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Dr. John AntoniwBioinformatics and plant virology |
 |
| john.antoniw@rothamsted.ac.uk |
Developing databases and software for bioinformatics. Analysis of microarray data from Mycosphaerella graminicola cDNA arrays and Fusarium graminearum affymetrix chips. Annotation of the Fusarium graminearum genome for transcription factors together with Kim Hammond-Kosack and Martin Urban. Developing plant virus genome web databases and PC client software with Mike Adams, and the light leafspot forecast web software with Neal Evans. Developing molecular biology software (e.g. BioLab in The Molecular Biology Notebook with Nathalie Castells-Brooke) for use in education at A-level in schools and undergraduate level at universities.
Here is a list of some my software:
DPV Web
This site provides a comprehensive resource for plant virology including:
Electron micrographs of Plant Viruses
A selection of electron micrographs produced by plant pathologists at Rothamsted.
Light Leafspot Forecast
Prediction of the severity of light leafspot disease on Winter oilseed rape.
The Molecular Biology Notebook
A comprehensive package for the hands-on teaching of Molecular Biology.
OmniMap
Web site about the OmniMap software for displaying and analysing genome features. Although developed for fungal genomes it can be used with any genome without changes to the source code or recompiling. It links chromosome, genetic, transcriptomic, mutation, blast hits and other data.
KEON, J., ANTONIW, J.F., CARZANIGA, R., DELLER, S., WARD, J.L., BAKER, J.M., BEALE, M.H., HAMMOND-KOSACK, K., & RUDD, J. (2007). Transcriptional adaptation of Mycosphaerella graminicola to programmed cell death (PCD) of its susceptible wheat host. Molecular Plant-Microbe Interactions 20, 179-193.
CUOMO, C. A., GÜLDENER, U., XU, J.-U., TRAIL, F., TURGEON, B. G., DI PIETRO, A., WALTON, J. D., MA, L.-J., BAKER, S. E., REP, M., ADAM, A., ANTONIW, J., BALDWIN, T., CALVO, S., CHANG, Y.-L., DECAPRIO, D., GALE, L., GNERRE, S., GOSWAMI, R. S., HAMMOND-KOSACK, K., HARRIS, L. J., HILBURN, K., KENNELL, J., KROKEN, S., MAGNUSON, J. K., MANNHAUPT, G., MAUCELI, E., MEWES, H.-W., MITTERBAUER, R., MUEHLBAUER, G., MÜNSTERKÖTTER, M., NELSON, D., O'DONNELL, K., OUELLET, T., QI, W., QUESNEVILLE, H., RONCERO, M. I. G., SEONG, K.-Y., TETKO, I. V., URBAN, M., WAALWIJK, C., WARD, T., YAO, J., BIRREN, B. W. & KISTLER, H. C. (2007) The genome sequence of F. graminearum reveals localized diversity and pathogen specialization. Science, 317, 1400-1402.
COOLS, H. J., FRAAIJE, B.A., BEAN, T. P., ANTONIW, J. & LUCAS, J. A.(2007). Transcriptome profiling of the response of Mycosphaerella graminicola isolates to an azole fungicide using cDNA microarrays. Molecular Plant Pathology 8, 639-651.
ZHOU, J.-J., KAN, Y., ANTONIW, J., PICKETT, J.A. & FIELD, L.M. (2006) Genome and EST analyses and expression of a gene family with putative functions in insect chemoreception. Chemical Senses 31, 453-466.
LASSO, G., ANTONIW, J.F. & MULLINS, J.G.L. (2006) A combinatorial pattern discovery approach for the prediction of membrane dipping (re-entrant) loops. Bioinformatics 22, e290-e297.
ADAMS, M.J. & ANTONIW, J.F. (2006). DPVweb: a comprehensive database of plant and fungal virus genes and genomes. Nucleic Acids Research 34, Database issue, D382-D385.
