Research Output 1975 2020

The Plant Ontology Database: A community resource for plant structure and developmental stages controlled vocabulary and annotations

Avraham, S., Tung, C. W., Ilic, K., Jaiswal, P., Kellogg, E. A., Mccouch, S., Pujar, A., Reiser, L., Rhee, S. Y., Sachs, M. M., Schaeffer, M., Stein, L., Stevens, P., Vincent, L., Zapata, F. & Ware, D., Jan 1 2008, In : Nucleic acids research. 36, SUPPL. 1, p. D449-D454

Research output: Contribution to journalArticle

Controlled Vocabulary
Plant Structures
Databases
Web Browser
Genes

The plant cell/microbe coincubation assay for the analysis of plant-activated promutagens

Plewa, M. J., Wagner, E. D. & Gentile, J. M., Feb 1988, In : Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 197, 2, p. 207-219 13 p.

Research output: Contribution to journalArticle

Plant Cells
Tobacco
Daucus carota
Zea mays
Carbamates

The plant activation of m-phenylenediamine by Tradescantia clone 03 and clone 4430 cells in liquid suspension culture

Anderson, V. A., Plewa, M. J. & Gentile, J. M., Feb 1988, In : Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 197, 2, p. 303-312 10 p.

Research output: Contribution to journalArticle

Tradescantia
Suspensions
Clone Cells
Plant Cells
3-phenylenediamine

The pineapple genome and the evolution of CAM photosynthesis

Ming, R., VanBuren, R., Wai, C. M., Tang, H., Schatz, M. C., Bowers, J. E., Lyons, E., Wang, M. L., Chen, J., Biggers, E., Zhang, J., Huang, L., Zhang, L., Miao, W., Zhang, J., Ye, Z., Miao, C., Lin, Z., Wang, H., Zhou, H. & 50 others, Yim, W. C., Priest, H. D., Zheng, C., Woodhouse, M., Edger, P. P., Guyot, R., Guo, H. B., Guo, H., Zheng, G., Singh, R., Sharma, A., Min, X., Zheng, Y., Lee, H., Gurtowski, J., Sedlazeck, F. J., Harkess, A., McKain, M. R., Liao, Z., Fang, J., Liu, J., Zhang, X., Zhang, Q., Hu, W., Qin, Y., Wang, K., Chen, L. Y., Shirley, N., Lin, Y. R., Liu, L. Y., Hernandez, A. G., Wright, C. L., Bulone, V., Tuskan, G. A., Heath, K., Zee, F., Moore, P. H., Sunkar, R., Leebens-Mack, J. H., Mockler, T., Bennetzen, J. L., Freeling, M., Sankoff, D., Paterson, A. H., Zhu, X., Yang, X., Smith, J. A. C., Cushman, J. C., Paull, R. E. & Yu, Q., Dec 1 2015, In : Nature Genetics. 47, 12, p. 1435-1442 8 p.

Research output: Contribution to journalArticle

Ananas
Photosynthesis
Genome
Acids
Circadian Clocks
Phytochrome B
Nicotiana plumbaginifolia
Photoperiod
phytochrome
Tobacco

The phylogenomic roots of translation

Caetano-Anollés, D. & Caetano-Anollés, G., Jan 1 2016, Evolution of the Protein Synthesis Machinery and Its Regulation. Springer International Publishing, p. 9-30 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Transfer RNA
ribosomes
Ribosomes
translation (genetics)
Genetic Code

The phylogenomic roots of modern biochemistry: Origins of proteins, cofactors and protein biosynthesis

Caetano-Anolles, G., Kim, K. M. & Caetano-Anollés, D., Feb 2012, In : Journal of Molecular Evolution. 74, 1-2, p. 1-34 34 p.

Research output: Contribution to journalArticle

biochemistry
Protein Biosynthesis
Biochemistry
protein synthesis
protein

The performance of early-generation perennial winter cereals at 21 sites across four continents

Hayes, R. C., Wang, S., Newell, M. T., Turner, K., Larsen, J., Gazza, L., Anderson, J. A., Bell, L. W., Cattani, D. J., Frels, K., Galassi, E., Morgounov, A. I., Revell, C. K., Thapa, D. B., Sacks, E. J., Sameri, M., Wade, L. J., Westerbergh, A., Shamanin, V., Amanov, A. & 1 others, Li, G. D., Apr 9 2018, In : Sustainability (Switzerland). 10, 4, 1124.

