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Scientific Publications
2012 Publications TOP
Akinbo, O., Labuschagne, M., and Fregene, M. (2012). Increased storage protein from interspecific F1
hybrids between cassava (Manihot esculenta Crantz) and its wild progenitor (M. esculenta ssp. flabellifolia).
Euphytica, 1-9.
Akinbo, O., Labuschagne, M., and Fregene, M. (2012). Introgression of whitefly (Aleurotrachelus socialis)
resistance gene from F1 inter-specific hybrids into commercial cassava. Euphytica 183, 19-26.http:
Akinbo, O., Labuschagne, M., Marín, J., Ospina, C., Santos, L., Barrera, E., Gutiérrez, J., Ewa, F., Okogbenin, E., and Fregene, M. (2012).
QTL Analysis for Root Protein in a Backcross Family of Cassava Derived from <i>Manihot esculenta ssp <i>flabellifolia</i>. Tropical Plant Biology 5, 1-12.
Allen, D.K., Laclair, R.W., Ohlrogge, J.B., and Shachar-Hill, Y. (2012). Isotope labelling of Rubisco subunits provides in vivo information on
subcellular biosynthesis and exchange of amino acids between compartments. Plant Cell Environ.
| PubMed |
Chen, M., Markham, J.E., and Cahoon, E.B. (2012). Sphingolipid Delta8 unsaturation is important for glucosylceramide biosynthesis and
low-temperature performance in Arabidopsis. Plant J 69, 769-81.
| PubMed |
Galant, A., Koester, R.P., Ainsworth, E.A., Hicks, L.M., and Jez, J.M. (2012). From climate change to molecular response: redox proteomics of
ozone-induced responses in soybean. New Phytol.
| PubMed |
Guo, L., Mishra, G., Markham, J.E., Li, M., Tawfall, A., Welti, R., and Wang, X. (2012). Connections between Sphingosine Kinase and Phospholipase D in the Abscisic Acid Signaling
Pathway in Arabidopsis. J Biol Chem.
| PubMed |
Hansman, G.S., Taylor, D.W., McLellan, J.S., Smith, T.J., Georgiev, I., Tame, J.R., Park, S.Y., Yamazaki, M., Gondaira, F., Miki, M., Katayama, K., Murata, K., and Kwong, P.D. (2012).
Structural basis for broad detection of genogroup II noroviruses by a monoclonal antibody that binds to a site occluded in the viral particle. J Virol.
| PubMed |
Hasnain, G., Waller, J.C., Alvarez, S., Ravilious, G.E., Jez, J.M., and Hanson, A.D. (2012). Mutational analysis of YgfZ, a folate-dependent protein implicated in iron/sulphur
cluster metabolism. FEMS Microbiol Lett 326, 168-72.
| PubMed |
Leyva-Guerrero, E., Narayanan, N.N., Ihemere, U., and Sayre, R.T. (2012). Iron and protein biofortification of cassava: lessons learned. Curr Opin Biotechnol.
| PubMed |
Martyniuk, C.J., Alvarez, S., and Denslow, N.D. (2012). DIGE and iTRAQ as biomarker discovery tools in aquatic toxicology. Ecotoxicol Environ Saf 76, 3-10.
| PubMed |
Prochnik, S., Marri, P., Desany, B., Rabinowicz, P., Kodira, C., Mohiuddin, M., Rodriguez, F., Fauquet, C., Tohme, J., Harkins, T., Rokhsar, D., and Rounsley, S.
(2012). The Cassava Genome: Current Progress, Future Directions. Tropical Plant Biology, 1-7.
Ruzicka, D., Hausmann, N., Barrios-Masias, F., Jackson, L., and Schachtman, D. (2012).
Transcriptomic and metabolic responses of mycorrhizal roots to nitrogen patches under field conditions. Plant and Soil 350, 145-62.
Smith, T.J. (2012). Glutamate dehydrogenase: structure regulation, and its role in insulin homeostasis. In Monogenic Hyperinsulinemic Hypoglycemia Disorders,
C.A. Stanley and D.D. De León, eds (Basel: Karger), pp. 87-99.
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Strong, D.W., Thackray, L.B., Smith, T.J., and Virgin, H.W. (2012). Protruding domain of capsid protein is necessary and sufficient to determine murine norovirus
replication and pathogenesis in vivo. J Virol 86, 2950-8.
| PubMed |
Taylor, N.J., Halsey, M.E., Gaitan-Solis, E., Anderson, P., Gichuki, S., Miano, D., Bua, A., Alicai, T., and Fauquet, C. (2012). The VIRCA Project:
Virus resistant cassava for Africa. GM Crops and Food: Biotechnology in Agriculture and the Food Chain 3.
Tjellstrom, H., Yang, Z., Allen, D.K., and Ohlrogge, J.B. (2012). Rapid kinetic labeling of Arabidopsis cell suspension cultures: implications for models of
lipid export from plastids. Plant Physiol 158, 601-11.
| PubMed |
Vu, H.S., Tamura, P., Galeva, N.A., Chaturvedi, R., Roth, M.R., Williams, T.D., Wang, X., Shah, J., and Welti, R. (2012).
Direct infusion mass spectrometry of oxylipin-containing Arabidopsis membrane lipids reveals varied patterns in different stress responses. Plant Physiol 158, 324-39.
| PubMed |
Waller, J.C., Ellens, K.W., Hasnain, G., Alvarez, S., Rocca, J.R., and Hanson, A.D. (2012). Evidence that the folate-dependent proteins YgfZ and MnmEG have opposing effects
on growth and on activity of the iron-sulfur enzyme MiaB. J Bacteriol 194, 362-7.
| PubMed |
Waller, J.C., Ellens, K.W., Alvarez, S., Loizeau, K., Ravanel, S., and Hanson, A.D. (2012). Mitochondrial and plastidial COG0354 proteins have folate-dependent
functions in iron-sulphur cluster metabolism. J Exp Bot 63, 403-11.
| PubMed |
Wang, H., Alvarez, S., and Hicks, L.M. (2012). Comprehensive comparison of iTRAQ and label-free LC-based quantitative proteomics approaches using two Chlamydomonas reinhardtii
strains of interest for biofuels engineering. J Proteome Res 11, 487-501.
| PubMed |
Wang, H., Wang, S., Lu, Y., Alvarez, S., Hicks, L.M., Ge, X., and Xia, Y. (2012). Proteomic analysis of early-responsive redox-sensitive proteins in Arabidopsis. J Proteome Res 11
, 412-24.
| PubMed |
Wang, Y., and Yu, O. (2012). Synthetic scaffolds increased resveratrol biosynthesis in engineered yeast cells. J Biotechnol 157, 258-60.
| PubMed |
Wood, C.R., Wang, Z., Diener, D., Zones, J.M., Rosenbaum, J., and Umen, J.G. (2012). IFT Proteins Accumulate during Cell Division and Localize to the Cleavage Furrow in Chlamydomonas.
PLoS One 7, e30729.
| PubMed |
Yang, W.Y., Zheng, Y., Bahn, S.C., Pan, X.Q., Li, M.Y., Vu, H.S., Roth, M.R., Scheu, B., Welti, R., Hong, Y.Y., and Wang, X.M. (2012). The Patatin-Containing Phospholipase A pPLAIIalpha
Modulates Oxylipin Formation and Water Loss in Arabidopsis thaliana. Mol Plant.
| PubMed |
2011 Publications TOP
Abhary, M., Siritunga, D., Stevens, G., Taylor, N.J., and Fauquet, C.M.
(2011). Transgenic biofortification of the starchy staple cassava (Manihot esculenta) generates a novel sink for protein. PLoS One
6, e16256.
| PubMed |
Abhary, M., Siritunga, D., Stevens, G., Taylor, N.J., and Fauquet, C.M. (2011). Transgenic biofortification of the starchy staple cassava (Manihot esculenta) generates a novel sink for protein. PLoS One 6, e16256.
| PubMed |
Ali, M.B., Howard, S., Chen, S., Wang, Y., Yu, O., Kovacs, L.G., and Qiu, W. (2011). Berry skin development in Norton grape: distinct patterns of transcriptional regulation and flavonoid biosynthesis. BMC Plant Biol 11, 7.
| PubMed |
Allen, A., Islamovic, E., Kaur, J., Gold, S., Shah, D., and Smith, T.J. (2011).
Transgenic maize plants expressing the Totivirus antifungal protein, KP4, are highly resistant to corn smut. Plant Biotechnol J, doi:10.1111/j.467-7652.2011.00590.x.
| PubMed |
Alvarez, S., Hicks, L.M., and Pandey, S.
(2011). ABA-dependent and -independent G-protein signaling in Arabidopsis roots revealed through an iTRAQ proteomics approach. J Proteome Res
10, 3107-22.
| PubMed |
Alvarez, S., Galant, A., Jez, J.M., and Hicks, L.M. (2011).
Redox-regulatory mechanisms induced by oxidative stress in Brassica juncea roots monitored by 2-DE proteomics. Proteomics
11, 1346-1350.
| PubMed |
Alvarez, S., and Hicks, L.M. (2011).
Survey in plant root proteomics. In Sustainable Agriculture and New Biotechnologies (CRC Press)
pp. 215-56.
| Open Access – Abstract |
Amin, I., Patil, B.L., Briddon, R.W., Mansoor, S., and Fauquet, C.M.
(2011). A common set of developmental miRNAs are upregulated in Nicotiana benthamiana by diverse begomoviruses.Virol J
8, 238.
| PubMed |
Amin, I., Patil, B.L., Briddon, R.W., Mansoor, S., and Fauquet, C.M.
(2011). Comparison of phenotypes produced in response to transient expression of genes encoded by four distinct begomoviruses in Nicotiana benthamiana and their correlation with the levels of developmental miRNAs. Virol J
8, 143.
| PubMed |
Amin, I., Ilyas, M., Qazi, J., Bashir, R., Yadav, J.S., Mansoor, S., Fauquet, C.M., and Briddon, R.W.
(2011). Identification of a major pathogenicity determinant and suppressors of RNA silencing encoded by a South Pacific isolate of Banana bunchy top virus originating from Pakistan. Virus Genes
42, 272-81.
| PubMed |
An, Y.Q., and Lin, L.
(2011). Transcriptional regulatory programs underlying barley germination and regulatory functions of Gibberellin and abscisic acid. BMC Plant Biol
11, 105.
| PubMed |
Atwood, A., DeConde, R., Wang, S.S., Mockler, T.C., Sabir, J.S., Ideker, T., and Kay, S.A. (2011). Cell-autonomous circadian clock of hepatocytes drives rhythms in transcription and polyamine synthesis. Proc Natl Acad Sci U S A 108, 18560-5.
| PubMed |
Bailey, J., Powell, L., Sinanan, L., Neal, J., Li, M., Smith, T., and Bell, E.
(2011). A novel mechanism of V-type zinc inhibition of glutamate dehydrogenase results from disruption of subunit interactions necessary for efficient catalysis. FEBS J
278, 3140-51.
| PubMed |
Becker, A., Chao, D.Y., Zhang, X., Salt, D.E., and Baxter, I.
(2011). Bulk segregant analysis using single nucleotide polymorphism microarrays. PLoS One
6, e15993.
| PubMed |
Bisht, N.C., Jez, J.M., and Pandey, S. (2011). An elaborate heterotrimeric G-protein family from soybean expands the diversity of plant G-protein networks. New Phytol 190, 35-48.
| PubMed |
Blankenship, R.E., Tiede, D.M., Barber, J., Brudvig, G.W., Fleming, G., Ghirardi, M., Gunner, M.R., Junge, W., Kramer, D.M., Melis, A., Moore, T.A., Moser, C.C., Nocera, D.G., Nozik, A.J., Ort, D.R., Parson, W.W., Prince, R.C., and Sayre, R.T.
(2011). Comparing photosynthetic and photovoltaic efficiencies and recognizing the potential for improvement. Science
332, 805-9.
| PubMed |
Chao, D.Y., Gable, K., Chen, M., Baxter, I., Dietrich, C.R., Cahoon, E.B., Guerinot, M.L., Lahner, B., Lu, S., Markham, J.E., Morrissey, J., Han, G., Gupta, S.D., Harmon, J.M., Jaworski, J.G., Dunn, T.M., and Salt, D.E.
(2011). Sphingolipids in the root play an important role in regulating the leaf ionome in Arabidopsis thaliana. Plant Cell
23, 1061-81.
| PubMed |
Chen, H., and Xiong, L.
(2011). Genetic interaction of two abscisic acid signaling regulators, HY5 and FIERY1, in mediating lateral root formation. Plant Signal Behav
6, 123-5.
| PubMed |
Chen, H., Zhang, B., Hicks, L.M., and Xiong, L. (2011). A nucleotide metabolite controls stress-responsive gene expression and plant development. PLoS One 6,
e26661.
| PubMed |
Chen, X., Alonso, A.P., Allen, D.K., Reed, J.L., and Shachar-Hill, Y. (2011). Synergy between (13)C-metabolic flux analysis and flux balance analysis for understanding metabolic adaptation to anaerobiosis in E. coli. Metabolic engineering 13, 38-48.
| PubMed |
Cheng, Y., Zhou, W., El Sheery, N.I., Peters, C., Li, M., Wang, X., and Huang, J.
(2011). Characterization of the Arabidopsis glycerophosphodiester phosphodiesterase (GDPD) family reveals a role of the plastid-localized AtGDPD1 in maintaining cellular phosphate homeostasis under phosphate starvation. Plant J
66, 781-95.
| PubMed |
Choudhury, S.R., Bisht, N.C., Thompson, R., Todorov, O., and Pandey, S.
