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The biochemical mechanisms of the plant activation of promutagenic aromatic amines

Wagner, E. D., Verdier, M. M. & Plewa, M. J., 1990, In : Environmental and Molecular Mutagenesis. 15, 4, p. 236-244 9 p.

Research output: Contribution to journalArticle

Plant Cells
Amines
Ditiocarb
Catechin
Acetaminophen

The bracteatus pineapple genome and domestication of clonally propagated crops

Chen, L. Y., VanBuren, R., Paris, M., Zhou, H., Zhang, X., Wai, C. M., Yan, H., Chen, S., Alonge, M., Ramakrishnan, S., Liao, Z., Liu, J., Lin, J., Yue, J., Fatima, M., Lin, Z., Zhang, J., Huang, L., Wang, H., Hwa, T. Y. & 25 others, Kao, S. M., Choi, J. Y., Sharma, A., Song, J., Wang, L., Yim, W. C., Cushman, J. C., Paull, R. E., Matsumoto, T., Qin, Y., Wu, Q., Wang, J., Yu, Q., Wu, J., Zhang, S., Boches, P., Tung, C. W., Wang, M. L., Coppens d’Eeckenbrugge, G., Sanewski, G. M., Purugganan, M. D., Schatz, M. C., Bennetzen, J. L., Lexer, C. & Ming, R., Oct 1 2019, In : Nature Genetics. 51, 10, p. 1549-1558 10 p.

Research output: Contribution to journalArticle

Open Access
Ananas
Genome
Bromelains
Capsicum
South America

The clastogenic potential of triazine herbicide combinations found in potable water supplies

Taets, C., Aref, S. & Rayburn, A. L., Jan 1 1998, In : Environmental health perspectives. 106, 4, p. 197-201 5 p.

Research output: Contribution to journalArticle

Triazines
Water Supply
Herbicides
Drinking Water
Atrazine

The clonal structure of Quercus geminata revealed by conserved microsatellite loci

Ainsworth, E. A., Tranel, P. J., Drake, B. G. & Long, S. P., Feb 1 2003, In : Molecular ecology. 12, 2, p. 527-532 6 p.

Research output: Contribution to journalArticle

Quercus
Microsatellite Repeats
microsatellite repeats
loci
scrub

The coevolutionary roots of biochemistry and cellular organization challenge the RNA world paradigm

Caetano-Anollés, G. & Seufferheld, M. J., Jan 1 2013, In : Journal of Molecular Microbiology and Biotechnology. 23, 1-2, p. 152-177 26 p.

Research output: Contribution to journalArticle

Cellular Structures
Biochemistry
RNA
Molecular Structure
Nucleic Acids

The coffee genome provides insight into the convergent evolution of caffeine biosynthesis

Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., Aury, J. M., Bento, P., Bernard, M., Bocs, S., Campa, C., Cenci, A., Combes, M. C., Crouzillat, D., Da Silva, C., Daddiego, L. & 44 others, De Bellis, F., Dussert, S., Garsmeur, O., Gayraud, T., Guignon, V., Jahn, K., Jamilloux, V., Joët, T., Labadie, K., Lan, T., Leclercq, J., Lepelley, M., Leroy, T., Li, L. T., Librado, P., Lopez, L., Muñoz, A., Noel, B., Pallavicini, A., Perrotta, G., Poncet, V., Pot, D., Priyono, Rigoreau, M., Rouard, M., Rozas, J., Tranchant-Dubreuil, C., VanBuren, R., Zhang, Q., Andrade, A. C., Argout, X., Bertrand, B., De Kochko, A., Graziosi, G., Henry, R. J., Jayarama, Ming, R., Nagai, C., Rounsley, S., Sankoff, D., Giuliano, G., Albert, V. A., Wincker, P. & Lashermes, P., Sep 5 2014, In : Science. 345, 6201, p. 1181-1184 4 p.