Research output: Contribution to journalArticle

cereal
wheat
breeding
parents
winter

The papaya genome project: Fruitful insights, a decade later

Nguyen, J. K. & Ming, R., Jan 1 2019, In : Acta Horticulturae. 1250, p. 111-121 11 p.

Research output: Contribution to journalArticle

papayas
Y chromosome
genome
domestication
chromosomes

The orphan gene ybjN conveys pleiotropic effects on multicellular behavior and survival of Escherichia coli

Wang, D., Calla, B., Vimolmangkang, S., Wu, X., Korban, S. S., Huber, S. C., Clough, S. J. & Zhao, Y., Sep 27 2011, In : PloS one. 6, 9, e25293.

Research output: Contribution to journalArticle

Escherichia coli
Genes
mutants
Acid resistance
acid tolerance

The origins of C4 Grasslands: Integrating evolutionary and ecosystem science

Edwards, E. J., Osborne, C. P., Strömberg, C. A. E., Smith, S. A., Bond, W. J., Christin, P. A., Cousins, A. B., Duvall, M. R., Fox, D. L., Freckleton, R. P., Ghannoum, O., Hartwell, J., Huang, Y., Janis, C. M., Keeley, J. E., Kellogg, E. A., Knapp, A. K., Leakey, A. D. B., Nelson, D. M., Saarela, J. M. & 5 others, Sage, R. F., Sala, O. E., Salamin, N., Still, C. J. & Tipple, B., Apr 30 2010, In : Science. 328, 5978, p. 587-591 5 p.

Research output: Contribution to journalReview article

Ecosystem
Photosynthesis
Poaceae
Research
Grassland

The origin of the non-recombining region of sex chromosomes in Carica and Vasconcellea

Wu, X., Wang, J., Na, J. K., Yu, Q., Moore, R. C., Zee, F., Huber, S. C. & Ming, R., Sep 1 2010, In : Plant Journal. 63, 5, p. 801-810 10 p.

Research output: Contribution to journalArticle

Vasconcellea
Carica
Sex Chromosomes
sex chromosomes
Alleles
Metabolic Networks and Pathways
Proteins
Nucleotides
Prebiotics
Hydrolases

The Origin of modern 5s rRNA: A case of relating models of structural history to phylogenetic data

Sun, F. J. & Caetano-Anolles, G., Jul 1 2010, In : Journal of Molecular Evolution. 71, 1, p. 3-5 3 p.

Research output: Contribution to journalArticle

Structural Models
Genomic Segmental Duplications
ribosomal RNA
phylogenetics
history

The origin of bermudagrass (Cynodon) off-types inferred by DNA amplification fingerprinting

Caetano-Anollés, G., Callahan, L. M. & Gresshoff, P. M., Jan 1 1997, In : Crop Science. 37, 1, p. 81-87 7 p.

Research output: Contribution to journalArticle

Cynodon
Cynodon dactylon
cultivars
DNA
genetic relationships

The origin and evolution of tRNA inferred from phylogenetic analysis of structure

Sun, F. J. & Caetano-Anollés, G., Jan 1 2008, In : Journal of Molecular Evolution. 66, 1, p. 21-35 15 p.

Research output: Contribution to journalArticle

Transfer RNA
phylogenetics
RNA
phylogeny
genetic code

The origin and evolution of the archaeal domain

Caetano-Anollés, G. & Kim, K. M., 2014, In : Archaea. 2014, 915828.

Research output: Contribution to journalEditorial

Archaeal Proteins
Biological Evolution
Archaea

The origin and evolution of modern metabolism

Caetano-Anolles, G., Mainzer, L. S., Gee, H., Caetano-Anollés, D., Kim, H. S. & Mittenthal, J. E., Feb 1 2009, In : International Journal of Biochemistry and Cell Biology. 41, 2, p. 285-297 13 p.

Research output: Contribution to journalReview article

Metabolism
Enzymes
Genomics
Nucleotides
Prebiotics

The origin, evolution and structure of the protein world

Caetano-Anollés, G., Wang, M., Caetano-Anollés, D. & Mittenthal, J. E., Feb 1 2009, In : Biochemical Journal. 417, 3, p. 621-637 17 p.

