard, M. R., Scott, H. W., Teitgen, A. M., Perera, M. A., Mhaske, V., Jose, A., Zheng, X., Crispin, M., Wurtele, E. S., Jones, D., Hur, M., Góngora-Castillo, E., Buell, C. R., Minto, R. E. & Nikolau, B. J. 2016 (Accepted/In press) In : Plant Journal.

Research output: Research - peer-reviewArticle

Branched Chain Amino Acids
Metabolomics
Amines
Enzymes
metabolomics

Self-fertility in a cultivated diploid potato population examined with the Infinium 8303 potato single-nucleotide polymorphism array

Peterson, B. A., Holt, S. H., Laimbeer, F. P. E., Doulis, A. G., Coombs, J., Douches, D. S., Hardigan, M. A., Buell, C. R. & Veilleux, R. E. Nov 1 2016 In : Plant Genome. 9, 3

Research output: Research - peer-reviewArticle

Solanum tuberosum
Diploidy
Single Nucleotide Polymorphism
Fertility
Population
3 Citations

Susceptibility of maize to stalk rot caused by Fusarium graminearum deoxynivalenol and zearalenone mutants

Quesada-Ocampo, L. M., Al-Haddad, J., Scruggs, A. C., Buell, C. R. & Trail, F. Aug 1 2016 In : Phytopathology. 106, 8, p. 920-927 8 p.

Research output: Research - peer-reviewArticle

zearalenone
Fusarium graminearum
deoxynivalenol
mutants
corn
2015
8 Citations

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, C. Y., Vaillancourt, B., Wei, C. L., Schmutz, J., Kaeppler, S. M., Casler, M. D. & Buell, C. R. Nov 1 2015 In : Plant Journal. 84, 4, p. 800-815 16 p.

Research output: Research - peer-reviewArticle

Panicum virgatum
ecotypes
population structure
Ecotype
Exome
26 Citations

Gene amplification of 5-enol-pyruvylshikimate-3-phosphate synthase in glyphosate-resistant Kochia scoparia

Wiersma, A. T., Gaines, T. A., Preston, C., Hamilton, J. P., Giacomini, D., Robin Buell, C., Leach, J. E. & Westra, P. 2015 In : Planta. 241, 2, p. 463-474 12 p.

Research output: Research - peer-reviewArticle

Bassia scoparia
glyphosate
polymerase chain reaction
phosphates
Gene Amplification
4 Citations

Genetic map and QTL analysis of agronomic traits in a diploid potato population using single nucleotide polymorphism markers

Manrique-Carpintero, N. C., Coombs, J. J., Cui, Y., Veilleux, R. E., Robin Buell, C. & Douches, D. Oct 1 2015 In : Crop Science. 55, 6, p. 2566-2579 14 p.

Research output: Research - peer-reviewArticle

agronomic traits
single nucleotide polymorphism
quantitative trait loci
tubers
diploidy
36 Citations

Genome-guided investigation of plant natural product biosynthesis

Kellner, F., Kim, J., Clavijo, B. J., Hamilton, J. P., Childs, K. L., Vaillancourt, B., Cepela, J., Habermann, M., Steuernagel, B., Clissold, L., Mclay, K., Buell, C. R. & O'Connor, S. E. May 1 2015 In : Plant Journal. 82, 4, p. 680-692 13 p.

Research output: Research - peer-reviewArticle

biosynthesis
genome
Biological Products
Genome
Catharanthus roseus
3 Citations

Shared genomic regions between derivatives of a large segregating population of maize identified using bulked segregant analysis sequencing and traditional linkage analysis

Haase, N. J., Beissinger, T., Hirsch, C. N., Vaillancourt, B., Deshpande, S., Barry, K., Robin Buell, C., Kaeppler, S. M. & de Leon, N. 2015 In : G3: Genes, Genomes, Genetics. 5, 8, p. 1593-1602 10 p.

Research output: Research - peer-reviewArticle

Zea mays
Population
Plant Development
Chromosome Mapping
Quantitative Trait Loci
8 Citations

Taxonomy and genetic differentiation among wild and cultivated germplasm of solanum sect. Petota

Hardigan, M. A., Bamberg, J., Buell, C. R. & Douches, D. S. 2015 In : Plant Genome. 8, 1

Research output: Research - peer-reviewArticle

Solanum
single nucleotide polymorphism
germplasm
taxonomy
genetic variation
11 Citations

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

Zuluaga, A. P., Solé, M., Lu, H., Góngora-Castillo, E., Vaillancourt, B., Coll, N., Buell, C. R. & Valls, M. Mar 26 2015 In : BMC Genomics. 16, 1, 246

Research output: Research - peer-reviewArticle

Ralstonia solanacearum
Solanum
Solanum tuberosum
Transcriptome
RNA
2014
31 Citations

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

Owens, B. F., Lipka, A. E., Magallanes-Lundback, M., Tiede, T., Diepenbrock, C. H., Kandianis, C. B., Kim, E., Cepela, J., Mateos-Hernandez, M., Robin Buell, C., Buckler, E. S., DellaPenna, D., Gore, M. A. & Rocheford, T. Dec 1 2014 In : Genetics. 198, 4, p. 1699-1716 18 p.

Research output: Research - peer-reviewArticle

Carotenoids
Zea mays
Genome
Biofortification
Provitamins
23 Citations

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

Beissinger, T. M., Hirsch, C. N., Vaillancourt, B., Deshpande, S., Barry, K., Robin Buell, C., Kaeppler, S. M., Gianola, D. & de Leon, N. 2014 In : Genetics. 196, 3, p. 829-840 12 p.

Research output: Research - peer-reviewArticle

Zea mays
Ear
Genome
Population
Population Density
19 Citations

A root-expressed l-phenylalanine: 4-hydroxyphenylpyruvate aminotransferase is required for tropane alkaloid biosynthesis in atropa belladonna

Bedewitz, M. A., Góngora-Castillo, E., Uebler, J. B., Gonzales-Vigil, E., Wiegert-Rininger, K. E., Childs, K. L., Hamilton, J. P., Vaillancourt, B., Yeo, Y. S., Chappell, J., Della, D., Daniel Jones, A., Robin Buell, C. & Barry, C. S. Sep 1 2014 In : Plant Cell. 26, 9, p. 3745-3762 18 p.

Research output: Research - peer-reviewArticle

Hyoscyamine
Atropa belladonna
Tropanes
Scopolamine Hydrobromide
Transaminases
20 Citations

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, G. A., Wu, Y., Zhang, W., Novák, P., Buell, C. R., Macas, J. & Jiang, J. 2014 In : Plant Cell. 26, 4, p. 1436-1447 12 p.

Research output: Research - peer-reviewArticle

centromeres
Solanum
nucleotide sequences
DNA
Centromere
31 Citations

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

Külahoglu, C., Denton, A. K., Sommer, M., Maß, J., Schliesky, S., Wrobel, T. J., Berckmans, B., Gongora-Castillo, E., Robin Buell, C., Simon, R., De Veylder, L., Bräutigam, A. & Weber, A. P. M. Aug 1 2014 In : Plant Cell. 26, 8, p. 3243-3260 18 p.

Research output: Research - peer-reviewArticle

Cleomaceae
C4 plants
C3 plants
transcriptome
photosynthesis
1 Citations

Correction: Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays (PLoS ONE)

Sekhon, R. S., Briskine, R., Hirsch, C. N., Myers, C. L., Springer, N. M., Buell, C. R., De Leon, N. & Kaeppler, S. M. Jan 3 2014 In : PLoS One. 9, 1

Research output: Research - peer-reviewArticle

3 Citations

Generation of transcript assemblies and identification of single nucleotide polymorphisms from seven lowland and upland cultivars of Switchgrass

Childs, K. L., Nandety, A., Hirsch, C. N., Góngora-Castillo, E., Schmutz, J., Kaeppler, S. M., Casler, M. D. & Robin Buell, C. 2014 In : Plant Genome. 7, 2

Research output: Research - peer-reviewArticle

Panicum virgatum
single nucleotide polymorphism
lowlands
highlands
cultivars
12 Citations

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

Hirsch, C. N., Flint-Garcia, S. A., Beissinger, T. M., Eichten, S. R., Deshpande, S., Barry, K., McMullen, M. D., Holland, J. B., Buckler, E. S., Springer, N., Buell, C. R., de Leon, N. & Kaeppler, S. M. Sep 1 2014 In : Genetics. 198, 1, p. 409-421 13 p.

Research output: Research - peer-reviewArticle

Zea mays
Seeds
Population
Genome
Single Nucleotide Polymorphism
73 Citations

Insights into the maize pan-genome and pan-transcriptome

Hirsch, C. N., Foerster, J. M., Johnson, J. M., Sekhon, R. S., Muttoni, G., Vaillancourt, B., Peñagaricano, F., Lindquist, E., Pedraza, M. A., Barry, K., de Leon, N., Kaeppler, S. M. & Robin Buell, C. Jan 2014 In : Plant Cell. 26, 1, p. 121-135 15 p.

Research output: Research - peer-reviewArticle

transcriptome
genome
corn
Transcriptome
Zea mays
11 Citations

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, K. L., Vaillancourt, B., Crisovan, E., Nandety, A., Gerhardt, D. J., Richmond, T. A., Jeddeloh, J. A., Kaeppler, S. M., Casler, M. D. & Buell, C. R. 2014 In : Plant Journal. 79, 6, p. 993-1008 16 p.