Research output: Contribution to journalArticle

Coffee
Caffeine
Genome
Methyltransferases
Coffea

The comet assay: Genotoxic damage or nuclear fragmentation?

Rundell, M. S., Wagner, E. D. & Plewa, M. J., Sep 18 2003, In : Environmental and Molecular Mutagenesis. 42, 2, p. 61-67 7 p.

Research output: Contribution to journalArticle

Comet Assay
comet
Assays
fragmentation
Mutagens

The complete chloroplast genome of a gynodioecious deciduous orchid Satyrium ciliatum (Orchidaceae) female

Ma, X., Lin, H., Chen, Y., Lan, S. & Ming, R., Jul 3 2019, In : Mitochondrial DNA Part B: Resources. 4, 2, p. 3876-3877 2 p.

Research output: Contribution to journalArticle

Open Access
Orchidaceae
Chloroplast Genome
Genes
Base Composition
Transfer RNA

The complete chloroplast genomes of three Korean Echinochloa crus-galli accessions

Nah, G., Im, J. H., Kim, J. W., Kim, K., Lim, J., Choi, A. Y., Choi, I. Y., Yang, T. J., Park, T. S., Lee, D. K. & Kim, D. S., Nov 1 2016, In : Mitochondrial DNA Part A: DNA Mapping, Sequencing, and Analysis. 27, 6, p. 4357-4358 2 p.

Research output: Contribution to journalArticle

Echinochloa
Chloroplast Genome
Genome Size
Genome
Genes

The complete nucleotide sequence of apple mosaic virus RNA-3

Shiel, P. J., Alrefai, R. H., Domier, L. L., Korban, S. S. & Berger, P. H., Jul 1 1995, In : Archives of Virology. 140, 7, p. 1247-1256 10 p.

Research output: Contribution to journalArticle

Ilarvirus
Mosaic Viruses
Malus
RNA
Bromoviridae

The crystal structure of Erwinia amylovora AmyR, a member of the YbjN protein family, shows similarity to type III secretion chaperones but suggests different cellular functions

Bartho, J. D., Bellini, D., Wuerges, J., Demitri, N., Toccafondi, M., Schmitt, A. O., Zhao, Y., Walsh, M. A. & Benini, S., Apr 2017, In : PloS one. 12, 4, e0176049.

Research output: Contribution to journalArticle

Erwinia amylovora
crystal structure
Crystal structure
secretion
Proteins

The detection of weak recombinogenic activities in the herbicides alachlor and propachlor using a plant-activation bioassay

Gentile, J. M., Wagner, E. D. & Plewa, M. J., Jan 1977, In : Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 48, 1, p. 113-115 3 p.

Research output: Contribution to journalArticle

Acetanilides
Mutagens
Herbicides
Biological Assay
Genetic Recombination

The development of putative adventitious shoots from a chimeral thornless rose (Rosa multiflora Thunb. ex J. Murr.) in vitro

Rosu, A., Skirvin, R. M., Bein, A., Norton, M. A., Kushad, M. & Otterbacher, A. G., Jan 1 1995, In : Journal of Horticultural Science. 70, 6, p. 901-907 7 p.

Research output: Contribution to journalArticle

Rosa multiflora
adventitious shoots
Rosa

The distribution and impact of viral lineages in domains of life

Nasir, A., Forterre, P., Kim, K. M. & Caetano-Anollés, G., Jan 1 2014, In : Frontiers in Microbiology. 5, APR, 194.

Research output: Contribution to journalArticle

Replicon
Capsid
Viruses

The Draft Genome of Kochia scoparia and the Mechanism of Glyphosate Resistance via Transposon-Mediated EPSPS Tandem Gene Duplication

Patterson, E. L., Saski, C. A., Sloan, D. B., Tranel, P. J., Westra, P. & Gaines, T. A., Oct 1 2019, In : Genome biology and evolution. 11, 10, p. 2927-2940 14 p.