Research output: Contribution to journalReview article

Proteome
Proteins
Protein folding
Prebiotics
Biochemistry

The organization of domains in proteins obeys Menzerath-Altmann's law of language

Shahzad, K., Mittenthal, J. E. & Caetano-Anollés, G., Aug 11 2015, In : BMC Systems Biology. 9, 1, 44.

Research output: Contribution to journalArticle

Proteome
Language
Organizations
Proteins
Protein

The nucleotide sequence of apple mosaic virus coat protein gene has no similarity with other Bromoviridae coat protein genes

Alrefai, R. H., Shiel, P. J., Domier, L. L., D'Arcy, C. J., Berger, P. H. & Korban, S. S., Jan 1 1994, In : Journal of General Virology. 75, 10, p. 2847-2850 4 p.

Research output: Contribution to journalArticle

Bromoviridae
Mosaic Viruses
Capsid Proteins
Malus
Ilarvirus

The nonselective nature of a modified single-seed descent breeding procedure

Gourmet, C., Kolb, F. L., Brown, C. M., Smyth, C. A., Biradar, D. P. & Rayburn, A. L., Jan 1 1997, In : Crop Science. 37, 5, p. 1434-1437 4 p.

Research output: Contribution to journalArticle

Barley yellow dwarf virus
breeding
seeds
nuclear genome
Spermatophytina

The non-photochemical reduction of plastoquinone in leaves

Groom, Q. J., Kramer, D. M., Crofts, A. R. & Ort, D. R., Jun 1 1993, In : Photosynthesis research. 36, 3, p. 205-215 11 p.

Research output: Contribution to journalArticle

Plastoquinone
Amaranthus
malic enzyme
far-red light
photosystem I

The natural history of transfer RNA and its interactions with the ribosome

Caetano-Anollés, G. & Sun, F. J., Jan 1 2014, In : Frontiers in Genetics. 5, MAY, 127.

Research output: Contribution to journalArticle

Transfer RNA
Natural History
Ribosomes
Protein Biosynthesis
Genetic Code

The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data

Koc, I. & Caetano-Anolles, G., May 2017, In : PloS one. 12, 5, e0176129.

Research output: Contribution to journalArticle

Gene Ontology
Phylogeny
Natural History
natural history
Ontology

The Natural History of Biocatalytic Mechanisms

Nath, N., Mitchell, J. B. O. & Caetano-Anollés, G., May 2014, In : PLoS computational biology. 10, 5, e1003642.

Research output: Contribution to journalArticle

Natural History
natural history
Fold
Enzymes
fold

The MANAGE Drain Concentration database: A new tool compiling North American drainage nutrient concentrations

Hertzberger, A., Pittelkow, C. M., Harmel, R. D. & Christianson, L. E., May 1 2019, In : Agricultural Water Management. 216, p. 113-117 5 p.

Research output: Contribution to journalArticle

Open Access
drain
drainage
nutrient content
nutrient loss
nutrient

The maize O2 and PBF proteins act additively to promote transcription from storage protein gene promoters in rice endosperm cells

Hwang, Y. S., Ciceri, P., Parsons, R. L., Moose, S. P., Schmidt, R. J. & Huang, N., Oct 2004, In : Plant and Cell Physiology. 45, 10, p. 1509-1518 10 p.

Research output: Contribution to journalArticle

Prolamins
Endosperm
prolamins
storage proteins
endosperm

The Maize macrohairless1 Locus Specifically Promotes Leaf Blade Macrohair Initiation and Responds to Factors Regulating Leaf Identity

Moose, S. P., Lauter, N. & Carlson, S. R., Mar 1 2004, In : Genetics. 166, 3, p. 1451-1461 11 p.

Research output: Contribution to journalArticle

Zea mays
Trichomes
Chromosomes, Human, Pair 9
Morphogenesis
Insects

The maize enr system of r1 haplotype-specific aleurone color enhancement factors

Stinard, P. S., Kermicle, J. L. & Sachs, M. M., Feb 20 2009, In : Journal of Heredity. 100, 2, p. 217-228 12 p.