(2011). Conventional and novel gƔ protein families constitute the heterotrimeric g-protein signaling network in soybean. PLoS One
6, e23361.
| PubMed |
Cuellar, W.J., Cruzado, R.K., Fuentes, S., Untiveros, M., Soto-Aguilar, M., and Kreuze, J.F. (2011). Sequence characterization of a Peruvian isolate of Sweet potato chlorotic stunt virus: further variability and a model for p22 acquisition. Virus Res 157, 111-5.
| PubMed |
Dai, S., Wei, X., Pei, L., Thompson, R.L., Liu, Y., Heard, J.E., Ruff, T.G., and Beachy, R.N.
(2011). Brother of LUX arrhythmo is a component of the Arabidopsis circadian clock. Plant Cell
23, 961-72.
| PubMed |
Deng, Y., Mao, G., Stutz, W., and Yu, O.
(2011). Generation of composite plants in Medicago truncatula used for nodulation assays. J Vis Exp
49, doi: 10.3791/2633.
| PubMed |
Diaz Chavez, M.L., Rolf, M., Gesell, A., and Kutchan, T.M.
(2011). Characterization of two methylenedioxy bridge-forming cytochrome P450-dependent enzymes of alkaloid formation in the Mexican prickly poppy Argemone mexicana. Arch Biochem Biophys
507, 186-193.
| PubMed |
Frolich, N., Dees, C., Paetz, C., Ren, X., Lohse, M.J., Nikolaev, V.O., and Zenk, M.H. (2011). Distinct pharmacological properties of morphine metabolites at G(i)-protein and beta-arrestin signaling pathways activated by the human mu-opioid receptor. Biochem Pharmacol, doi:10.1016/j.bcp.2011.1003.1001.
| PubMed |
Gesell, A., Diaz Chavez, M.L., Kramell, R., Piotrowski, M., Macheroux, P., and Kutchan, T.M.
(2011). Heterologous expression of two FAD-dependent oxidases with (S)-tetrahydroprotoberberine oxidase activity from Argemone mexicana and Berberis wilsoniae in insect cells. Planta
, doi:10.1007/s00425-011-1357-4
| PubMed |
Grobe, N., Ren, X., Kutchan, T.M., and Zenk, M.H. (2011). An (R)-specific N-methyltransferase involved in human morphine biosynthesis. Arch Biochem Biophys 506, 42-47.
| PubMed |
Guo, L., Mishra, G., Taylor, K., and Wang, X.
(2011). Phosphatidic acid binds and stimulates Arabidopsis sphingosine kinases. J Biol Chem
286, 13336-45.
| PubMed |
Gutierrez-Gonzalez, J., Vuong, T., Zhong, R., Yu, O., Lee, J.-D., Shannon, G., Ellersieck, M., Nguyen, H., and Sleper, D.
(2011). Major locus and other novel additive and epistatic loci involved in modulation of isoflavone concentration in soybean seeds. TAG Theoretical and Applied Genetics
123, doi: 10.1007/s00122-011-1673-x.
| PubMed |
He, Z., Siripornadulsil, S., Sayre, R.T., Traina, S.J., and Weavers, L.K.
(2011). Removal of mercury from sediment by ultrasound combined with biomass (transgenic Chlamydomonas reinhardtii). Chemosphere
83, 1249-54.
| PubMed |
Herman, E.M., and Burks, A.W.
(2011). The impact of plant biotechnology on food allergy. Curr Opin Biotechnol
22, 224-30.
| PubMed |
Higashi, Y., Kutchan, T.M., and Smith, T.J.
(2011). The atomic structure of salutaridine reductase from the opium poppy (Papaver somniferum). J Biol Chem
286, 6532-6541.
| PubMed |
Kaur, J., Sagaram, U.S., and Shah, D. (2011). Can plant defensins be used to engineer durable commercially useful fungal resistance in crop plants? Fungal Biology Reviews 25, 128-35.
Li, M., Bahn, S.C., Guo, L., Musgrave, W., Berg, H., Welti, R., and Wang, X.
(2011). Patatin-related phospholipase pPLAIIIb-induced changes in lipid metabolism alter cellulose content and cell elongation in Arabidopsis. Plant Cell
23, 1107-23.
| PubMed |
Li, B., Li, Q., Su, Y., Chen, H., Xiong, L., Mi, G., Kronzucker, H.J., and Shi, W.
(2011). Shoot-supplied ammonium targets the root auxin influx carrier AUX1 and inhibits lateral root emergence in Arabidopsis. Plant Cell Environ
34, 933-46.
| PubMed |
Li, M., Li, C., Allen, A., Stanley, C.A., and Smith, T.J. (2011). The structure and allosteric regulation of glutamate dehydrogenase. Neurochem Int 59, 445-55.
| PubMed |
Li, M., Li, C., Allen, A., Stanley, C.A., and Smith, T.J. (2011). The structure and allosteric regulation of mammalian glutamate dehydrogenase. Arch Biochem Biophys.
| PubMed |
Libault, M., Govindarajulu, M., Berg, R.H., Ong, Y.T., Puricelli, K., Taylor, C.G., Xu, D., and Stacey, G. (2011). A dual-targeted soybean protein is involved in Bradyrhizobium japonicum
infection of soybean root hair and cortical cells. Mol Plant Microbe Interact 24, 1051-60.
| PubMed |
Li, M., Li, C., Allen, A., Stanley, C.A., and Smith, T.J.
(2011). The structure and allosteric regulation of glutamate dehydrogenase. Neurochem Int
59, 445-55.
| PubMed |
Liberton, M., Austin, J.R., 2nd, Berg, R.H., and Pakrasi, H.B.
(2011). Insights into the complex 3-D architecture of thylakoid membranes in unicellular cyanobacterium Cyanothece sp. ATCC 51142. Plant Signal Behav
6, 566-69.
| PubMed |
Liberton, M., Austin, J.R., 2nd, Berg, R.H., and Pakrasi, H.B.
(2011). Unique thylakoid membrane architecture of a unicellular N2-fixing cyanobacterium revealed by electron tomography. Plant Physiol
155, 1656-66.
| PubMed |
Lu, Y., Li, C., Wang, H., Chen, H., Berg, H., and Xia, Y. (2011). AtPPR2, an Arabidopsis pentatricopeptide repeat protein, binds to plastid 23S rRNA and plays an important role in the
first mitotic division during gametogenesis and in cell proliferation during embryogenesis. Plant J 67, 13-25.
| PubMed |
Markham, J.E., Molino, D., Gissot, L., Bellec, Y., Hematy, K., Marion, J., Belcram, K., Palauqui, J.C., Satiat-Jeunemaitre, B., and Faure, J.D. (2011). Sphingolipids
containing very-long-chain Fatty acids define a secretory pathway for specific polar plasma membrane protein targeting in Arabidopsis. Plant Cell 23, 2362-78.
| PubMed |
Mbanzibwa, D.R., Tian, Y.P., Tugume, A.K., Patil, B.L., Yadav, J.S., Bagewadi, B., Abarshi, M.M., Alicai, T., Changadeya, W., Mkumbira, J., Muli, M.B., Mukasa, S.B., Tairo, F., Baguma, Y., Kyamanywa, S., Kullaya, A., Maruthi, M.N., Fauquet, C.M., and Valkonen, J.P. (2011). Evolution of cassava brown streak disease-associated viruses. J Gen Virol 92, 974-987.
| PubMed |
Narayanan, N.N., Ihemere, U., Ellery, C., and Sayre, R.T.
(2011). Overexpression of hydroxynitrile lyase in cassava roots elevates protein and free amino acids while reducing residual cyanogen levels. PLoS One
6, e21996.
| PubMed |
Negi, S., Kharshiing, E.V., and Sharma, R. (2011). NO way! Is nitric oxide level in tomato regulated by a mammalian IKK/NF-kappaB like signaling pathway? Plant Signal Behav 6, 1049-52.
| PubMed |
Pakrasi, H.B., and Smith, T.J. (2011). Zinc binding protein, ZnuA. In Handbook of Metalloproteins, A. Messerschmidt, ed (Chichester, UK: John Wiley & Sons, Ltd), pp. 746-754.
Pandey, S.
(2011). More (G-proteins) please! Identification of an elaborate network of G-proteins in soybean. Plant Signal Behav
6, 780-82.
| PubMed |
Pandey, S.
(2011). Plant hormone perception at the plasma membrane. In The Plant Plasma Membrane, A.S. Murphy, B. Schulz, and W. Peer, eds (Heidelberg: Springer)
, pp. 401-22
| Open Access – Abstract |
Patil, B.L., and Fauquet, C.M. (2011). Ecology of Plant Viruses, with Special Reference to Geminiviruses. In Studies in Viral Ecology (John Wiley & Sons, Inc.), pp. 272-306.
Patil, B.L., Ogwok, E., Wagaba, H., Mohammed, I.U., Yadav, J.S., Bagewadi, B., Taylor, N.J., Kreuze, J.F., Maruthi, M.N., Alicai, T., and Fauquet, C.M. (2011). RNAi-mediated resistance to diverse isolates belonging to two virus species involved in Cassava brown streak disease. Mol Plant Pathol 12, 31-41.
| PubMed |
Perrine, Z., and Sayre, R.
(2011).Modulating the redox potential of the stable electron acceptor, QB, in mutagenized photosystem II reaction centers. Biochemistry
50, 1454-64.
| PubMed |
Rajamani, S., Teplitski, M., Kumar, A., Krediet, C.J., Sayre, R.T., and Bauer, W.D. (2011). N-Acyl homoserine lactone lactonase, AiiA, Inactivation of quorum-sensing agonists
produced by chlamydomonas reinhardtii (Chlorphyta) and characterization of aiiA transgenic algAE. Journal of Phycology 47, 1219-27.
| PubMed |
Rajamani, S., and Sayre, R.T. (2011). A sensitive fluorescence reporter for monitoring quorum sensing regulated protease production in Vibrio harveyi.
J Microbiol Methods 84, 189-93.
| PubMed |
Sagaram, U.S., Pandurangi, R., Kaur, J., Smith, T.J., and Shah, D.M. (2011). Structure-activity determinants in antifungal plant defensins MsDef1 and MtDef4 with different modes
of action against Fusarium graminearum. PLoS One 6, e18550.
| PubMed |
Salas, J.J., Markham, J.E., Martinez-Force, E., and Garces, R. (2011). Characterization of sphingolipids from sunflower seeds with altered fatty acid composition. J Agric Food Chem 59
, 12486-92.
| PubMed |
Saucedo-Garcia, M., Guevara-Garcia, A., Gonzalez-Solis, A., Cruz-Garcia, F., Vazquez-Santana, S., Markham, J.E., Lozano-Rosas, M.G., Dietrich, C.R., Ramos-Vega, M., Cahoon, E.B., and Gavilanes-Ruiz, M.
(2011). MPK6, sphinganine and the LCB2a gene from serine palmitoyltransferase are required in the signaling pathway that mediates cell death induced by long chain bases in Arabidopsis. New Phytol 191
, 943-57.
| PubMed |
Sayre, R., Beeching, J.R., Cahoon, E.B., Egesi, C., Fauquet, C., Fellman, J., Fregene, M., Gruissem, W., Mallowa, S., Manary, M., Maziya-Dixon, B., Mbanaso, A., Schachtman, D.P., Siritunga, D., Taylor, N., Vanderschuren, H., and Zhang, P.
(2011).). The BioCassava plus program: biofortification of cassava for sub-Saharan Africa. Annu Rev Plant Biol
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Sayre, R.T. (2011). Biofortification of cassava for Africa: the BioCassava Plus program. In Access not excess: the search for better nutrition, C. Pasternak, ed (St. Ives, Cambridgeshire, UK: Smith-Gordon), pp. 113-120.
Schmidt, M.A., Barbazuk, W.B., Sandford, M., May, G., Song, Z., Zhou, W., Nikolau, B.J., and Herman, E.M.
(2011). Silencing of soybean seed storage proteins results in a rebalanced protein composition preserving seed protein content without major collateral changes in the metabolome and transcriptome. Plant Physiol
156, 330-45.
| PubMed |
Shi, C.Y., Yang, H., Wei, C.L., Yu, O., Zhang, Z.Z., Jiang, C.J., Sun, J., Li, Y.Y., Chen, Q., Xia, T., and Wan, X.C. (2011). Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds. BMC Genomics 12, 131.
| PubMed |
Shin, R., Jez, J.M., Basra, A., Zhang, B., and Schachtman, D.P. (2011). 14-3-3 proteins fine-tune plant nutrient metabolism. FEBS Lett 585, 143-7.
| PubMed |
Smith, T.J. (2011). Crop fungal resistance developed using genetic engineering and antifungal proteins from viruses. ISB News Report Nov 2011, 4-6.
| PubMed |
Smith, T.J. (2011). Engineering fungal resistance in crop plants using antifungal proteins from viruses. ISB News Report May 2011, 8-10.
| PubMed |
Smith, T.J., and Stanley, C.A. (2011). Glutamate Dehydrogenase. In Amino Acids in Human Nutrition and Health, J.P.F. D'Mello, ed (Oxford: CABI Publishing), pp. 3-23.
Smith, T.J.
(2011). Engineering fungal resistance in crop plants using antifungal proteins from viruses. ISB News Report
2011, 8-10.
| PubMed |
Smith, T.J., and Stanley, C.A. (2011).
Glutamate Dehydrogenase. In Amino Acids in Human Nutrition and Health, F. D'Mello, ed (Oxford: CABI Publishing)
Smith, T.J.
(2011). Green Tea Polyphenols in drug discovery - a success or failure? Expert Opin Drug Discov
6, 589-95.
| PubMed |
Smith, T.J.