ADAMS , M.J., ANTONIW, J.F. & FAUQUET, C.M. (2005). Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology 150, 459-479
KEON, J., ANTONIW, J.F., RUDD, J., SKINNER, W., HARGREAVES, J. & HAMMOND-KOSACK, K.E. (2005). Analysis of expressed sequence tags from the wheat leaf blotch pathogen Mycosphaerella graminicola (anamorph Septoria tritici). Fungal Genetics and Biology 42, 376-389
ADAMS, M.J., ANTONIW, J.F. & BEAUDOIN, F. (2005). Overview and analysis of the polyprotein cleavage sites in the family Potyviridae. Molecular Plant Pathology 6, 471-487
KEON, J., RUDD, J.J., ANTONIW, J., SKINNER, W., HARGREAVES, J. & HAMMOND-KOSACK, K. (2005). Metabolic and stress adaptation by Mycosphaerella graminicola during sporulation in its host revealed through microarray transcription profiling. Molecular Plant Pathology 6, 527-540
ADAMS, M.J. & ANTONIW, J.F. (2004). Codon usage bias amongst plant viruses. Archives of Virology 149, 113-135
CHEN, J., ZHENG, H.-Y., LIN, L., ADAMS, M.J., ANTONIW, J.F., ZHAO, M.-F., SHANG, Y.F., & CHEN, J.-P. (2004). A virus related to Soybean mosaic virus from Pinellia ternata in China and its comparison with local soybean SMV isolates. Archives of Virology 149, 349-363
CHEN, J., ZHENG, H.-Y., ANTONIW, J.F., ADAMS, M.J., CHEN, J.-P. & LIN, L. (2004). Detection and classification of allexiviruses from garlic in China. Archives of Virology 149, 435-445
LIN, L., ZHENG, H.-Y., CHEN, J., CHEN, J.-P., ZHANG, Q.-Y., ZHAO, M.-F., ANTONIW, J.F. & ADAMS, M.J. (2004). A new potyvirus from tuberose (Polianthes tuberosa) in China. Archives of Virology 149, 1469-1480
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. & FAUQUET, C.M. (2004). The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Archives of Virology 149, 1045-1060
PASTORI, G.M., KIDDLE, G., ANTONIW, J.F., BERNARD, S., VELJOVIC-JOVANOVIC, S., VERRIER, P.J., NOCTOR, G. & FOYER, C.H. (2003) Leaf vitamin C contents modulate plant defense transcripts and regulate genes that control development through hormone signaling. Plant Cell, 15, 939-951
KIDDLE, G., PASTORI, G.M., BERNARD, S., PIGNOCCHI, C., ANTONIW, J.F., VERRIER, P.J. & FOYER, C.H. (2003) Effects of leaf ascorbate content on defense and photosynthetic gene expression in Arabidopsis thaliana. Antioxidants & Redox Signalling 5, 23-32
ZHENG, H.-Y., CHEN, J., ZHAO, M.-F., LIN, L., CHEN, J.-P., ANTONIW, J.F. & ADAMS, M.J. (2003). Occurrence and sequences of Lily mottle virus and Lily symptomless virus in plants grown from imported bulbs in Zhejiang province, China. Archives of Virology 148, 2419-2428.
TAHIRI-ALAOUI, A., LINGUA, G., AVROVA, A., SAMPO, S., FUSCONI, A., ANTONIW, J.F. & BERTA, G. (2002) A cullin gene is induced in tomato roots forming arbuscular mycorrhizae. Canadian Journal of Botany, 80, 607-616
TOGAWA, R.C., ANTONIW, J.F. & MULLINS, J.G.L. (2001) TMCompare: transmembrane region sequence and structure. Bioinformatics, 17, 1238-1239
ADAMS, M.J., ANTONIW, J.F. & MULLINS, J.G.L. (2001) Plant virus transmission by plasmodiophorid fungi is associated with distinctive transmembrane regions of virus-encoded proteins. Archives of Virology, 146, 1139-1153
ANTONIW, J.F., CASTELLS-BROOKE, N., DANN, L., MOORE, B., MULLINS, J.G.L. & VERRIER, P. (1999) Software: "Molecular Biology Notebook". Wellesbourne, Warwick, UK: Association of Applied Biologists.
ADAMS, M.J., ANTONIW, J.F., BARKER, H., JONES, A.T., MURANT, A.F., & ROBINSON, D. (1998) Software: "Descriptions of Plant Viruses on CD-ROM". Wellesbourne, Warwick, UK: Association of Applied Biologists.
ADAMS, M.J. & ANTONIW, J.F. (2005). Membrane proteins in plant viruses. In: Viral membrane proteins: structure, function, drug design. Ed. W. Fisher. Kluwer
ANTONIW, J.F. (2002) Alphacryptovirus. Chapter in book: "The Springer Index of Viruses". C.A. Tidona & G. Darai (Editors) