Publications 1992 2017

2017
2 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: Contribution to journalArticle

Base Composition
Ribosomes
Oryza sativa
Messenger RNA
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: Contribution to journalArticle

blueberries
Blueberry Plant
Hypocalcemia
Vaccinium
Library Catalogs
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: Contribution to journalLetter

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: Contribution to journalArticle

endopolyploidy
Endoreduplication
Protoplasts
Solanum tuberosum
Flow Cytometry

Technology turbocharges functional genomics

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

Research output: Contribution to journalComment/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 In : Bioenergy Research. p. 1-14 14 p.

Research output: Contribution to journalArticle

flowering
Genes
Panicum virgatum
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: Contribution to journalArticle

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: Contribution to journalArticle

RNA Sequence Analysis
Atlases
Zea mays
Gene Expression
Genes
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: Contribution to journalArticle

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: Contribution to journalArticle

Solanum tuberosum
Diploidy
Chromosomes, Human, Pair 2
Chromosomes, Human, Pair 12
Chromosomes, Human, Pair 9
9 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: Contribution to journalArticle

corn
Transcriptome
Zea mays
inbred lines
Genome
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 In : New Phytologist.

Research output: Contribution to journalArticle

flowering
Exome
Genome
Panicum virgatum
Biomass
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: Contribution to journalArticle

Haplotypes
Cyclic AMP Receptor Protein
Agglutination Tests
haplotypes
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 In : Plant Journal.

Research output: Contribution to journalArticle

Branched Chain Amino Acids
Metabolomics
Amines
Enzymes
amides

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: Contribution to journalArticle

Solanum tuberosum
Diploidy
Single Nucleotide Polymorphism
Fertility
potatoes
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: Contribution to journalArticle

deoxynivalenol
Fusarium graminearum
zearalenone
corn
lesions (plant)
2015
7 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: Contribution to journalArticle

ecotypes
Ecotype
Exome
Panicum virgatum
genes
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: Contribution to journalArticle

Bassia scoparia
Gene Amplification
Phosphates
glyphosate
phosphates
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: Contribution to journalArticle

tubers
quantitative trait loci
potatoes
specific gravity
agronomic traits
34 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: Contribution to journalArticle

genome
Biological Products
Genome
Catharanthus roseus
Catharanthus
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: Contribution to journalArticle

Zea mays
Plant Development
Chromosome Mapping
Quantitative Trait Loci
Poaceae
7 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: Contribution to journalArticle

Solanum
single nucleotide polymorphism
Single Nucleotide Polymorphism
germplasm
potatoes
10 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: Contribution to journalArticle

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: Contribution to journalArticle

Carotenoids
Zea mays
Genome
Genes
Cereals
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: Contribution to journalArticle

Zea mays
Ear
Genome
Population Density
Gene Frequency
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: Contribution to journalArticle

Hyoscyamine
Atropa belladonna
Tropanes
Scopolamine Hydrobromide
Transaminases
19 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: Contribution to journalArticle

Solanum
Centromere
DNA
centromeres
Solanum tuberosum
32 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: Contribution to journalArticle

Atlases
Gene Regulatory Networks
Photosynthesis
Transcriptome
Gene Expression
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: Contribution to journalArticle

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: Contribution to journalArticle

Panicum virgatum
Single Nucleotide Polymorphism
single nucleotide polymorphism
cultivars
lowlands
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: Contribution to journalArticle

Zea mays
Seeds
Cereals
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: Contribution to journalArticle

Transcriptome
Zea mays
Genome
genome
corn
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: Contribution to journalArticle

DNA Copy Number Variations
Exome
Panicum
Polyploidy
Poaceae
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: Contribution to journalArticle

Zea mays
Seeds
seeds
genes
Cereals
19 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: Contribution to journalArticle

Quantitative Trait Loci
Zea mays
quantitative trait loci
Soil
phenotypic variation
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: Contribution to journalArticle

Plant Genome
Genome
Cyclic AMP Receptor Protein
Exome
Food Supply
23 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: Contribution to journalArticle

Solanum tuberosum
Breeding
Genotype
Phenotype
potatoes
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: Contribution to journalArticle

germplasm
potatoes
Solanaceae
Solanum tuberosum
Breeding

Timber! Felling the loblolly pine genome

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

Research output: Contribution to journalArticle

Pinus taeda
Genome
genome
Haploidy
DNA
2 Citations
Cytokinins
Meristem
Solanum tuberosum
Cell Proliferation
Transcriptome
23 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: Contribution to journalArticle

Gene Expression Profiling
Zea mays
Embryonic Development
Genes
genes
2013
10 Citations
Solanum tuberosum
Transcriptome
Genes
genes
potatoes
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: Contribution to journalArticle

Computational Biology
Transcriptome
Genome
Cyclic AMP Receptor Protein
Gene Expression Profiling
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: Contribution to journalArticle

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: Contribution to journalArticle

beta Carotene
Carotenoids
Arabidopsis
Seeds
carotenoids
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: Contribution to journalArticle

Oomycetes
Genomics
Virulence
Cyclic AMP Receptor Protein
Pythium
14 Citations

Copy number variation in potato - An asexually propagated autotetraploid species

Iovene, M., Zhang, T., Lou, Q., Buell, C. R. & Jiang, J. Jul 2013 In : Plant Journal. 75, 1, p. 80-89 10 p.

Research output: Contribution to journalArticle

potatoes
Solanum tuberosum
Bacterial Artificial Chromosomes
Fluorescence In Situ Hybridization
Genes
26 Citations

Coupling deep transcriptome analysis with untargeted metabolic profiling in ophiorrhiza pumila to further the understanding of the biosynthesis of the anti-cancer alkaloid camptothecin and anthraquinones

Yamazaki, M., Mochida, K., Asano, T., Nakabayashi, R., Chiba, M., Udomson, N., Yamazaki, Y., Goodenowe, D. B., Sankawa, U., Yoshida, T., Toyoda, A., Totoki, Y., Sakaki, Y., Góngora-Castillo, E., Buell, C. R., Sakurai, T. & Saito, K. May 2013 In : Plant and Cell Physiology. 54, 5, p. 686-696 11 p.

Research output: Contribution to journalArticle

Camptothecin
Anthraquinones
Gene Expression Profiling
Alkaloids
Cell Culture Techniques
21 Citations

Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis

Yeo, Y. S. , Nybo, S. E. , Chittiboyina, A. G. , Weerasooriya, A. D. , Wang, Y. H. , Góngora-Castillo, E. , Vaillancourt, B. , Buell, C. R. , Dellapenna, D. , Celiz, M. D. , Daniel Jones, A. , Wurtele, E. S. , Ransom, N. , Dudareva, N. , Shaaban, K. A. , Tibrewal, N. , Chandra, S. , Smillie, T. , Khan, I. A. , Coates, R. M. & 2 others Watt, D. S. & Chappell, J. Feb 1 2013 In : Journal of Biological Chemistry. 288, 5, p. 3163-3173 11 p.

Research output: Contribution to journalArticle

Valerian
Sesquiterpenes
Terpenes
Biosynthesis
Hyperostosis, Cortical, Congenital
33 Citations

Genome-wide analysis of branched-chain amino acid levels in Arabidopsis Seeds

Angelovici, R., Lipka, A. E., Deason, N., Gonzalez-Jorge, S., Lin, H., Cepela, J., Buell, R., Gore, M. A. & DellaPenna, D. Dec 2013 In : Plant Cell. 25, 12, p. 4827-4843 17 p.

Research output: Contribution to journalArticle

Branched Chain Amino Acids
Arabidopsis
Seeds
Genome
branched chain amino acids