Research output: Contribution to journalArticle

Open Access
glyphosate
Bassia scoparia
3-Phosphoshikimate 1-Carboxyvinyltransferase
Gene Duplication
gene duplication

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

Studer, A. J., Schnable, J. C., Weissmann, S., Kolbe, A. R., McKain, M. R., Shao, Y., Cousins, A. B., Kellogg, E. A. & Brutnell, T. P., Oct 28 2016, In : Genome biology. 17, 1, 223.

Research output: Contribution to journalArticle

Poaceae
Setaria viridis
genome
grass
Sorghum

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

Ming, R., Hou, S., Feng, Y., Yu, Q., Dionne-Laporte, A., Saw, J. H., Senin, P., Wang, W., Ly, B. V., Lewis, K. L. T., Salzberg, S. L., Feng, L., Jones, M. R., Skelton, R. L., Murray, J. E., Chen, C., Qian, W., Shen, J., Du, P., Eustice, M. & 65 others, Tong, E., Tang, H., Lyons, E., Paull, R. E., Michael, T. P., Wall, K., Rice, D. W., Albert, H., Wang, M. L., Zhu, Y. J., Schatz, M., Nagarajan, N., Acob, R. A., Guan, P., Blas, A., Wai, C. M., Ackerman, C. M., Ren, Y., Liu, C., Wang, J., Wang, J., Na, J. K., Shakirov, E. V., Haas, B., Thimmapuram, J., Nelson, D., Wang, X., Bowers, J. E., Gschwend, A. R., Delcher, A. L., Singh, R., Suzuki, J. Y., Tripathi, S., Neupane, K., Wei, H., Irikura, B., Paidi, M., Jiang, N., Zhang, W., Presting, G., Windsor, A., Navajas-Pérez, R., Torres, M. J., Feltus, F. A., Porter, B., Li, Y., Burroughs, A. M., Luo, M. C., Liu, L., Christopher, D. A., Mount, S. M., Moore, P. H., Sugimura, T., Jiang, J., Schuler, M. A., Friedman, V., Mitchell-Olds, T., Shippen, D. E., Depamphilis, C. W., Palmer, J. D., Freeling, M., Paterson, A. H., Gonsalves, D., Wang, L. & Alam, M., Apr 24 2008, In : Nature. 452, 7190, p. 991-996 6 p.

Research output: Contribution to journalArticle

Carica
Fruit
Genome
Angiosperms
Genes

The Dsl transposable element acts as an intron in the mutant allele Adh1-Fm335 and is spliced from the message

Dennis, E. S., Sachs, M. M., Gerlach, W. L., Beach, L. & Peacock, W. J., May 11 1988, In : Nucleic acids research. 16, 9, p. 3815-3828 14 p.

Research output: Contribution to journalArticle

DNA Transposable Elements
Introns
Alleles
5' Untranslated Regions
Transcription Initiation Site

The dwarf phenotype of the Arabidopsis ac15 mutant is suppressed by a mutation in an upstream ORF of a bHLH gene

Imai, A., Hanzawa, Y., Komura, M., Yamamoto, K. T., Komeda, Y. & Takahashi, T., Sep 1 2006, In : Development. 133, 18, p. 3575-3585 11 p.

Research output: Contribution to journalArticle

ORF
Arabidopsis
Open Reading Frames
phenotype
mutation

The early history and emergence of molecular functions and modular scale-free network behavior

Aziz, M. F., Caetano-Anollés, K. & Caetano-Anolles, G., Apr 28 2016, In : Scientific Reports. 6, 25058.