Research output: Contribution to journalArticle

Haplotypes
Zea mays
Color
Alleles

The Kalanchoë genome provides insights into convergent evolution and building blocks of crassulacean acid metabolism

Yang, X., Hu, R., Yin, H., Jenkins, J., Shu, S., Tang, H., Liu, D., Weighill, D. A., Cheol Yim, W., Ha, J., Heyduk, K., Goodstein, D. M., Guo, H. B., Moseley, R. C., Fitzek, E., Jawdy, S., Zhang, Z., Xie, M., Hartwell, J., Grimwood, J. & 29 others, Abraham, P. E., Mewalal, R., Beltrán, J. D., Boxall, S. F., Dever, L. V., Palla, K. J., Albion, R., Garcia, T., Mayer, J. A., Don Lim, S., Man Wai, C., Peluso, P., Van Buren, R., De Paoli, H. C., Borland, A. M., Guo, H., Chen, J. G., Muchero, W., Yin, Y., Jacobson, D. A., Tschaplinski, T. J., Hettich, R. L., Ming, R., Winter, K., Leebens-Mack, J. H., Smith, J. A. C., Cushman, J. C., Schmutz, J. & Tuskan, G. A., Dec 1 2017, In : Nature communications. 8, 1, 1899.

Research output: Contribution to journalArticle

genome
metabolism
Metabolism
Genes
Genome

The IPM paradigm: Concepts, strategies and tactics

Gray, M., Ratcliffe, S. T. & Ratcliffe, S. T., Jan 1 2008, Integrated Pest Management: Concepts, Tactics, Strategies and Case Studies. Cambridge University Press, p. 1-13 13 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

pests
Insects
Food
dietary fiber
Plant Weeds

The involvement of the photoinhibition of photosystem II and impaired membrane energization in the reduced quantum yield of carbon assimilation in chilled maize

Ortiz-Lopez, A., Nie, G. Y., Ort, D. R. & Baker, N. R., Apr 1990, In : Planta. 181, 1, p. 78-84 7 p.

Research output: Contribution to journalArticle

Photosystem II Protein Complex
photoinhibition
photosystem II
Zea mays
Carbon

The International Comet Assay Workshop

Anderson, D. & Plewa, M. J., Jan 1 1998, In : Mutagenesis. 13, 1, p. 67-73 7 p.

Research output: Contribution to journalReview article

Comet Assay
Electrophoresis
Assays
Education
DNA Repair

The interaction of the novel 30C02 cyst nematode effector protein with a plant β-1,3-endoglucanase may suppress host defence to promote parasitism

Hamamouch, N., Li, C., Hewezi, T., Baum, T. J., Mitchum, M. G., Hussey, R. S., Vodkin, L. O. & Davis, E. L., Jun 13 2012, In : Journal of experimental botany. 63, 10, p. 3683-3696 14 p.

Research output: Contribution to journalArticle

cyst nematodes
Cellulase
endo-1,4-beta-glucanase
Cysts
parasitism

The interaction of soybean aphids and soybean cyst nematodes on selected resistant and susceptible soybean lines

Heeren, J. R., Steffey, K. L., Tinsley, N. A., Estes, R. E., Niblack, T. L. & Gray, M., Nov 1 2012, In : Journal of Applied Entomology. 136, 9, p. 646-655 10 p.

Research output: Contribution to journalArticle

Aphis glycines
Heterodera glycines
pests
soybeans
Aphidoidea

The Inheritance Pattern of 24 nt siRNA Clusters in Arabidopsis Hybrids Is Influenced by Proximity to Transposable Elements

Li, Y., Varala, K., Moose, S. P. & Hudson, M. E., Oct 31 2012, In : PloS one. 7, 10, e47043.

Research output: Contribution to journalArticle

Inheritance Patterns
DNA Transposable Elements
small interfering RNA
Arabidopsis
transposons

The inheritance of a branching type in soybean

Nelson, R., Jan 1 1996, In : Crop Science. 36, 5, p. 1150-1152 3 p.

Research output: Contribution to journalArticle

branching
inheritance (genetics)
soybeans
branches
loci

The influence of rising tropospheric carbon dioxide and ozone on plant productivity

Ainsworth, E. A., Lemonnier, P. & Wedow, J. M., Jan 1 2020, In : Plant Biology. 22, S1, p. 5-11 7 p.