(2011). ). Structural studies on antibody recognition and neutralization of viruses. Curr Opin Virol
1, 150-56.
| PubMed |
Song, C.X., Szulwach, K.E., Fu, Y., Dai, Q., Yi, C., Li, X., Li, Y., Chen, C.H., Zhang, W., Jian, X., Wang, J., Zhang, L., Looney, T.J., Zhang, B., Godley, L.A., Hicks, L.M., Lahn, B.T., Jin, P., and He, C.
(2011). Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine. Nat Biotechnol
29, 68-72.
| PubMed |
Sorek, N., Gutman, O., Bar, E., Abu-Abied, M., Feng, X., Running, M.P., Lewinsohn, E., Ori, N., Sadot, E., Henis, Y.I., and Yalovsky, S. (2011). Differential effects of prenylation and s-acylation on type I and II ROPS membrane interaction and function. Plant Physiol 155, 706-20.
| PubMed |
Thiele, I., Hyduke, D.R., Steeb, B., Fankam, G., Allen, D.K., Bazzani, S., Charusanti, P., Chen, F.C., Fleming, R.M., Hsiung, C.A., De Keersmaecker, S.C., Liao, Y.C., Marchal, K., Mo, M.L., Ozdemir, E., Raghunathan, A., Reed, J.L., Shin, S.I., Sigurbjornsdottir, S., Steinmann, J., Sudarsan, S., Swainston, N., Thijs, I.M., Zengler, K., Palsson, B.O., Adkins, J.N., and Bumann, D.
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2008 Publications TOP
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Berg, R.H., and Beachy, R.N. (2008). Fluorescent protein applications in plants. Methods Cell Biol 85, 153-177.
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Chen, H., Hu, J., Chen, P.R., Lan, L., Li, Z., Hicks, L.M., Dinner, A.R., and He, C. (2008). The Pseudomonas aeruginosa multidrug efflux regulator MexR uses an oxidation-sensing mechanism. Proc Natl Acad Sci U S A 105, 13586-13591.
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Koropatkin, N.M., Martens, E.C., Gordon, J.I., and Smith, T.J. (2008). Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices. Structure 16, 1105-1115.
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Nagamune, K., Hicks, L.M., Fux, B., Brossier, F., Chini, E.N., and Sibley, L.D.
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Nomura, T., Quesada, A.L., and Kutchan, T.M.
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Pan, X., Welti, R., and Wang, X. (2008). Simultaneous quantification of major phytohormones and related compounds in crude plant extracts by liquid chromatography-electrospray tandem mass spectrometry. Phytochemistry 69, 1773-1781.
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Pandey, S., Monshausen, G.B., Ding, L., and Assmann, S.M. (2008). Regulation of root-wave response by extra large and conventional G proteins in Arabidopsis thaliana. Plant J 55, 311-322.
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Phillips, G., El Yacoubi, B., Lyons, B., Alvarez, S., Iwata-Reuyl, D., and de Crecy-Lagard, V. (2008). Biosynthesis of 7-deazaguanosine-modified tRNA nucleosides: a new role for GTP cyclohydrolase I. J Bacteriol 190, 7876-7884.
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Qi, Z., Hampton, C.R., Shin, R., Barkla, B.J., White, P.J., and Schachtman, D.P. (2008). The high affinity K+ transporter AtHAK5 plays a physiological role in planta at very low K+ concentrations and provides a caesium uptake pathway in Arabidopsis. J Exp Bot 59, 595-607.
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Schmidt, M., and Herman, E. (2008). Suppression of soybean oleosin produces micro-oil bodies that aggregate into oil body/ER complexes. Molec Plant 1, 910-924
Schmidt, M.A., and Herman, E.M. (2008). Proteome rebalancing in soybean seeds can be exploited to enhance foreign protein accumulation. Plant Biotechnol J 6, 832-842.
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Schroeder, A.C., Kumaran, S., Hicks, L.M., Cahoon, R.E., Halls, C., Yu, O., and Jez, J.M. (2008). Contributions of conserved serine and tyrosine residues to catalysis, ligand binding, and cofactor processing in the active site of tyrosine ammonia lyase. Phytochemistry 69, 1496-1506.
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Silvester, W.B., Berg, R.H., Schwintzer, C.R., and Tjepkema, J.D. (2008). Oxygen responses, hemoglobin and the structure and function of vesicles. In Actinorhizal Symbioses, K. Pawlowski and W.H. Newton, eds (Dordrecht: Springer), pp. 105-146.
Smith, T.J., and Stanley, C.A. (2008). Untangling the glutamate dehydrogenase allosteric nightmare. Trends Biochem Sci 33, 557-564.
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Wang, W., Yang, X., Tangchaiburana, S., Ndeh, R., Markham, J.E., Tsegaye, Y., Dunn, T.M., Wang, G.L., Bellizzi, M., Parsons, J.F., Morrissey, D., Bravo, J.E., Lynch, D.V., and Xiao, S. (2008). An inositolphosphorylceramide synthase is involved in regulation of plant programmed cell death associated with defense in Arabidopsis. Plant Cell 20, 3163-3179.
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Winkler, A., Lyskowski, A., Riedl, S., Puhl, M., Kutchan, T.M., Macheroux, P., and Gruber, K. (2008). A concerted mechanism for berberine bridge enzyme. Nat Chem Biol 4, 739-741.
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Yu, O., and Jez, J.M. (2008). Nature's assembly line: biosynthesis of simple phenylpropanoids and polyketides. Plant J 54, 750-762.
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Zeng, Q., and Running, M.P. (2008). Protein lipid modification and plant
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Zhang, J., and Yu, O. (2008). Metabolic engineering of isoflavone biosynthesis in seeds. In Modification of seed composition to promote health and nutrition, H. Krishnan, ed. (Madison, WI: ASA/CCSA/SSSA), pp. 151-177.
Zubieta, C., Arkus, K.A., Cahoon, R.E., and Jez, J.M.
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2007 Publications TOP
Abhary, J., Patil, B.L., and Fauquet, C.M. (2007). Molecular biodiversity, taxonomy and nomenclature of Tomato yellow leaf curl-like viruses. In Tomato yellow leaf curl virus disease: Management, molecular biology, breeding for resistance, H. Czosnek, ed (Netherlands: Springer), pp. 85-118.
Asurmendi, S., Berg, R.H., Smith, T.J., Bendahmane, M., and Beachy, R.N. (2007). Aggregation of TMV CP plays a role in CP functions and in coat-protein-mediated resistance. Virology 366, 98-106.
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Barrows, F., Bellis, D., Krogdahl, A., Silverstein, J., Herman, E., Sealey, W., Rust, M., and Gatlin, I.D. (2007). Report of the plant products in aquafeed strategic planning workshop: An integrated, interdisciplinary research roadmap for increasing utilization of plant feedstuffs in diets for carnivorous fish. Aquaculture Res 38, 551-579
Bazzini, A.A., Hopp, H.E., Beachy, R.N., and Asurmendi, S. (2007). Infection and coaccumulation of tobacco mosaic virus proteins alter microRNA levels, correlating with symptom and plant development. Proc Natl Acad Sci U S A 104, 12157-12162.
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Bendahmane, M., Chen, I., Asurmendi, S., Bazzini, A.A., Szecsi, J., and Beachy, R.N. (2007). Coat protein-mediated resistance to TMV infection of Nicotiana tabacum involves multiple modes of interference by coat protein. Virology 366, 107-116.
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Brendza, K.M., Haakenson, W., Cahoon, R.E., Hicks, L.M., Palavalli, L.H., Chiapelli, B.J., McLaird, M., McCarter, J.P., Williams, D.J., Hresko, M.C., and Jez, J.M. (2007). Phosphoethanolamine N-methyltransferase (PMT-1) catalyses the first reaction of a new pathway for phosphocholine biosynthesis in Caenorhabditis elegans. Biochem J 404, 439-448.
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Cahoon, E.B., Shockey, J.M., Dietrich, C.R., Gidda, S.K., Mullen, R.T., and Dyer, J.M. (2007). Engineering oilseeds for sustainable production of industrial and nutritional feedstocks: solving bottlenecks in fatty acid flux. Curr Opin Plant Biol 10, 236-244.
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Devaiah, S.P., Pan, X., Hong, Y., Roth, M., Welti, R., and Wang, X. (2007). Enhancing seed quality and viability by suppressing phospholipase D in Arabidopsis. Plant J 50, 950-957.
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Earley, K.W., Shook, M.S., Brower-Toland, B., Hicks, L., and Pikaard, C.S. (2007). In vitro specificities of Arabidopsis co-activator histone acetyltransferases: implications for histone hyperacetylation in gene activation. Plant J 52, 615-626.
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Graham, T.L., Graham, M.Y., Subramanian, S., and Yu, O. (2007). RNAi silencing of genes for elicitation or biosynthesis of 5-deoxyisoflavonoids suppresses race-specific resistance and hypersensitive cell death in Phytophthora sojae infected tissues. Plant Physiol 144, 728-740.
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Hicks, L.M., Cahoon, R.E., Bonner, E.R., Rivard, R.S., Sheffield, J., and Jez, J.M. (2007). Thiol-based regulation of redox-active glutamate-cysteine ligase from Arabidopsis thaliana. Plant Cell 19, 2653-2661.
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Katpally, U., Kakani, K., Reade, R., Dryden, K., Rochon, D., and Smith, T.J. (2007). Structures of T=1 and T=3 particles of cucumber necrosis virus: evidence of internal scaffolding. J Mol Biol 365, 502-512.
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Subramanian, S., Stacey, G., and Yu, O. (2007). Distinct, crucial roles of flavonoids during legume nodulation. Trends Plant Sci 12, 282-285.
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Wei, B., Randich, A.M., Bhattacharyya-Pakrasi, M., Pakrasi, H.B., and Smith, T.J. (2007). Possible regulatory role for the histidine-rich loop in the zinc transport protein, ZnuA. Biochemistry 46, 8734-8743.
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Xiong, L. (2007). Abscisic acid in plant response and adaptation to drought and salt stress. In Advances in Molecular Breeding Toward Drought and Salt Tolerant Crops, M.A. Jenks, P.M. Hasegawa, and S.M. Jain, eds (Dordrecht, The Netherlands: Springer), pp. 193-221.
Yang, W., Devaiah, S.P., Pan, X., Isaac, G., Welti, R., and Wang, X. (2007). AtPLAI is an acyl hydrolase involved in basal jasmonic acid production and Arabidopsis resistance to Botrytis cinerea. J Biol Chem 282, 18116-18128.
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Zhang, J., Subramanian, S., Zhang, Y., and Yu, O. (2007). Flavone synthases from Medicago truncatula are flavanone-2-hydroxylases and are important for nodulation. Plant Physiol 144, 741-751.
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Zhu, J., Alvarez, S., Marsh, E.L., Lenoble, M.E., Cho, I.J., Sivaguru, M., Chen, S., Nguyen, H.T., Wu, Y., Schachtman, D.P., and Sharp, R.E. (2007). Cell wall proteome in the maize primary root elongation zone. II. Region-specific changes in water soluble and lightly ionically bound proteins under water deficit. Plant Physiol 145, 1533-1548.
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2006 Publications TOP
Alvarez, S., Goodger, J.Q., Marsh, E.L., Chen, S., Asirvatham, V.S., and Schachtman, D.P. (2006). Characterization of the maize xylem sap proteome. J Proteome Res 5, 963-972.
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Bazzini, A.A., Asurmendi, S., Hopp, H.E., and Beachy, R.N. (2006). TMV and PVX coat proteins confer heterologous interference to PVX and TMV infection, respectively. J Gen Virol 87, 1005-1012.
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Bazzini, A.A., Hopp, H.E., Beachy, R.N., and Asurmendi, S. (2006). Posttranscriptional gene silencing does not play a significant role in PVX coat protein-mediated resistance. Phytopathology 96, 1175-1178.
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Chabaud, M., Boisson-Dernier, A., Zhang, J., Taylor, C.G., Yu, O., and Barker, D.G. (2006). Agrobacterium rhizogenes-mediated root transformation. In The Medicago truncatula handbook, U. Mathesius, ed (Ardmore, OK: Samuel Roberts Noble Found.), pp.1-8.
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Chan, A.P., Pertea, G., Cheung, F., Lee, D., Zheng, L., Whitelaw, C., Pontaroli, A.C., SanMiguel, P., Yuan, Y., Bennetzen, J., Barbazuk, W.B., Quackenbush, J., and Rabinowicz, P.D. (2006). The TIGR Maize Database. Nucleic Acids Res 34, D771-776.
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Chen, M., Han, G., Dietrich, C.R., Dunn, T.M., and Cahoon, E.B. (2006). The essential nature of sphingolipids in plants as revealed by the functional identification and characterization of the Arabidopsis LCB1 subunit of serine palmitoyltransferase. Plant Cell 18, 3576-3593.
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Chen, S. (2006). Rapid protein identification using direct infusion nanoelectrospray ionization mass spectrometry. Proteomics 6, 16-25.
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Dai, S., Zhang, Z., Bick, J., and Beachy, R.N. (2006). Essential role of the Box II cis element and cognate host factors in regulating the promoter of Rice tungro bacilliform virus. J Gen Virol 87, 715-722.
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Davies, C., Shin, R., Liu, W., Thomas, M.R., and Schachtman, D.P. (2006). Transporters expressed during grape berry (Vitis vinifera L.) development are associated with an increase in berry size and berry potassium accumulation. J Exp Bot 57, 3209-3216.
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Devaiah, S.P., Roth, M.R., Baughman, E., Li, M., Tamura, P., Jeannotte, R., Welti, R., and Wang, X. (2006). Quantitative profiling of polar glycerolipid species from organs of wild-type Arabidopsis and a phospholipase Da knockout mutant. Phytochemistry 67, 1907-1924.
