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The bench scientist's guide to statistical analysis of RNA-Seq data

Yendrek, C. R., Ainsworth, E. A. & Thimmapuram, J., Sep 18 2012, In : BMC Research Notes. 5, 506.

Research output: Contribution to journalArticle

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

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

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

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

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

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

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

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

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

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

The conversion of the corn/soybean ecosystem to no-till agriculture may result in a carbon sink

Bernacchi, C. J., Hollinger, S. E. & Meyers, T., Nov 1 2005, In : Global change biology. 11, 11, p. 1867-1872 6 p.

Research output: Contribution to journalArticle

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

The data-intensive farm management project: Changing agronomic research through on-farm precision experimentation

Bullock, D. S., Boerngen, M., Tao, H., Maxwell, B., Luck, J. D., Shiratsuchi, L., Puntel, L. & Martin, N. F., Nov 1 2019, In : Agronomy Journal. 111, 6, p. 2736-2746 11 p.

Research output: Contribution to journalArticle

Open Access

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

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

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

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. & Gaut, B., Oct 1 2019, In : Genome biology and evolution. 11, 10, p. 2927-2940 14 p.

Research output: Contribution to journalArticle

Open Access

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

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

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

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

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

Research output: Contribution to journalArticle

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The effects of O3 fumigation during leaf development on photosynthesis of wheat and pea: An in vivo analysis

Farage, P. K. & Long, S. P., Jan 1 1999, In : Photosynthesis research. 59, 1, p. 1-7 7 p.

Research output: Contribution to journalArticle

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

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

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

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

Research output: Contribution to journalArticle

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

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 1 2004, In : Crop Science. 44, 4, p. 1341-1347 7 p.

Research output: Contribution to journalArticle

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

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