Research output: Contribution to journalArticle

Amino Acid Motifs
Metabolic Networks and Pathways
Amino Acid Sequence
History
Protein Domains

The effect of artificial selection on phenotypic plasticity in maize

Gage, J. L., Jarquin, D., Romay, C., Lorenz, A., Buckler, E. S., Kaeppler, S., Alkhalifah, N., Bohn, M., Campbell, D. A., Edwards, J., Ertl, D., Flint-Garcia, S., Gardiner, J., Good, B., Hirsch, C. N., Holland, J., Hooker, D. C., Knoll, J., Kolkman, J., Kruger, G. & 20 others, Lauter, N., Lawrence-Dill, C. J., Lee, E., Lynch, J., Murray, S. C., Nelson, R., Petzoldt, J., Rocheford, T., Schnable, J., Schnable, P. S., Scully, B., Smith, M., Springer, N. M., Srinivasan, S., Walton, R., Weldekidan, T., Wisser, R. J., Xu, W., Yu, J. & De Leon, N., Dec 1 2017, In : Nature communications. 8, 1, 1348.

Research output: Contribution to journalArticle

plastic properties
Zea mays
Plasticity
Crops
Genotype

The effect of assay composition, detergent solubilization and reconstitution on red beet (Beta vulgaris L.) plasma membrane H+-ATPase kinetic properties

Giannini, J. L. & Briskin, D. P., 1989, In : Plant Science. 60, 2, p. 189-193 5 p.

Research output: Contribution to journalArticle

H-transporting ATP synthase
Beta vulgaris
Proton-Translocating ATPases
beets
solubilization

The effect of breed and individual heterosis on the feed efficiency, performance, and carcass characteristics of feedlot steers

Retallick, K. M., Faulkner, D. B., Rodriguez-Zas, S. L., Nkrumah, J. D. & Shike, D. W., Nov 1 2013, In : Journal of animal science. 91, 11, p. 5161-5166 6 p.

Research output: Contribution to journalArticle

Hybrid Vigor
heterosis
feedlots
carcass characteristics
feed conversion

The effect of drying method and storage on color characteristics of paprika

Topuz, A., Feng, H. & Kushad, M., Dec 1 2009, In : LWT - Food Science and Technology. 42, 10, p. 1667-1673 7 p.

Research output: Contribution to journalArticle

paprika
Capsicum
Color
drying
color

The effect of fungicide seed protectants, seeding rates, and reduced rates of herbicides on no-till soybean

Bradley, C., Wax, L. M., Ebelhar, S. A., Bollero, G. A. & Pedersen, W. L., Oct 22 2001, In : Crop Protection. 20, 7, p. 615-622 8 p.

Research output: Contribution to journalArticle

no-tillage
fungicides
sowing
herbicides
soybeans

The effect of glyceollin on proton leakage in Phytophthora megasperma f. sp. glycinea plasma membrane and red beet tonoplast vesicles

Giannini, J. L., Holt, J. S. & Briskin, D. P., 1990, In : Plant Science. 68, 1, p. 39-45 7 p.

Research output: Contribution to journalArticle

Phytophthora megasperma
Phytophthora
Beta vulgaris
tonoplast
beets

The effect of glyceollin on soybean (Glycine max L.) tonoplast and plasma membrane vesicles

Giannini, J. L., Holt, J. S. & Briskin, D. P., 1991, In : Plant Science. 74, 2, p. 203-211 9 p.

Research output: Contribution to journalArticle

tonoplast
Soybeans
Glycine max
plasma membrane
Adenosine Triphosphate

The effect of leaf-level spatial variability in photosynthetic capacity on biochemical parameter estimates using the Farquhar model: A theoretical analysis

Chen, C. P., Zhu, X. G. & Long, S. P., Oct 1 2008, In : Plant physiology. 148, 2, p. 1139-1147 9 p.

Research output: Contribution to journalArticle

Photosynthesis
Theoretical Models
leaves
Trioses
Light

The effect of rhg1 on reproduction of Heterodera glycines in the field and greenhouse and associated effects on agronomic traits

Brucker, E., Niblack, T., Kopisch-Obuch, F. J. & Diers, B. W., Sep 1 2005, In : Crop Science. 45, 5, p. 1721-1727 7 p.