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Fargette, D., Konate, G., Fauquet, C., Muller, E., Peterschmitt, M., and Thresh, J.M. (2006). Molecular ecology and emergence of tropical plant viruses. Annu Rev Phytopathol 44, 235-260.
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Fauquet, C.M. (2006). The diversity of single-stranded DNA viruses. Biodiversity 7, 38-44
Fujiki, M., Kawakami, S., Kim, R.W., and Beachy, R.N. (2006). Domains of tobacco mosaic virus movement protein essential for its membrane association. J Gen Virol 87, 2699-2707.
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Hammes, U.Z., Nielsen, E., Honaas, L.A., Taylor, C.G., and Schachtman, D.P. (2006). AtCAT6, a sink-tissue-localized transporter for essential amino acids in Arabidopsis. Plant J 48, 414-426.
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Hankoua, B.B., Taylor, N.J., Ng, S.Y.C., Fawole, I., Puonti-Kaerlas, J., Padmanabhan, C., Yadav, J.S., Fauquet, C.M., Dixon, A.G.O., and Fondong, V.N. (2006). Production of the first transgenic cassava in Africa via direct shoot organogenesis from friable embryogenic calli and germination of maturing somatic embryos. AfrJBiotechnol 5, 1700-1712
Herman, E.M., Rotter, K., Premakumar, R., Elwinger, G., Bae, H., Ehler-King, L., Chen, S., and Livingston, D.P., 3rd. (2006). Additional freeze hardiness in wheat acquired by exposure to -3 degreesC is associated with extensive physiological, morphological, and molecular changes. J Exp Bot 57, 3601-3618. (cover article)
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Joseph, L.M., Hymowitz, T., Schmidt, M.A., and Herman, E.M. (2006). Evaluation of glycine germplasm for nulls of the immunodominant allergen p34/Gly m BD 30k. Crop Sci 46, 1755-1763. (cover article)
Koropatkin, N.M., Pakrasi, H.B., and Smith, T.J. (2006). Atomic structure of a nitrate-binding protein crucial for photosynthetic productivity. Proc Natl Acad Sci U S A 103, 9820-9825.
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Kouassi, N.K., Chen, L., Sire, C., Bangratz-Reyser, M., Beachy, R.N., Fauquet, C.M., and Brugidou, C. (2006). Expression of rice yellow mottle virus coat protein enhances virus infection in transgenic plants. Arch Virol 151, 2111-2122.
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Li, C., Allen, A., Kwagh, J., Doliba, N.M., Qin, W., Najafi, H., Collins, H.W., Matschinsky, F.M., Stanley, C.A., and Smith, T.J. (2006). Green tea polyphenols modulate insulin secretion by inhibiting glutamate dehydrogenase. J Biol Chem 281, 10214-10221.
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Li, M., Qin, C., Welti, R., and Wang, X. (2006). Double knockouts of phospholipases Dz1 and Dz2 in Arabidopsis affect root elongation during phosphate-limited growth but do not affect root hair patterning. Plant Physiol 140, 761-770.
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Li, M., Welti, R., and Wang, X. (2006). Quantitative profiling of Arabidopsis polar glycerolipids in response to phosphorus starvation. Roles of phospholipases Dz1 and Dz2 in phosphatidylcholine hydrolysis and digalactosyldiacylglycerol accumulation in phosphorus-starved plants. Plant Physiol 142, 750-761.
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Markham, J.E., Li, J., Cahoon, E.B., and Jaworski, J.G. (2006). Separation and identification of major plant sphingolipid classes from leaves. J Biol Chem 281, 22684-22694.
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Mishra, G., Zhang, W., Deng, F., Zhao, J., and Wang, X. (2006). A bifurcating pathway directs abscisic acid effects on stomatal closure and opening in Arabidopsis. Science 312, 264-266.
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Ndunguru, J., Legg, J.P., Fofana, I.B.F., Aveling, T.A.S., Thompson, G., and Fauquet, C.M. (2006). Identification of a defective molecule derived from DNA-A of the bipartite begomovirus of East African cassava mosaic virus. Plant Pathol 55, 2-10
Palavalli, L.H., Brendza, K.M., Haakenson, W., Cahoon, R.E., McLaird, M., Hicks, L.M., McCarter, J.P., Williams, D.J., Hresko, M.C., and Jez, J.M. (2006). Defining the role of phosphomethylethanolamine N-methyltransferase from Caenorhabditis elegans in phosphocholine biosynthesis by biochemical and kinetic analysis. Biochemistry 45, 6056-6065.
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Paul, S., Gable, K., Beaudoin, F., Cahoon, E., Jaworski, J., Napier, J.A., and Dunn, T.M. (2006). Members of the Arabidopsis FAE1-like 3-ketoacyl-CoA synthase gene family substitute for the Elop proteins of Saccharomyces cerevisiae. J Biol Chem 281, 9018-9029.
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Petruccelli, S., Otegui, M.S., Lareu, F., Tran Dinh, O., Fitchette, A.C., Circosta, A., Rumbo, M., Bardor, M., Carcamo, R., Gomord, V., and Beachy, R.N. (2006). A KDEL-tagged monoclonal antibody is efficiently retained in the endoplasmic reticulum in leaves, but is both partially secreted and sorted to protein storage vacuoles in seeds. Plant Biotechnol J 4, 511-527.
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Platten, J.D., Cotsaftis, O., Berthomieu, P., Bohnert, H., Davenport, R.J., Fairbairn, D.J., Horie, T., Leigh, R.A., Lin, H.X., Luan, S., Maser, P., Pantoja, O., Rodriguez-Navarro, A., Schachtman, D.P., Schroeder, J.I., Sentenac, H., Uozumi, N., Very, A.A., Zhu, J.K., Dennis, E.S., and Tester, M. (2006). Nomenclature for HKT transporters, key determinants of plant salinity tolerance. Trends Plant Sci 11, 372-374.
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Preuss, M.L., Schmitz, A.J., Thole, J.M., Bonner, H.K., Otegui, M.S., and Nielsen, E. (2006). A role for the RabA4b effector protein PI-4Kbeta1 in polarized expansion of root hair cells in Arabidopsis thaliana. J Cell Biol 172, 991-998.
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Qin, C., Li, M., Qin, W., Bahn, S.C., Wang, C., and Wang, X. (2006). Expression and characterization of Arabidopsis phospholipase Dg2. Biochim Biophys Acta 1761, 1450-1458.
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Rajashekar, C.B., Zhou, H.E., Zhang, Y., Li, W., and Wang, X. (2006). Suppression of phospholipase Da1 induces freezing tolerance in Arabidopsis: response of cold-responsive genes and osmolyte accumulation. J Plant Physiol 163, 916-926.
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Ralston, L., and Yu, O. (2006). Metabolons involving plant cytochrome P450s. Phytochem Rev 5, 459-472.
Raven, P., Fauquet, C., Swaminathan, M.S., Borlaug, N., and Samper, C. (2006). Where next for genome sequencing? Science 311, 468.
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Sheffield, J., Taylor, N., Fauquet, C., and Chen, S. (2006). The cassava (Manihot esculenta Crantz) root proteome: protein identification and differential expression. Proteomics 6, 1588-1598.
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Subramanian, S., Stacey, G., and Yu, O. (2006). Endogenous isoflavones are essential for the establishment of symbiosis between soybean and Bradyrhizobium japonicum. Plant J 48, 261-273.
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Taylor, C.G., Fuchs, B., Collier, R., and Lutke, W.K. (2006). Generation of composite plants using Agrobacterium rhizogenes. Methods Mol Biol 343, 155-167.
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Wang, X. (2006). Phospholipid-derived signaling in plant response to temperature and water stresses. Genet Eng (N Y) 27, 57-66.
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Wang, X., Devaiah, S.P., Zhang, W., and Welti, R. (2006). Signaling functions of phosphatidic acid. Prog Lipid Res 45, 250-278.
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Wang, X., Li, W., Li, M., and Welti, R. (2006). Profiling lipid changes in plant response to low temperatures. Physiol Plant 126, 90-96
Xiong, L., and Ishitani, M. (2006). Stress signal transduction: components, pathways, and network integration. In Abiotic Stress Tolerance in Plants: Toward the Improvement of Global Environment and Food., A.K. Rai and T. Takabe, eds (Dordrecht, The Netherlands: Springer), pp. 3-29.
Xiong, L., Wang, R.G., Mao, G., and Koczan, J.M. (2006). Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic Acid. Plant Physiol 142, 1065-1074.
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Yang, Y., Hammes, U.Z., Taylor, C.G., Schachtman, D.P., and Nielsen, E. (2006). High-affinity auxin transport by the AUX1 influx carrier protein. Curr Biol 16, 1123-1127.
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Yu, O. (2006). Metabolic engineering of the plant phenylpropanoid pathway. In Encyclopedia of Plant and Crop Science (London: Taylor & Francis), DOI: 10.1081/E-EPCS-120010589
Yu, O., Matsuno, M., and Subramanian, S. (2006). Flavonoids in flowers: Genetics and Biochemistry. In Floriculture, ornamental and plant biotechnology: Advances and topical issues J.A.T.d. Silva, ed (Isleworth, UK: Global Science Books), pp. 283-293.
Zhang, Y., Li, S.Z., Li, J., Pan, X., Cahoon, R.E., Jaworski, J.G., Wang, X., Jez, J.M., Chen, F., and Yu, O. (2006). Using unnatural protein fusions to engineer resveratrol biosynthesis in yeast and Mammalian cells. J Am Chem Soc 128, 13030-13031.
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Zhu, J., Chen, S., Alvarez, S., Asirvatham, V.S., Schachtman, D.P., Wu, Y., and Sharp, R.E. (2006). Cell wall proteome in the maize primary root elongation zone. I. Extraction and identification of water-soluble and lightly ionically bound proteins. Plant Physiol 140, 311-325.
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2005 Publications TOP
Adams, M.J., Antoniw, J.F., and Fauquet, C.M. (2005). Molecular criteria for genus and species discrimination within the family Potyviridae. Arch Virol 150, 459-479.
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Altpeter, F., Niranjan, B., Beachy, R., Bock, R., Capell, T., Christou, P., Daniell, H., Karabi, D., Swapan, D., Dix, P.J., Fauquet, C., Huang, N., Ajay, K., Mooibroek, H., Nicholson, L., Thi Thanh, N., Nugent, G., Raemakers, K., Romano, A., Somers, D.A., Stoger, E., Taylor, N., and Visser, R. (2005). Particle bombardment and the genetic enhancement of crops: myths and realities. Mol Breed 15, 305-327
Aroca, R., Amodeo, G., Fernandez-Illescas, S., Herman, E.M., Chaumont, F., and Chrispeels, M.J. (2005). The role of aquaporins and membrane damage in chilling and hydrogen peroxide induced changes in the hydraulic conductance of maize roots. Plant Physiol 137, 341-353.
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Bae, H., Herman, E., Bailey, B., Bae, H.-J., and Sicher, R. (2005). Exogenous trehalose alters Arabidopsis transcripts involved in cell wall modification, abiotic stress, nitrogen metabolism, and plant defense. Physiol Plant 125, 114-126
Bae, H., Herman, E., and Sicher, R. (2005). Exogenous trehalose promotes nonstructural carbohydrate accumulation and induces chemical detoxification and stress response proteins in Arabidopsis thaliana grown in liquid culture. Plant Sci 168, 1293-1301.
Open Access – Full |
Barbazuk, W.B., Bedell, J.A., and Rabinowicz, P.D. (2005). Reduced representation sequencing: a success in maize and a promise for other plant genomes. Bioessays 27, 839-848.
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Bommert, P., Lunde, C., Nardmann, J., Vollbrecht, E., Running, M., Jackson, D., Hake, S., and Werr, W. (2005). Thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development 132, 1235-1245.
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Bonner, E.R., Cahoon, R.E., Knapke, S.M., and Jez, J.M. (2005). Molecular basis of cysteine biosynthesis in plants: structural and functional analysis of O-acetylserine sulfhydrylase from Arabidopsis thaliana. J Biol Chem 280, 38803-38813.
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Chellappan, P., Vanitharani, R., and Fauquet, C.M. (2005). MicroRNA-binding viral protein interferes with Arabidopsis development. Proc Natl Acad Sci U S A 102, 10381-10386.
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Chellappan, P., Vanitharani, R., Ogbe, F., and Fauquet, C.M. (2005). Effect of temperature on geminivirus-induced RNA silencing in plants. Plant Physiol 138, 1828-1841.
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Chen, H., and Xiong, L. (2005). Pyridoxine is required for post-embryonic root development and tolerance to osmotic and oxidative stresses. Plant J 44, 396-408.
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Chinnusamy, V., Xiong, L., and Zhu, J.K. (2005). Use of Genetic Engineering and Molecular Biology Approaches for Crop Improvement for Stress Environments. In Abiotic Stresses: Plant Resistance through Breeding and Molecular Approaches., M. Ashraf and P.J.C. Harris, eds (Binghamton, NY: Haworth Press), pp. 47-107.
Collier, R., Fuchs, B., Walter, N., Kevin Lutke, W., and Taylor, C.G. (2005). Ex vitro composite plants: an inexpensive, rapid method for root biology. Plant J 43, 449-457.
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Fauquet, C.M., and Fargette, D. (2005). International Committee on Taxonomy of Viruses and the 3,142 unassigned species. Virol J 2, 64.
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Fauquet, C.M., Mayo, M.A., Maniloff, J., Desselberger, U., and Ball, L.A. (2005). Virus Taxonomy: Classification and Nomenclature of Viruses: Eighth Report of the International Committee on the Taxonomy of Viruses (Oxford: Academic Press). 586 p.