Research output: Contribution to journalReview article

Open Access
ozone
carbon dioxide
productivity
terrestrial ecosystem
pollutants

The influence of photosynthetic acclimation to rising CO2 and warmer temperatures on leaf and canopy photosynthesis models

Bagley, J., Rosenthal, D. M., Ruiz-Vera, U. M., Siebers, M. H., Kumar, P., Ort, D. R. & Bernacchi, C. J., Feb 2015, In : Global Biogeochemical Cycles. 29, 2, p. 194-206 13 p.

Research output: Contribution to journalArticle

Photosynthesis
acclimation
photosynthesis
canopy
temperature

The influence of drought and heat stress on long-term carbon fluxes of bioenergy crops grown in the Midwestern USA

Joo, E., Hussain, M. Z., Zeri, M., Masters, M. D., Miller, J. N., Gomez-Casanovas, N., DeLucia, E. H. & Bernacchi, C. J., Sep 1 2016, In : Plant Cell and Environment. 39, 9, p. 1928-1940 13 p.

Research output: Contribution to journalArticle

Carbon Cycle
Droughts
energy crops
Miscanthus
Ecosystem

The important but weakening maize yield benefit of grain filling prolongation in the US Midwest

Zhu, P., Jin, Z., Zhuang, Q., Ciais, P., Bernacchi, C., Wang, X., Makowski, D. & Lobell, D., Oct 2018, In : Global change biology. 24, 10, p. 4718-4730 13 p.

Research output: Contribution to journalArticle

maize
food security
Crops
Drought
crop yield

The importance of using realistic evolutionary models for retrodicting proteomes

Kim, K. M., Nasir, A. & Caetano-Anollés, G., Apr 1 2014, In : Biochimie. 99, 1, p. 129-137 9 p.

Research output: Contribution to journalArticle

Planetary Evolution
Proteome
Molecular Models
Molecular Evolution
Phylogeny

The importance of space, time, and stochasticity to the demography and management of Alliaria petiolata

Evans, J. A., Davis, A. S., Raghu, S., Ragavendran, A., Landis, D. A. & Schemske, D. W., Jul 2012, In : Ecological Applications. 22, 5, p. 1497-1511 15 p.

Research output: Contribution to journalArticle

biocontrol agent
stochasticity
demography
fecundity
population modeling

The importance of phenolic metabolism to limit the growth of Phakopsora pachyrhizi

Lygin, A. V., Li, S., Vittal, R., Widholm, J. M., Hartman, G. L. & Lozovaya, V. V., Dec 1 2009, In : Phytopathology. 99, 12, p. 1412-1420 9 p.

Research output: Contribution to journalArticle

Phakopsora pachyrhizi
soybeans
metabolism
genotype
soybean rust
Breeding
breeding
Forests
intraspecific variation

The impacts of fluctuating light on crop performance

Slattery, R. A., Walker, B. J., Weber, A. P. M. & Ort, D. R., Feb 2018, In : Plant physiology. 176, 2, p. 990-1003 14 p.

Research output: Contribution to journalArticle

Light
Photosynthesis
crops
canopy
C4 photosynthesis

The impact of water management practices on subtropical pasture methane emissions and ecosystem service payments

Chamberlain, S. D., Groffman, P. M., Boughton, E. H., Gomez-Casanovas, N., DeLucia, E. H., Bernacchi, C. J. & Sparks, J. P., Jun 2017, In : Ecological Applications. 27, 4, p. 1199-1209 11 p.

Research output: Contribution to journalArticle

ecosystem service
water management
management practice
pasture
methane

The Impact of Rye Cover Crops on Weeds, Insects, and Diseases in Snap Bean Cropping Systems

Bottenberg, H., Masiunas, J., Eastman, C. & Eastburn, D. M., Jan 11 1997, In : Journal of Sustainable Agriculture. 9, 2-3, p. 131-155 25 p.

Research output: Contribution to journalArticle

cover crop
green beans
mulch
cover crops
rye

The impact of rye cover crops on weed populations in a tomato cropping system

Masiunas, J. B., Weston, L. A. & Weller, S. C., Jan 1 1995, In : Weed Science. 43, 2, p. 318-323 6 p.

Research output: Contribution to journalArticle

cover crops
rye
cropping systems
weeds
tomatoes