Research output: Contribution to journalArticle

Heterodera glycines
agronomic traits
greenhouses
isogenic lines
greenhouse production

The effect of solar irradiance on the mortality of Phakopsora pachyrhizi urediniospores

Isard, S. A., Dufault, N. S., Miles, M. R., Hartman, G. L., Russo, J. M., De Wolf, E. D. & Morel, W., Jul 1 2006, In : Plant disease. 90, 7, p. 941-945 5 p.

Research output: Contribution to journalArticle

Phakopsora pachyrhizi
solar radiation
soybean rust
germination
viability

The effect of weed-free period and nitrogen on eastern black nightshade competition with english pea

Croster, M. P. & Masiunas, J., Feb 1 1998, In : HortScience. 33, 1, p. 88-91 4 p.

Research output: Contribution to journalArticle

peas
weeds
nitrogen
Solanum ptycanthum
Pisum sativum

The effects of artificial selection on sugar metabolism and transporter genes in grape

Xin, H., Zhang, J., Zhu, W., Wang, N., Fang, P., Han, Y., Ming, R. & Li, S., Oct 1 2013, In : Tree Genetics and Genomes. 9, 5, p. 1343-1349 7 p.

Research output: Contribution to journalArticle

artificial selection
Vitis
transporters
grapes
sugar

The effects of chilling in the dark and in the light on photosynthesis of tomato: electron transfer reactions

Kee, S. C., Martin, B. & Ort, D. R., Jan 1 1986, In : Photosynthesis research. 8, 1, p. 41-51 11 p.

Research output: Contribution to journalArticle

Chilling
Photosynthesis
Lycopersicon esculentum
electron transfer
photosynthesis

The effects of chilling in the light on ribulose-1,5-bisphosphate carboxylase/oxygenase activation in tomato (Lycopersicon esculentum Mill.)

Byrd, G. T., Ort, D. R. & Ogren, W. L., Jan 1 1995, In : Plant physiology. 107, 2, p. 585-591 7 p.

Research output: Contribution to journalArticle

ribulose 1,5-diphosphate
oxygenases
Solanum lycopersicum var. lycopersicum
tomatoes
cold treatment

The effects of chloroplast coupling factor reduction on the energetics of activation and on the energetics and efficiency of ATP formation.

Hangarter, R. P., Grandoni, P. & Ort, D. R., Oct 5 1987, In : The Journal of biological chemistry. 262, 28, p. 13513-13519 7 p.

Research output: Contribution to journalArticle

Chloroplast Proton-Translocating ATPases
Adenosine Triphosphate
Chemical activation
Adenosine Diphosphate
Thylakoids
photoinhibition
Zea mays
Temperature
Growth
leaves

The effects of elevated CO2 concentration on soybean gene expression. An analysis of growing and mature leaves

Ainsworth, E. A., Rogers, A., Vodkin, L. O., Walter, A. & Schurr, U., Sep 1 2006, In : Plant physiology. 142, 1, p. 135-147 13 p.

Research output: Contribution to journalArticle

Soybeans
carbon dioxide
soybeans
Gene Expression
gene expression

The effects of gibberellic acid on sex expression and secondary sexual characteristics in papaya

Han, J., Murray, J. E., Yu, Q., Moore, P. H. & Ming, R., Mar 2014, In : HortScience. 49, 3, p. 378-383 6 p.

Research output: Contribution to journalArticle

papayas
gibberellic acid
gibberellins
gender
Carica papaya

The EPSPS Pro106Ser substitution solely accounts for glyphosate resistance in a goosegrass (Eleusine indica) population from Tennessee, United States

Janel, L. H., Riggins, C. W., Steckel, L. E. & Tranel, P. J., Jun 1 2016, In : Journal of Integrative Agriculture. 15, 6, p. 1304-1312 9 p.