Fauquet, C.M., Sawyer, S., Idris, A.M., and Brown, J.K. (2005). Sequence analysis and classification of apparent recombinant begomoviruses infecting tomato in the nile and mediterranean basins. Phytopathology 95, 549-555.
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Fauquet, C.M., and Stanley, J. (2005). Revising the way we conceive and name viruses below the species level: a review of geminivirus taxonomy calls for new standardized isolate descriptors. Arch Virol 150, 2151-2179.
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Ge, X., Dietrich, C., Matsuno, M., Li, G., Berg, H., and Xia, Y. (2005). An Arabidopsis aspartic protease functions as an anti-cell-death component in reproduction and embryogenesis. EMBO Rep 6, 282-288.
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Goodger, J.Q., Sharp, R.E., Marsh, E.L., and Schachtman, D.P. (2005). Relationships between xylem sap constituents and leaf conductance of well-watered and water-stressed maize across three xylem sap sampling techniques. J Exp Bot 56, 2389-2400.
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Hammes, U.Z., Schachtman, D.P., Berg, R.H., Nielsen, E., Koch, W., McIntyre, L.M., and Taylor, C.G. (2005). Nematode-induced changes of transporter gene expression in Arabidopsis roots. Mol Plant Microbe Interact 18, 1247-1257.
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Hanks, J.N., Snyder, A.K., Graham, M.A., Shah, R.K., Blaylock, L.A., Harrison, M.J., and Shah, D.M. (2005). Defensin gene family in Medicago truncatula: structure, expression and induction by signal molecules. Plant Mol Biol 58, 385-399.
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Johnson, C.D., Chary, S.N., Chernoff, E.A., Zeng, Q., Running, M.P., and Crowell, D.N. (2005). Protein geranylgeranyltransferase I is involved in specific aspects of abscisic acid and auxin signaling in Arabidopsis. Plant Physiol 139, 722-733.
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Kouassi, N.K., N'Guessan, P., Albar, L., Fauquet, C.M., and Brugidou, C. (2005). Distribution and characterization of Rice yellow mottle virus: a threat to African farmers. Plant Disease 89, 124-133
Marmey, P., Rojas-Mendoza, A., de Kochko, A., Beachy, R.N., and Fauquet, C.M. (2005). Characterization of the protease domain of Rice tungro bacilliform virus responsible for the processing of the capsid protein from the polyprotein. Virol J 2, 33-45.
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Ndunguru, J., Legg, J.P., Aveling, T.A., Thompson, G., and Fauquet, C.M. (2005). Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses. Virol J 2, 21.
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Ndunguru, J., Taylor, N.J., Yadav, J., Aly, H., Legg, J.P., Aveling, T., Thompson, G., and Fauquet, C.M. (2005). Application of FTA technology for sampling, recovery and molecular characterization of viral pathogens and virus-derived transgenes from plant tissues. Virol J 2, 45.
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Nielsen, E. (2005). Rab GTPases in plant endocytosis. In Plant Endocytosis., J. Šamaj, F. Baluška, and D. Menzel, eds (Dordrecht, The Netherlands: Springer), pp. 177-196.
Ralston, L., Subramanian, S., Matsuno, M., and Yu, O. (2005). Partial reconstruction of flavonoid and isoflavonoid biosynthesis in yeast using soybean type I and type II chalcone isomerases. Plant Physiol 137, 1375-1388.
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Shin, R., Berg, R.H., and Schachtman, D.P. (2005). Reactive oxygen species and root hairs in Arabidopsis root response to nitrogen, phosphorus and potassium deficiency. Plant Cell Physiol 46, 1350-1357.
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Subramanian, S., Graham, M.Y., Yu, O., and Graham, T.L. (2005). RNA interference of soybean isoflavone synthase genes leads to silencing in tissues distal to the transformation site and to enhanced susceptibility to Phytophthora sojae. Plant Physiol 137, 1345-1353.
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Vanitharani, R., Chellappan, P., and Fauquet, C.M. (2005). Geminiviruses and RNA silencing. Trends Plant Sci 10, 144-151.
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Voigt, B., Timmers, A.C., Samaj, J., Hlavacka, A., Ueda, T., Preuss, M., Nielsen, E., Mathur, J., Emans, N., Stenmark, H., Nakano, A., Baluska, F., and Menzel, D. (2005). Actin-based motility of endosomes is linked to the polar tip growth of root hairs. Eur J Cell Biol 84, 609-621.
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Voloudakis, A.E., Aleman-Verdaguer, M.E., Padgett, H.S., and Beachy, R.N. (2005). Characterization of resistance in transgenic Nicotiana benthamiana encoding N-terminal deletion and assembly mutants of the tobacco etch potyvirus coat protein. Arch Virol 150, 2567-2582.
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Wang, X. (2005). Regulatory functions of phospholipase D and phosphatidic acid in plant growth, development, and stress responses. Plant Physiol 139, 566-573.
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Welti, R., Shah, J., LeVine, S., Esch, S.W., Williams, T.D., and Wang, X. (2005). High throughput lipid profiling to identify and characterize genes invovled in lipid metabolism, signaling, and stress response. In Functional Lipidomics, L. Feng and G. Prestwich, eds (Boca Raton, Florida: CRC Press), pp. 308-320.
Wendl, M.C., and Barbazuk, W.B. (2005). Extension of Lander-Waterman theory for sequencing filtered DNA libraries. BMC Bioinformatics 6, 245.
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Yadav, J.S., Fauquet, C.M., and Beachy, R.N. (2005). Control of plant virus diseases. In Encyclopedia of Plant and Crop Science, R.M. Goodman, ed (New York: Taylor & Francis), DOI: 10.1081/E-EPCS-120019914.
Yu, O., and McGonigle, B. (2005). Metabolic engineering of isoflavone biosynthesis. Adv Agron 86, 147-190
Zhang, W., Yu, L., Zhang, Y., and Wang, X. (2005). Phospholipase D in the signaling networks of plant response to abscisic acid and reactive oxygen species. Biochim Biophys Acta 1736, 1-9.
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Adams, M.J., Antoniw, J.F., Bar-Joseph, M., Brunt, A.A., Candresse, T., Foster, G.D., Martelli, G.P., Milne, R.G., Zavriev, S.K., and Fauquet, C.M. (2004). The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Arch Virol 149, 1045-1060.
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2004 Publications TOP
Ahn, S.J., Shin, R., and Schachtman, D.P. (2004). Expression of KT/KUP genes in Arabidopsis and the role of root hairs in K+ uptake. Plant Physiol 134, 1135-1145.
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Allen, A., Kwagh, J., Fang, J., Stanley, C.A., and Smith, T.J. (2004). Evolution of glutamate dehydrogenase regulation of insulin homeostasis is an example of molecular exaptation. Biochemistry 43, 14431-14443.
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Asurmendi, S., Berg, R.H., Koo, J.C., and Beachy, R.N. (2004). Coat protein regulates formation of replication complexes during TMV infection. Proc Natl Acad Sci U S A 101, 1415-1420.
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Asurmendi, S., Berg, R.H., Koo, J.C., and Beachy, R.N. (2004). Coat protein regulates formation of replication complexes during tobacco mosaic virus infection. Proc Natl Acad Sci U S A 101, 1415-1420.
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Bachvaroff, T.R., Concepcion, G.T., Rogers, C.R., Herman, E.M., and Delwiche, C.F. (2004). Dinoflagellate expressed sequence tag data indicate massive transfer of chloroplast genes to the nuclear genome. Protist 155, 65-78.
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Beachy, R.N. (2004). Continuing the effort. AgBioForum 7, 1
Bennett, J.O., Yu, O., Heatherly, L.G., and Krishnan, H.B. (2004). Accumulation of genistein and daidzein, soybean isoflavones implicated in promoting human health, is significantly elevated by irrigation. J Agric Food Chem 52, 7574-7579.
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Berg, R.H. (2004). Evaluation of spectral imaging for plant cell analysis. J Microsc 214, 174-181.
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Berry, S.D., Fondong, V.N., Rey, C., Rogan, D., Fauquet, C.M., and Brown, J.K. (2004). Molecular evidence for five distinct Bemisia tabaci (Homoptera: Aleyrodidae) geographic haplotypes associated with cassava plants in sub-Saharan Africa. Ann Entomol Soc of Am 97, 852-859
Brill, L.M., Dechongkit, S., DeLaBarre, B., Stroebel, J., Beachy, R.N., and Yeager, M. (2004). Dimerization of recombinant TMV movement protein. J Virol 78, 3372-3377.
| PubMed |
Chellappan, P., Masona, M.V., Vanitharani, R., Taylor, N.J., and Fauquet, C.M. (2004). Broad spectrum resistance to ssDNA viruses associated with transgene-induced gene silencing in cassava. Plant Mol Biol 56, 601-611.
| PubMed |
Chellappan, P., Vanitharani, R., Pita, J., and Fauquet, C.M. (2004). Short interfering RNA accumulation correlates with host recovery in DNA virus-infected hosts, and gene silencing targets specific viral sequences. J Virol 78, 7465-7477.
| PubMed |
Clifton, S.W., Minx, P., Fauron, C.M., Gibson, M., Allen, J.O., Sun, H., Thompson, M., Barbazuk, W.B., Kanuganti, S., Tayloe, C., Meyer, L., Wilson, R.K., and Newton, K.J. (2004). Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136, 3486-3503.
| PubMed |
Cui, X., Tao, X., Xie, Y., Fauquet, C.M., and Zhou, X. (2004). A DNAbeta associated with Tomato yellow leaf curl China virus is required for symptom induction. J Virol 78, 13966-13974.
| PubMed |
Dai, S., Zhang, Z., Chen, S., and Beachy, R.N. (2004). RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease. Proc Natl Acad Sci U S A 101, 687-692.
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de Villiers, E.M., Fauquet, C., Broker, T.R., Bernard, H.U., and zur Hausen, H. (2004). Classification of papillomaviruses. Virology 324, 17-27.
| PubMed |
Fargette, D., Pinel, A., Abubakar, Z., Traore, O., Brugidou, C., Fatogoma, S., Hebrard, E., Choisy, M., Sere, Y., Fauquet, C., and Konate, G. (2004). Inferring the evolutionary history of rice yellow mottle virus from genomic, phylogenetic, and phylogeographic studies. J Virol 78, 3252-3261.
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Fauquet, C.M. (2004). Viral classification and nomenclature. In Encyclopedia of Life Sciences (London John Wiley & Sons). DOI: 10.1038/npg.els.0004323
Fauquet, C.M. (2004). Family Geminiviridae. In Viruses and virus diseases of Poaceae (Gramineae), H. Lapierre and P.-A. Signoret, eds (Versailles, France: INRA Editions), p. 304-312.
Fauquet, C.M., and Tohme, J. (2004). The global cassava partnership for genetic improvement. Plant Mol Biol 56, v-x.
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Fofana, I.B., Sangare, A., Collier, R., Taylor, C., and Fauquet, C.M. (2004). A geminivirus-induced gene silencing system for gene function validation in cassava. Plant Mol Biol 56, 613-624.
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Herman, E. (2004). Allergenic responses to legume proteins. In Genomics for Legume Crops, E. Brummer and R. Wilson, eds (Urbana,
IL: AOCS Press), pp. 326-347.
Herman, E. (2004). The process of accumulation of seed proteins and the prospects of using biotechnology to improve crops. . In Handbook of Seed Science and Technology, A. Basra, ed (Philadelphia: Haworth Press), pp. 195-225.
Herman, E. (2004). Characterization and elimination of an immunodominant soybean allergen. Crop Sci 45, 462-467
Herman, E., and Schmidt, M. (2004). Endoplasmic reticulum to vacuole trafficking of endoplasmic reticulum bodies provides an alternate pathway for protein transfer to the vacuole. Plant Physiol 136, 3440-3446.
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Hossain, T., Rosenberg, I., Selhub, J., Kishore, G.M., Beachy, R.N., and Schubert, K.R. (2004). Enhancement of folates in plants through metabolic engineering Proc Natl Acad Sci U S A 101, 5158-5163.
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Jez, J.M., Cahoon, R.E., and Chen, S. (2004). Arabidopsis thaliana glutamate-cysteine ligase: functional properties, kinetic mechanism, and regulation of activity. J Biol Chem 279, 33463-33470.
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Kawakami, S., Watanabe, Y., and Beachy, R.N. (2004). Tobacco mosaic virus infection spreads cell to cell as intact replication complexes. Proc Natl Acad Sci U S A 101, 6291-6296.
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Ke, J., Schmidt, T., Chase, E., Bozarth, R.F., and Smith, T.J. (2004). Structure of Cowpea mottle virus: a consensus in the genus Carmovirus. Virology 321, 349-358.
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Koo, J.C., Asurmendi, S., Bick, J., Woodford-Thomas, T., and Beachy, R.N. (2004). Ecdysone agonist-inducible expression of a coat protein gene from tobacco mosaic virus confers viral resistance in transgenic Arabidopsis. Plant J 37, 439-448.
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Legg, J.P., and Fauquet, C.M. (2004). Cassava mosaic geminiviruses in Africa. Plant Mol Biol 56, 585-599.
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Li, W., Li, M., Zhang, W., Welti, R., and Wang, X. (2004). The plasma membrane-bound phospholipase Dd enhances freezing tolerance in Arabidopsis thaliana. Nat Biotechnol 22, 427-433.
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Pappan, K., Zheng, L., Krishnamoorthi, R., and Wang, X. (2004). Evidence for and characterization of Ca2+ binding to the catalytic region of Arabidopsis thaliana phospholipase Db. J Biol Chem 279, 47833-47839.