Research output: Research - peer-reviewArticle

Panicum virgatum
polyploidy
nucleotides
genetic polymorphism
grasses
17 Citations

Phenotypic and transcriptional analysis of divergently selected maize populations reveals the role of developmental timing in seed size determination

Sekhon, R. S., Hirsch, C. N., Childs, K. L., Breitzman, M. W., Kell, P., Duvick, S., Spalding, E. P., Robin Buell, C., de Leon, N. & Kaeppler, S. M. 2014 In : Plant Physiology. 165, 2, p. 658-669 12 p.

Research output: Research - peer-reviewArticle

Zea mays
Seeds
Population
corn
seeds
21 Citations

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

Burton, A. L., Johnson, J. M., Foerster, J. M., Hirsch, C. N., Buell, C. R., Hanlon, M. T., Kaeppler, S. M., Brown, K. M. & Lynch, J. P. Oct 25 2014 In : Theoretical And Applied Genetics. 127, 11, p. 2293-2311 19 p.

Research output: Research - peer-reviewArticle

phenotypic variation
quantitative trait loci
Zea mays
corn
Quantitative Trait Loci
9 Citations

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

Hirsch, C. D., Evans, J., Buell, C. R. & Hirsch, C. N. 2014 In : Briefings in Functional Genomics and Proteomics. 13, 4, p. 257-267 11 p., elt051

Research output: Research - peer-reviewArticle

Plant Genome
Genome
Genes
Exome
Food Supply
26 Citations

Spud DB: A resource for mining sequences, genotypes, and phenotypes to accelerate potato breeding

Hirsch, C. D., Hamilton, J. P., Childs, K. L., Cepela, J., Crisovan, E., Vaillancourt, B., Hirsch, C. N., Habermann, M., Neal, B. & Buell, C. R. 2014 In : Plant Genome. 7, 1

Research output: Research - peer-reviewArticle

potatoes
phenotype
genotype
breeding
Solanum tuberosum
5 Citations

The Contribution of the Solanaceae Coordinated Agricultural Project to Potato Breeding

Douches, D., Hirsch, C. N., Manrique-Carpintero, N. C., Massa, A. N., Coombs, J., Hardigan, M., Bisognin, D., De Jong, W. & Buell, C. R. Dec 1 2014 In : Potato Research. 57, 3-4, p. 215-224 10 p.

Research output: Research - peer-reviewArticle

Solanaceae
germplasm
potatoes
breeding
Solanum tuberosum

Timber! Felling the loblolly pine genome

Hamilton, J. P. & Buell, C. R. Mar 31 2014 In : Genome Biology. 15, 3, 111

Research output: Research - peer-reviewArticle

felling
Pinus taeda
genome
Genome
timber
3 Citations
Cytokinins
Meristem
Solanum tuberosum
Cell Proliferation
Growth
25 Citations

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

Salvo, S. A. G. D., Hirsch, C. N., Buell, C. R., Kaeppler, S. M. & Kaeppler, H. F. Oct 30 2014 In : PLoS One. 9, 10, e111407

Research output: Research - peer-reviewArticle

transcriptomics
somatic embryogenesis
embryogenesis
corn
genes
2013
11 Citations
biotic stress
transcriptomics
Solanum tuberosum
abiotic stress
stress response
25 Citations

Bioinformatics challenges in de novo transcriptome assembly using short read sequences in the absence of a reference genome sequence

Góngora-Castillo, E. & Buell, C. R. Apr 2013 In : Natural Product Reports. 30, 4, p. 490-500 11 p.

Research output: Research - peer-reviewArticle

Computational Biology
Transcriptome
Genome
Bioinformatics
Genes
15 Citations

Carbohydrate-Active Enzymes in Pythium and Their Role in Plant Cell Wall and Storage Polysaccharide Degradation

Zerillo, M. M., Adhikari, B. N., Hamilton, J. P., Buell, C. R., Lévesque, C. A. & Tisserat, N. Sep 12 2013 In : PLoS One. 8, 9, e72572

Research output: Research - peer-reviewArticle

Pythium
Plant Cells
Cell Wall
Polysaccharides
Carbohydrates
56 Citations

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

Gonzalez-Jorge, S., Ha, S. H., Magallanes-Lundback, M., Gilliland, L. U., Zhou, A., Lipka, A. E., Nguyen, Y. N., Angelovici, R., Lin, H., Cepela, J., Little, H., Buell, C. R., Gore, M. A. & DellaPenna, D. Dec 2013 In : Plant Cell. 25, 12, p. 4812-4826 15 p.

Research output: Research - peer-reviewArticle

beta-carotene
carotenoids
Arabidopsis
seeds
beta Carotene
38 Citations

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

Adhikari, B. N., Hamilton, J. P., Zerillo, M. M., Tisserat, N., Lévesque, C. A. & Buell, C. R. Oct 4 2013 In : PLoS One. 8, 10, e75072

Research output: Research - peer-reviewArticle

Oomycetes
virulence
genomics
Genomics
Virulence