Research output: Contribution to journalArticle

glyphosate
3-Phosphoshikimate 1-Carboxyvinyltransferase
Eleusine
Eleusine indica
substitution
Erwinia amylovora
Gene Expression
Peptides
Xanthomonas
Acids
proteome
ancestry
fold
history
protein

The evolutionary history of the structure of 5S ribosomal RNA

Sun, F. J. & Caetano-Anollés, G., Nov 1 2009, In : Journal of Molecular Evolution. 69, 5, p. 430-443 14 p.

Research output: Contribution to journalArticle

5S Ribosomal RNA
RNA
domain structure
History
ribosomal RNA

The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World

Wang, M. & Caetano-Anolles, G., Jan 14 2009, In : Structure. 17, 1, p. 66-78 13 p.

Research output: Contribution to journalArticle

Proteome
Mechanics
Genome
Proteins
Censuses

The evolutionary significance of the long variable arm in transfer RNA

Sun, F. J. & Caetano-Anolles, G., Jan 1 2009, In : Complexity. 14, 5, p. 26-39 14 p.

Research output: Contribution to journalArticle

Amino acids
Biochemistry
Molecules
Bacteriophages
Transfer RNA

The FAR1 locus encodes a novel nuclear protein specific to phytochrome A signaling

Hudson, M., Ringli, C., Boylan, M. T. & Quail, P. H., Aug 1 1999, In : Genes and Development. 13, 15, p. 2017-2027 11 p.

Research output: Contribution to journalArticle

Phytochrome A
Phytochrome
Nuclear Proteins
Arabidopsis
Light

The fate of nitrogen-15 ammonium sulfate applied to Kentucky bluegrass and perennial ryegrass turfs

Engelsjord, M. E., Branham, B. E. & Horgan, B. P., Jul 2004, In : Crop Science. 44, 4, p. 1341-1347 7 p.

Research output: Contribution to journalArticle

Poa pratensis
thatch
Lolium perenne
ammonium sulfate
nitrogen fertilizers

The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway

Hudson, M. E., Lisch, D. R. & Quail, P. H., May 1 2003, In : Plant Journal. 34, 4, p. 453-471 19 p.

Research output: Contribution to journalArticle

Phytochrome A
Transposases
gene expression regulation
Gene Expression Regulation
phytochrome

The fungicide captan reduces nuclear DNA content in maize seedlings

Rayburn, A. L., Pedersen, W. L. & McMurphy, L. M., 1993, In : Pesticide Science. 37, 1, p. 79-82 4 p.

Research output: Contribution to journalArticle

Captan
captan
Seedlings
nuclear genome
Zea mays

The genetic architecture of maize flowering time

Buckler, E. S., Holland, J. B., Bradbury, P. J., Acharya, C. B., Brown, P. J., Browne, C., Ersoz, E., Flint-Garcia, S., Garcia, A., Glaubitz, J. C., Goodman, M. M., Harjes, C., Guill, K., Kroon, D. E., Larsson, S., Lepak, N. K., Li, H., Mitchell, S. E., Pressoir, G., Peiffer, J. A. & 16 others, Rosas, M. O., Rocheford, T. R., Romay, M. C., Romero, S., Salvo, S., Villeda, H. S., Da Silva, H. S., Sun, Q., Tian, F., Upadyayula, N., Ware, D., Yates, H., Yu, J., Zhang, Z., Kresovich, S. & McMullen, M. D., Aug 17 2009, In : Science. 325, 5941, p. 714-718 5 p.

Research output: Contribution to journalArticle

Zea mays
Quantitative Trait Loci
Arabidopsis
Population

The genetic architecture of seed composition in soybean is refined by genome-wide association scans across multiple populations

Vaughn, J. N., Nelson, R. L., Song, Q., Cregan, P. B. & Li, Z., Jan 1 2014, In : G3: Genes, Genomes, Genetics. 4, 11, p. 2283-2294 12 p.

Research output: Contribution to journalArticle

Genome-Wide Association Study
Soybeans
Seeds
Essential Amino Acids
Population