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Preuss, M.L., Serna, J., Falbel, T.G., Bednarek, S.Y., and Nielsen, E. (2004). The Arabidopsis Rab GTPase RabA4b localizes to the tips of growing root hair cells. Plant Cell 16, 1589-1603.
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Ramesh, S.A., Choimes, S., and Schachtman, D.P. (2004). Over-expression of an Arabidopsis zinc transporter in hordeum vulgare increases short-term zinc uptake after zinc deprivation and seed zinc content. Plant Mol Biol 54, 373-385.
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Running, Mark P. (2004). Flowering Plant Embryology: With Emphasis on Economic Species. By Nels R Lersten. Q Rev Biol 79, 428-428.
| Open Access – Abstract |
Running, M.P., Lavy, M., Sternberg, H., Galichet, A., Gruissem, W., Hake, S., Ori, N., and Yalovsky, S. (2004). Enlarged meristems and delayed growth in plp mutants result from lack of CaaX prenyltransferases. Proc Natl Acad Sci U S A 101, 7815-7820.
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Shin, R., and Schachtman, D.P. (2004). Hydrogen peroxide mediates plant root cell response to nutrient deprivation. Proc Natl Acad Sci U S A 101, 8827-8832.
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Smith, T.J. (2004). MolViewX: a molecular visualization program for the Macintosh OS X system. J Appl Cryst 37, 654-657
Spelbrink, R.G., Dilmac, N., Allen, A., Smith, T.J., Shah, D.M., and Hockerman, G.H. (2004). Differential antifungal and calcium channel-blocking activity among structurally related plant defensins. Plant Physiol 135, 2055-2067.
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Springer, N.M., Xu, X., and Barbazuk, W.B. (2004). Utility of different gene enrichment approaches toward identifying and sequencing the maize gene space. Plant Physiol 136, 3023-3033.
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Subramanian, S., Hu, X., Lu, G., Odelland, J.T., and Yu, O. (2004). The promoters of two isoflavone synthase genes respond differentially to nodulation and defense signals in transgenic soybean roots. Plant Mol Biol 54, 623-639.
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Subramanian, S., Xu, L., Lu, G., Odell, J., and Yu, O. (2004). The promoters of the isoflavone synthase genes respond differentially to nodulation and defense signals in transgenic soybean roots. Plant Mol Biol 54, 623-639
Taylor, N., Kent, L., and Fauquet, C. (2004). Progress and challenges for the deployment of transgenic technologies in cassava. AgBioForum 7, 51-56.
| Open Access – Full |
Taylor, N., Kent, L., and Fauquet, C. (2004). Special issue: Progress, achievements and constraints for plant biotechnology in developing countries. In AgBioForum, N. Taylor, L. Kent, and C. Fauquet, eds (Columbia, MO: University of Missouri-Columbia), pp. 1-95.
Taylor, N.J., Chavarriaga, P., Raemakers, K., Siritunga, D., and Zhang, P. (2004). Development and application of transgenic technologies in cassava. Plant Mol Biol 56, 671-688.
| PubMed |
Vanitharani, R., Chellappan, P., and Fauquet, C.M. (2004). RNAi and gene silencing phenomena mediated by viral suppressors in plants. In RNA Interference Technology: From Basic Science to Drug Development, K. Appasani, ed (Cambridge, UK: Cambridge University), pp. 280-302.
Vanitharani, R., Chellappan, P., Pita, J.S., and Fauquet, C.M. (2004). Differential roles of AC2 and AC4 of cassava geminiviruses in mediating synergism and suppression of posttranscriptional gene silencing. J Virol 78, 9487-9498.
| PubMed |
Voloudakis, A.E., Malpica, C.A., Aleman-Verdaguer, M.E., Stark, D.M., Fauquet, C.M., and Beachy, R.N. (2004). Structural characterization of Tobacco etch virus coat protein mutants. Arch Virol 149, 699-712.
| PubMed |
Wang, X. (2004). Lipid signaling. Curr Opin Plant Biol 7, 329-336.
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Welti, R., and Wang, X. (2004). Lipid species profiling: a high-throughput approach to identify lipid compositional changes and determine the function of genes involved in lipid metabolism and signaling. Curr Opin Plant Biol 7, 337-344.
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Xiong, L., Lee, H., Huang, R., and Zhu, J.K. (2004). A single amino acid substitution in the Arabidopsis FIERY1/HOS2 protein confers cold signaling specificity and lithium tolerance. Plant J 40, 536-545.
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Zhang, W., Qin, C., Zhao, J., and Wang, X. (2004). Phospholipase Da1-derived phosphatidic acid interacts with ABI1 phosphatase 2C and regulates abscisic acid signaling. Proc Natl Acad Sci U S A 101, 9508-9513.
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Zhao, J., and Wang, X. (2004). Arabidopsis phospholipase Da1 interacts with the heterotrimeric G-protein a-subunit through a motif analogous to the DRY motif in G-protein-coupled receptors. J Biol Chem 279, 1794-1800.
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2003 Publications TOP
Atkinson, R.C., Beachy, R.N., Conway, G., Cordova, F.A., Fox, M.A., Holbrook, K.A., Klessig, D.F., McCormick, R.L., McPherson, P.M., Rawlings, H.R., 3rd, Rapson, R., Vanderhoef, L.N., Wiley, J.D., and Young, C.E. (2003). Public sector collaboration for agricultural IP management. Science 301, 174-175.
| PubMed |
Banerjee, S., Schmidt, T., Fang, J., Stanley, C.A., and Smith, T.J. (2003). Structural studies on ADP activation of mammalian glutamate dehydrogenase and the evolution of regulation. Biochemistry 42, 3446-3456.
| PubMed |
Banerjee, S., Wei, B., Bhattacharyya-Pakrasi, M., Pakrasi, H.B., and Smith, T.J. (2003). Structural determinants of metal specificity in the zinc transport protein ZnuA from synechocystis 6803. J Mol Biol 333, 1061-1069.
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Beachy, R.N. (2003). IP policies and serving the public. Science 299, 473.
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Chakraborty, S., Pandey, P.K., Banerjee, M.K., Kalloo, G., and Fauquet, C.M. (2003). A new begomovirus species causing tomato leaf curl disease in Varanasi, India. Plant Disease 87, 313-313
Chakraborty, S., Pandey, P.K., Banerjee, M.K., Kalloo, G., and Fauquet, C.M. (2003). Tomato leaf curl Gujarat virus, a New Begomovirus Species Causing a Severe Leaf Curl Disease of Tomato in Varanasi, India. Phytopathology 93, 1485-1495.
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Dai, S., Petruccelli, S., Ordiz, M.I., Zhang, Z., Chen, S., and Beachy, R.N. (2003). Functional analysis of RF2a, a rice transcription factor. J Biol Chem 278, 36396-36402.
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Dwivedi, R.S., Breiman, A., and Herman, E.M. (2003). Differential distribution of the cognate and heat-stress-induced isoforms of high Mr cis-trans prolyl peptidyl isomerase (FKBP) in the cytoplasm and nucleoplasm. J Exp Bot 54, 2679-2689.
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Fauquet, C.M., Bisaro, D.M., Briddon, R.W., Brown, J.K., Harrison, B.D., Rybicki, E.P., Stenger, D.C., and Stanley, J. (2003). Revision of taxonomic criteria for species demarcation in the family Geminiviridae, and an updated list of begomovirus species. Arch Virol 148, 405-421.
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Fauquet, C.M., and Stanley, J. (2003). Geminivirus classification and nomenclature: progress and problems. Ann Appl Biol 142, 165-189
Fofana, I.B.F., Sangaré, A., Ndunguru, J., Kahn, K., and Fauquet, C.M. (2003). Principles for control of virus diseases in developing countries. In Virus and virus-like diseases of major crops in developing countries, G. Loebenstein and G. Thottappilly, eds (Dordrecht,
the Netherlands: Kluwer Academic Publishers), pp. 31-54.
Herman, E.M. (2003). Genetically modified soybeans and food allergies. J Exp Bot 54, 1317-1319.
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Herman, E.M., Helm, R.M., Jung, R., and Kinney, A.J. (2003). Genetic modification removes an immunodominant allergen from soybean. Plant Physiol 132, 36-43.
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Hinz, G., and Herman, E. (2003). Sorting of storage proteins in the plant Golgi apparatus. In The Golgi apparatus and the plant secretory pathway. Annual Plant Reviews, D. Robinson, ed (Oxford: Blackwell Publishing), pp. 141-164.
Jaworski, J., and Cahoon, E.B. (2003). Industrial oils from transgenic plants. Curr Opin Plant Biol 6, 178-184.
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Kusner, D.J., Barton, J.A., Qin, C., Wang, X., and Iyer, S.S. (2003). Evolutionary conservation of physical and functional interactions between phospholipase D and actin. Arch Biochem Biophys 412, 231-241.
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Lotrakul, P., Valverde, R.A., Clark, C.A., and Fauquet, C.M. (2003). Properties of a begomovirus isolated from sweet potato [Ipomoea batatas (L.) Lam.] infected with sweet potato leaf curl virus. Rev Mex Fitopatol 21, 128-136.
Lu, H., and Skolnick, J. (2003). Application of statistical potentials to protein structure refinement from low resolution ab initio models. Biopolymers 70, 575-584.
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Maggio, A., Bressan, R.A., Ruggiero, C., Xiong, L., and Grub, S. (2003). Salt Tolerance: Placing Advances in Molecular Genetics into a Physiological and Agronomic Context. In Abiotic Stresses in Plants., L. Sanità di Toppi and B. Pawlik-Skowronska, eds (Dordrecht, The Netherlands: Springer), pp. 53-69.
Mansoor, S., Briddon, R.W., Bull, S.E., Bedford, I.D., Bashir, A., Hussain, M., Saeed, M., Zafar, Y., Malik, K.A., Fauquet, C., and Markham, P.G. (2003). Cotton leaf curl disease is associated with multiple monopartite begomoviruses supported by single DNA beta. Arch Virol 148, 1969-1986.
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Mayo, M.A., Fauquet, C.M., and Maniloff, J. (2003). Taxonomic proposals on the Web: new ICTV consultative procedures. Arch Virol 148, 609-611.
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Mendez-Lozano, J., Torres-Pacheco, I., Fauquet, C.M., and Rivera-Bustamante, R.F. (2003). Interactions between Geminiviruses in a naturally occurring mixture: Pepper huasteco virus and Pepper golden mosaic virus. Phytopathology 93, 270-277.
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Mpelasoka, B.S., Schachtman, D.P., Treeby, M.T., and Thomas, M.R. (2003). A review of potassium nutrition in grapevines with special emphasis on berry accumulation. Aust J Grape and Wine Res 9, 154-168
Pokarowski, P., Kolinski, A., and Skolnick, J. (2003). A minimal physically realistic protein-like lattice model: designing an energy landscape that ensures all-or-none folding to a unique native state. Biophys J 84, 1518-1526.
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Ramesh, S.A., Shin, R., Eide, D.J., and Schachtman, D.P. (2003). Differential metal selectivity and gene expression of two zinc transporters from rice. Plant Physiol 133, 126-134.
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Reisdorph, N., Thomas, J.J., Katpally, U., Chase, E., Harris, K., Siuzdak, G., and Smith, T.J. (2003). Human rhinovirus capsid dynamics is controlled by canyon flexibility. Virology 314, 34-44.
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Schachtman, D.P., and Thomas, M.R. (2003). A rapid method for generating sufficient amounts of uniform genotype-specific material from woody perennials such as grapevine for ion transport studies. Plant Soil 263, 195-199
Smith, T.J. (2003). Structural studies on antibody-virus complexes. Adv Protein Chem 64, 409-453.
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Storey, R., Schachtman, D.P., and Thomas, M.R. (2003). Root structure and cellular chloride, sodium and potassium distribution in salinized grapevines. Plant Cell Environ 26, 789-800.
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Storey, R., Wyn Jones, R.G., Schachtman, D.P., and Treeby, M.T. (2003). Calcium accumulating cells in the meristematic region of grapevine root apices. Funct Plant Biol 30, 719-727
Vanitharani, R., Chellappan, P., and Fauquet, C.M. (2003). Short interfering RNA-mediated interference of gene expression and viral DNA accumulation in cultured plant cells. Proc Natl Acad Sci U S A 100, 9632-9636.
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Vernoud, V., Horton, A.C., Yang, Z., and Nielsen, E. (2003). Analysis of the small GTPase gene superfamily of Arabidopsis. Plant Physiol 131, 1191-1208.
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Welti, R., Wang, X., and Williams, T.D. (2003). Electrospray ionization tandem mass spectrometry scan modes for plant chloroplast lipids. Anal Biochem 314, 149-152.
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Whitelaw, C.A., Barbazuk, W.B., Pertea, G., Chan, A.P., Cheung, F., Lee, Y., Zheng, L., van Heeringen, S., Karamycheva, S., Bennetzen, J.L., SanMiguel, P., Lakey, N., Bedell, J., Yuan, Y., Budiman, M.A., Resnick, A., Van Aken, S., Utterback, T., Riedmuller, S., Williams, M., Feldblyum, T., Schubert, K., Beachy, R., Fraser, C.M., and Quackenbush, J. (2003). Enrichment of gene-coding sequences in maize by genome filtration. Science 302, 2118-2120.
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Xiong, L., and Zhu, J.K. (2003). Regulation of abscisic acid biosynthesis. Plant Physiol 133, 29-36.
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Yu, O., Shi, J., Hession, A.O., Maxwell, C.A., McGonigle, B., and Odell, J.T. (2003). Metabolic engineering to increase isoflavone biosynthesis in soybean seed. Phytochemistry 63, 753-763.
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Zhou, X., Xie, Y., Tao, X., Zhang, Z., Li, Z., and Fauquet, C.M. (2003). Characterization of DNAbeta associated with begomoviruses in China and evidence for co-evolution with their cognate viral DNA-A. J Gen Virol 84, 237-247.
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2002 Publications TOP
Beachy, R.N., and Ordiz, M.I. (2002). The fingers of gene regulation in plants. ISB News Report Dec 2002, 5-6
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Bendahmane, M., Szecsi, J., Chen, I., Berg, R.H., and Beachy, R.N. (2002). Characterization of mutant tobacco mosaic virus coat protein that interferes with virus cell-to-cell movement. Proc Natl Acad Sci U S A 99, 3645-3650.
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Bowman, V.D., Chase, E.S., Franz, A.W., Chipman, P.R., Zhang, X., Perry, K.L., Baker, T.S., and Smith, T.J. (2002). An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons. J Virol 76, 12250-12258.
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Brugidou, C., Opalka, N., Yeager, M., Beachy, R.N., and Fauquet, C. (2002). Stability of Rice Yellow Mottle Virus and cellular compartmentalization during the infection process in Oryza sativa (L.). Virology 297, 98-108.
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Fang, J., Hsu, B.Y., MacMullen, C.M., Poncz, M., Smith, T.J., and Stanley, C.A. (2002). Expression, purification and characterization of human glutamate dehydrogenase (GDH) allosteric regulatory mutations. Biochem J 363, 81-87.
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Fargette, D., Pinel, A., Halimi, H., Brugidou, C., Fauquet, C., and Van, R.M. (2002). Comparison of molecular and immunological typing of isolates of Rice yellow mottle virus. Arch Virol 147, 583-596.
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Fauquet, C.M., and Taylor, N. (2002). The potential for biotechnology to improve the nutritional value of cassava. Food Nutr Bull 23, 364-366.
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Fetrow, J.S., Giammona, A., Kolinski, A., and Skolnick, J. (2002). The protein folding problem: a biophysical enigma. Curr Pharm Biotechnol 3, 329-347.
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Gage, M.J., Rane, S.G., Hockerman, G.H., and Smith, T.J. (2002). The virally encoded fungal toxin KP4 specifically blocks L-type voltage-gated calcium channels. Mol Pharmacol 61, 936-944.
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Helm, R., Burkes, W., and Herman, E. (2002). Hypoallergenic foods- Soybeans and peanuts. ISB News Report Oct 2002, 3-5.
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Kihara, D., Zhang, Y., Lu, H., Kolinski, A., and Skolnick, J. (2002). Ab initio protein structure prediction on a genomic scale: application to the Mycoplasma genitalium genome. Proc Natl Acad Sci U S A 99, 5993-5998.
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Lu, L., Lu, H., and Skolnick, J. (2002). MULTIPROSPECTOR: an algorithm for the prediction of protein-protein interactions by multimeric threading. Proteins 49, 350-364.
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Mayo, M.A., Maniloff, J., Regenmortel, M.H.V.v., and Fauquet, C.M. (2002). The type species in virus taxonomy. Arch Virol 147, 1271-1274
Munns, R., Husain, S., Rivelli, A.R., James, R., Condon, A.G., Lindsay, M., Lagudah, E., Schachtman, D.P., and Hare, R. (2002). Avenues for increasing salt tolerance of crops, and the role of physiologically-based selection traits. Plant and Soil 247, 93-105
Nielsen, N., and Herman, E. (2002). The future prospects for broadening soybean utilization by altering glycinin. In Plant Biopolymer Science, D. Renard, G. G.D Valle, and Y. Popineau, eds (London: RSC Publishing), pp. 13-23.
Okinaka, Y., Yang, C.H., Herman, E., Kinney, A., and Keen, N.T. (2002). The P34 syringolide elicitor receptor interacts with a soybean photorespiration enzyme, NADH-dependent hydroxypyruvate reductase. Mol Plant Microbe Interact 15, 1213-1218.
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Ordiz, M.I., Barbas, C.F., 3rd, and Beachy, R.N. (2002). Regulation of transgene expression in plants with polydactyl zinc finger transcription factors. Proc Natl Acad Sci U S A 99, 13290-13295.
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Running, Mark P. (2002). Developmental Biology of Flowering Plants. By V Raghavan. The Q Rev Biol 77, 204-205.
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Running, M.P. (2002). Nuclear Staining for Confocal Microscopy. In Arabidopsis: A Laboratory Manual, D. Weigel and J. Glazebrook, eds (Cold Spring Harbor, N.Y.: Cold Spring Harbor Laboratory Press), pp. 100-103.
Sikorski, A., Kolinski, A., and Skolnick, J. (2002). Computer simulations of protein folding with a small number of distance restraints. Acta Biochim Pol 49, 683-692.
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Skolnick, J., and Kolinski, A. (2002). A unified approach to the prediction of protein structure and function. Adv Chem Phys 120, 131-192
Smith, T.J. (2002). Antibody recognition of human rhinovirus. In Molecular Biology of Picornaviruses, E. Wimmer and B. Semler, eds (Washington DC: ASM Press), pp. 39-49.
Smith, T.J., Schmidt, T., Fang, J., Wu, J., Siuzdak, G., and Stanley, C.A. (2002). The structure of apo human glutamate dehydrogenase details subunit communication and allostery. J Mol Biol 318, 765-777.
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Stege, J.T., Guan, X., Ho, T., Beachy, R.N., and Barbas, C.F., 3rd. (2002). Controlling gene expression in plants using synthetic zinc finger transcription factors. Plant J 32, 1077-1086.
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Taylor, N., Masona, M.V., Schöpke, C., and Fauquet, C.M. (2002). Transgenic cassava for food security and economic development. In Transgenic Plants and Crops, G. Khachatourians, ed (New York: Marcel Dekker), pp. 523-546.
Taylor, N.J., and Fauquet, C.M. (2002). Microparticle bombardment as a tool in plant science and agricultural biotechnology. In DNA
and Cell Biology (Larchmont, NY: Mary Ann Liebert, Inc.), pp. 963-977.
van Regenmortel, M.H.V., and Fauquet, C.M. (2002). Only italicised species names of viruses have a taxonomic meaning. Arch Virol 147, 2247-2250.
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van Regenmortel, M.H.V., and Fauquet, C.M. (2002). Utilisation d’un système binomial pour les noms d’espèces virales. Qu’en pense la communauté des virologues? Virologie 6, 70-73.
Vinals, J., Kolinski, A., and Skolnick, J. (2002). Numerical study of the entropy loss of dimerization and the folding thermodynamics of the GCN4 leucine zipper. Biophys J 83, 2801-2811.
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Wojciechowski, M., and Skolnick, J. (2002). Docking of small ligands to low-resolution and theoretically predicted receptor structures. J Comput Chem 23, 189-197.
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Zhang, Y., Kihara, D., and Skolnick, J. (2002). Local energy landscape flattening: parallel hyperbolic Monte Carlo sampling of protein folding. Proteins 48, 192-201.
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Zhu, Q., Ordiz, M.I., Dabi, T., Beachy, R.N., and Lamb, C. (2002). Rice TATA binding protein interacts functionally with transcription factor IIB and the RF2a bZIP transcriptional activator in an enhanced plant in vitro transcription system. Plant Cell 14, 795-803.
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2001 TOP
Betancourt, M., and Skolnick, J. (2001). Finding the needle in the haystack: Educing native folds from ambiguous ab initio protein structure predictions. J Comput Chem 22, 339-353
Betancourt, M.R., and Skolnick, J. (2001). Universal similarity measure for comparing protein structures. Biopolymers 59, 305-309.
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Bigarre, L., Chazly, M., Salah, M., Ibrahim, M., Padidam, M., Nicole, M., Peterschmitt, M., Fauquet, C., and Thouvenel, J.C. (2001). Characterization of a new begomovirus from Egypt infecting hollyhock (Althea rosea). Eur J Plant Pathol 107, 701-711
Broo, K., Wei, J., Marshall, D., Brown, F., Smith, T.J., Johnson, J.E., Schneemann, A., and Siuzdak, G. (2001). Viral capsid mobility: a dynamic conduit for inactivation. Proc Natl Acad Sci U S A 98, 2274-2277.
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Bukhman, Y.V., and Skolnick, J. (2001). BioMolQuest: integrated database-based retrieval of protein structural and functional information. Bioinformatics 17, 468-478.
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Chatterji, A., Beachy, R.N., and Fauquet, C.M. (2001). Expression of the oligomerization domain of the replication-associated protein (Rep) of Tomato leaf curl New Delhi virus interferes with DNA accumulation of heterologous geminiviruses. J Biol Chem 276, 25631-25638.
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Dai, S., Carcamo, R., Zhang, Z., Chen, S., and Beachy, R.N. (2001). Bacterial cytosine deaminase gene used as a conditional negative selection marker in transgenic rice plants. Plant Cell Rep 20, 738-743
Dai, S., Zheng, P., Marmey, P., Zhang, S., Tian, W., Chen, S., Beachy, R.N., and Fauquet, C. (2001). Comparative analysis of transgenic rice plants obtained by Agrobaterium-mediated transformation and particle bombardment. Mol Breed 7, 25-33
Dai, S., Zheng, P., Marmey, P., Zhang, S., Tian, W., Chen, S., Beachy, R.N., and Fauquet, C. (2001). Comparative analysis of transgenic rice plants obtained by Agrobacterium-mediated transformation and particle bombardment. Mol Breed, 25-33
Di Gennaro, J.A., Siew, N., Hoffman, B.T., Zhang, L., Skolnick, J., Neilson, L.I., and Fetrow, J.S. (2001). Enhanced functional annotation of protein sequences via the use of structural descriptors. J Struct Biol 134, 232-245.
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Fauquet, C.M. (2001). Viral classification and nomenclature. In Encyclopedia of Life Sciences (London: Nature Publishing Group).
Fauquet, C.M., and Mayo, M.A. (2001). The 7th ICTV Report. Arch Virol 146, 189-194.
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Fetrow, J.S., Siew, N., Di Gennaro, J.A., Martinez-Yamout, M., Dyson, H.J., and Skolnick, J. (2001). Genomic-scale comparison of sequence- and structure-based methods of function prediction: does structure provide additional insight? Protein Sci 10, 1005-1014.
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Gage, M.J., Bruenn, J., Fischer, M., Sanders, D., and Smith, T.J. (2001). KP4 fungal toxin inhibits growth in Ustilago maydis by blocking calcium uptake. Mol Microbiol 41, 775-785.
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Gandikota, M., de Kochko, A., Chen, L., Ithal, N., Fauquet, C., and Reddy, A.R. (2001). Development of transgenic rice plants expressing maize anthocyanin genes and increased blast resistance. Mol Breed 7, 73-83
Gront, D., Kolinski, A., and Skolnick, J. (2001). A new combination of replica exchange Monte Carlo and histogram analysis for protein folding and thermodynamics. J Comput Phys 115, 1569-1574
Herman, E.M. (2001). A career as a U.S. Department of Agriculture-Agricultural Research Service scientist. Plant Physiol 127, 707-708.
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Kihara, D., Lu, H., Kolinski, A., and Skolnick, J. (2001). TOUCHSTONE: an ab initio protein structure prediction method that uses threading-based tertiary restraints. Proc Natl Acad Sci U S A 98, 10125-10130.
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Kinney, A.J., Jung, R., and Herman, E.M. (2001). Cosuppression of the alpha subunits of beta-conglycinin in transgenic soybean seeds induces the formation of endoplasmic reticulum-derived protein bodies. Plant Cell 13, 1165-1178.
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Kolinski, A., Betancourt, M.R., Kihara, D., Rotkiewicz, P., and Skolnick, J. (2001). Generalized comparative modeling (GENECOMP): a combination of sequence comparison, threading, and lattice modeling for protein structure prediction and refinement. Proteins 44, 133-149.
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Kotlizky, G., Katz, A., van der Laak, J., Boyko, V., Lapidot, M., Beachy, R.N., Heinlein, M., and Epel, B.L. (2001). A dysfunctional movement protein of tobacco mosaic virus interferes with targeting of wild-type movement protein to microtubules. Mol Plant Microbe Interact 14, 895-904.
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Lu, H., and Skolnick, J. (2001). A distance-dependent atomic knowledge-based potential for improved protein structure selection. Proteins 44, 223-232.
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MacMullen, C., Fang, J., Hsu, B.Y., Kelly, A., de Lonlay-Debeney, P., Saudubray, J.M., Ganguly, A., Smith, T.J., and Stanley, C.A. (2001). Hyperinsulinism/hyperammonemia syndrome in children with regulatory mutations in the inhibitory guanosine triphosphate-binding domain of glutamate dehydrogenase. J Clin Endocrinol Metab 86, 1782-1787.
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Madhuri, G., Kochko, A.d., Chen, L., Nagabhushana, I., Fauquet, C., and Reddy, A.R. (2001). Development of transgenic rice plants expressing maize anthocyanin genes and increased blast resistance. Mol Breed 7, 73-83
Masona, M.V., Taylor, N.J., Robertson, A.I., and Fauquet, C.M. (2001). Transferring a cassava (Manihot esculenta Crantz) genetic engineering capability to the African environment: progress and prospects. Euphytica 120, 43-48.
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Mendez-Lozano, J., Rivera-Bustamante, R.F., Fauquet, C.M., and Torre-Almaraz, R.d.l. (2001). Pepper huasteco virus and pepper golden mosaic virus are geminiviruses affecting tomatillo (Physalis ixocarpa) crops in Mexico. Plant Disease 85, 1291-1291
Ndjiondjop, M.N., Brugidou, C., Zang, S., Fargette, D., Ghesquiere, A., and Fauquet, C. (2001). High resistance to rice yellow mottle virus in two cultivated rice cultivars is correlated with failure of cell to cell movement. Physiol
Mol Plant Pathol 59, 309-316.
Petruccelli, S., Dai, S., Carcamo, R., Yin, Y., Chen, S., and Beachy, R.N. (2001). Transcription factor RF2a alters expression of the rice tungro bacilliform virus promoter in transgenic tobacco plants. Proc Natl Acad Sci U S A 98, 7635-7640.
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Pita, J.S., Fondong, V.N., Sangaré, A., Kokora, R.N.N., and Fauquet, C.M. (2001). Genomic and biological diversity of the African cassava geminiviruses. Euphytica 120, 115-125
Pita, J.S., Fondong, V.N., Sangare, A., Otim-Nape, G.W., Ogwal, S., and Fauquet, C.M. (2001). Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J Gen Virol 82, 655-665.
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Shy. G, Ehler. L, E, H., and G, G. (2001). Expression patterns of genes encoding endomembrane proteins support a reduced function of the Golgi in wheat endosperm during the onset of storage protein deposition. J Exp Bot 52, 707-708
Skolnick, J., and Kihara, D. (2001). Defrosting the frozen approximation: PROSPECTOR--a new approach to threading. Proteins 42, 319-331.
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Skolnick, J., and Kolinski, A. (2001). Computional studies of protein folding. Comput Sci Eng 3, 40-50
Skolnick, J., Kolinski, A., Kihara, D., Betancourt, M., Rotkiewicz, P., and Boniecki, M. (2001). Ab initio protein structure prediction via a combination of threading, lattice folding, clustering, and structure refinement. Proteins Suppl 5, 149-156.
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Smith, T.J. (2001). Antibody interactions with rhinovirus: lessons for mechanisms of neutralization and the role of immunity in viral evolution. Curr Top Microbiol Immunol 260, 1-28.
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Smith, T.J., Peterson, P.E., Schmidt, T., Fang, J., and Stanley, C.A. (2001). Structures of bovine glutamate dehydrogenase complexes elucidate the mechanism of purine regulation. J Mol Biol 307, 707-720.
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Taylor, N.J., Masona, M.V., Carcamo, R., Ho, T., Schöpke, C., and Fauquet, C.M. (2001). Production of embryogenic tissues and regeneration of transgenic plants in cassava (Manihot esculenta Crantz). Euphytica 120, 25-34
Wu, J.D., Yang, J.B., Xu, C.W., Li, L., Xiang, T.H., Ni, D.F., Wang, X.F., Jia, S.R., Tang, Y.X., Zhang, S., and Fauquet, C.M. (2001). Study on resistance gene to Bacterial Blight Xa21 transgenic rice and their hybrid combinations. Acta Agronomica Sinica 27, 29-34.
Zhang, Y., and Skolnick, J. (2001). Parallel-hat tempering: A Monte Carlo search scheme for the identification of low-energy structures. J Chem Physics 115, 5027-5032
2000 TOP
Beachy, R.N., and Heinlein, M. (2000). Role of P30 in replication and spread of TMV. Traffic 1, 540-544.
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Chatterji, A., Chatterji, U., Beachy, R.N., and Fauquet, C.M. (2000). Sequence parameters that determine specificity of binding of the replication-associated protein to its cognate site in two strains of tomato leaf curl virus-New Delhi. Virology 273, 341-350.
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Chatterji, A., and Fauquet, C.M. (2000). Ecology of plant viruses with special reference to whitefly transmitted geminiviruses (WTGs). In Viral Ecology, C.J. Hurst, ed (New York: Academic Press), pp. 322-352.
Fauquet, C.M., Maxwell, D.P., Gronenborn, B., and Stanley, J. (2000). Revised proposal for naming geminiviruses. Arch Virol 145, 1743-1761.
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Fauquet, C.M., and Pringle, C.R. (2000). Abbreviations for bacterial and fungal virus species names. Arch Virol 145, 197-203.
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Feig, M., Rotkiewicz, P., Kolinski, A., Skolnick, J., and Brooks, C.L., 3rd. (2000). Accurate reconstruction of all-atom protein representations from side-chain-based low-resolution models. Proteins 41, 86-97.
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Fondong, V.N., Pita, J.S., Rey, M.E., de Kochko, A., Beachy, R.N., and Fauquet, C.M. (2000). Evidence of synergism between African cassava mosaic virus and a new double-recombinant geminivirus infecting cassava in Cameroon. J Gen Virol 81, 287-297.
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Fondong, V.N., Thresh, J.M., and Fauquet, C. (2000). Field experiments in Cameroon on cassava mosaic virus disease and the reversion phenomenon in susceptible and resistant cassava cultivars. Int J Pest Manag 46, 211-217
Gilleland, H.E., Gilleland, L.B., Staczek, J., Harty, R.N., Garcia-Sastre, A., Palese, P., Brennan, F.R., Hamilton, W.D., Bendahmane, M., and Beachy, R.N. (2000). Chimeric animal and plant viruses expressing epitopes of outer membrane protein F as a combined vaccine against Pseudomonas aeruginosa lung infection. FEMS Immunol Med Microbiol 27, 291-297.
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Gront, D., Kolinski, A., and Skolnick, J. (2000). Comparison of three Monte Carlo conformational search strategies for protein-like polymer models: Identification of low energy structures and folding thermodynamics. J Chem Physics 113, 6065-6071
Ilkowski, B., Skolnick, J., and Kolinski, A. (2000). Helix-coil and beta sheet-coil transitions in a simplified, yet realistic protein model. Macromolecular Theory and Simulations 9, 523-533
Jung, W., Yu, O., Lau, S.M., O'Keefe, D.P., Odell, J., Fader, G., and McGonigle, B. (2000). Identification and expression of isoflavone synthase, the key enzyme for biosynthesis of isoflavones in legumes. Nat Biotechnol 18, 208-212.
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Kolinski, A., Rotkiewicz, P., Ilkowski, B., and Skolnick, J. (2000). Protein folding: Flexible lattice models. Progress of Theoret Phys Suppl 138, 292-300
Kolinski, A., Rotkiewicz, P., and Skolnick, J. (2000). Structure of proteins: New approach to molecular modeling. Pol J Chem 75, 587-599
Mas, P., and Beachy, R.N. (2000). Role of microtubules in the intracellular distribution of tobacco mosaic virus movement protein. Proc Natl Acad Sci U S A 97, 12345-12349.
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Mayo, M.A., and Fauquet, C.M. (2000). The current composition of ICTV. International Committee on Taxonomy of Viruses. Arch Virol 145, 1497-1504.
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Opalka, N., Tihova, M., Brugidou, C., Kumar, A., Beachy, R.N., Fauquet, C.M., and Yeager, M. (2000). Structure of native and expanded sobemoviruses by electron cryo-microscopy and image reconstruction. J Mol Biol 303, 197-211.
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Qu, C., Liljas, L., Opalka, N., Brugidou, C., Yeager, M., Beachy, R.N., Fauquet, C.M., Johnson, J.E., and Lin, T. (2000). 3D domain swapping of a molecular switch for quasi-equivalent symmetry modulates the stability of an icosahedral virus Structure 8, 1095-1103.
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Qu, C., Liljas, L., Opalka, N., Brugidou, C., Yeager, M., Beachy, R.N., Fauquet, C.M., Johnson, J.E., and Lin, T. (2000). 3D domain swapping modulates the stability of members of an icosahedral virus group. Structure 8, 1095-1103.
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Reichel, C., and Beachy, R.N. (2000). Degradation of tobacco mosaic virus movement protein by the 26S proteasome. J Virol 74, 3330-3337.
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Skolnick, J., and Fetrow, J.S. (2000). From genes to protein structure and function: novel applications of computational approaches in the genomic era. Trends Biotechnol 18, 34-39.
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Skolnick, J., Fetrow, J.S., and Kolinski, A. (2000). Structural genomics and its importance for gene function analysis. Nat Biotechnol 18, 283-287.
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Skolnick, J., Kolinski, A., and Ortiz, A. (2000). Derivation of protein-specific pair potentials based on weak sequence fragment similarity. Proteins 38, 3-16.
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Staczek, J., Bendahmane, M., Gilleland, L.B., Beachy, R.N., and Gilleland, H.E., Jr. (2000). Immunization with a chimeric tobacco mosaic virus containing an epitope of outer membrane protein F of Pseudomonas aeruginosa provides protection against challenge with P. aeruginosa. Vaccine 18, 2266-2274.
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Taylor, N.J., and Fauquet, C.M. (2000). Biotechnology’s Greatest Challenge. Forum for Applied Research and Public Policy 15, 51-58
van Regenmortel, M.H.V., Mayo, M.A., and Fauquet, C.M. (2000). Progrès en taxonomie virale. Virologie 4, 29-37
van Regenmortel, M.H.V., Mayo, M.A., Fauquet, C.M., and Maniloff, J. (2000). Virus nomenclature: consensus versus chaos. Arch Virol 145, 2227-2232.
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Yu, O., Jung, W., Shi, J., Croes, R.A., Fader, G.M., McGonigle, B., and Odell, J.T. (2000). Production of the isoflavones genistein and daidzein in non-legume dicot and monocot tissues. Plant Physiol 124, 781-794.
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1999 TOP
Chatterji, A., Padidam, M., Beachy, R.N., and Fauquet, C.M. (1999). Identification of replication specificity determinants in two strains of tomato leaf curl virus from New Delhi. J Virol 73, 5481-5489.
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Fauquet, C.M. (1999). Taxonomy, Classification and Nomenclature of Viruses. In Encyclopedia of Virology (London, U.K.: Academic Press, Harcourt Brace and Co.), pp. 1730-1756.
Fauquet, C.M., and Pringle, C.R. (1999). Abbreviations for invertebrate virus species names. Arch Virol 144, 2265-2271.
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Fauquet, C.M., and Pringle, C.R. (1999). Abbreviations for vertebrate virus species names. Arch Virol 144, 1865-1880.
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Fauquet, M.C., and Mayo, M.A. (1999). Abbreviations for plant virus names--1999. Arch Virol 144, 1249-1273.
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Huet, H., Mahendra, S., Wang, J., Sivamani, E., Ong, C.A., Chen, L., de Kochko, A., Beachy, R.N., and Fauquet, C. (1999). Near immunity to rice tungro spherical virus achieved in rice by a replicase-mediated resistance strategy. Phytopathology 89, 1022-1027.
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Kolinski, A., Rotkiewicz, P., Ilkowski, B., and Skolnick, J. (1999). A method for the improvement of threading-based protein models. Proteins 37, 592-610.
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Liu, D., Zhang, S., Fauquet, C., and Crawford, N.M. (1999). The Arabidopsis transposon Tag1 is active in rice, undergoing germinal transposition and restricted, late somatic excision. Mol Gen Genet 262, 413-420.
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Marmey, P., Bothner, B., Jacquot, E., de Kochko, A., Ong, C.A., Yot, P., Siuzdak, G., Beachy, R.N., and Fauquet, C.M. (1999). Rice tungro bacilliform virus open reading frame 3 encodes a single 37-kDa coat protein. Virology 253, 319-326.
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Ndjiondjop, M.N., Fargette, D., Fauquet, C., and Ghesquiere, A. (1999). The genetic basis of high resistance to rice yellow mottle virus (RYMV) in cultivars of two cultivated rice species. Plant Disease 83, 931-935
Padidam, M., Beachy, R.N., and Fauquet, C.M. (1999). A phage single-stranded DNA (ssDNA) binding protein complements ssDNA accumulation of a geminivirus and interferes with viral movement. J Virol 73, 1609-1616.
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Padidam, M., Reddy, V.S., Beachy, R.N., and Fauquet, C.M. (1999). Molecular characterization of a plant mitochondrial chaperone GrpE. Plant Mol Biol 39, 871-881.
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Padidam, M., Sawyer, S., and Fauquet, C.M. (1999). Possible emergence of new geminiviruses by frequent recombination. Virology 265, 218-225.
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Sangaré, A., Deng, D., Fauquet, C.M., and Beachy, R.N. (1999). Resistance to African cassava mosaic virus conferred by a mutant of the putative NTP-binding domain of the Rep gene (AC1) in Nicotiana benthamiana. Mol Breed 5, 95-102
Schubert, J., Fauquet, C., Merits, A., and Rabenstein, F. (1999). The complete nucleotide sequence of the ryegrass mosaic potyvirus indicates that it is a recombinant between members of two different genera in the family Potyviridae. Z Pflanzenk Pflanzen 106, 392-404
Sivamani, E., Huet, H., Ping, S., Ong, C., Kochko, A.d., Fauquet, C., and Beachy, R.N. (1999). Rice plant (Oryza sativa L.) containing rice tungro spherical virus (RTSV) coat protein transgenes are resistant to virus infection. Mol Breed 5, 177-185
Tao, L., Ling, D., Zhang, S., and Fauquet, C.M. (1999). Gene transformation by particle bombardment in Indica rice and inheritance of the foreign gene in host rice plants. Journal of Wuhan Botanical Research 17, 289-296
Taylor, N.J., Schöpke, C., Masona, M.V., and Fauquet, C.M. (1999). Development of genetic engineering technologies in cassava production. . Biotechnology International, II, 268-275
van Regenmortel, M.H.V., Fauquet, C.M., Bishop, D.H.L., Carstens, E.B., Estes, M.K., Lemon, S., Maniloff, J., Mayo, M.A., McGeoch, D.J., Pringle, C.R., and Wickner, R.B. (1999). Virus Taxonomy: Classification and Nomenclature of Viruses. Seventh Report of the International Committee on Taxonomy of Viruses. (London: Academic Press).
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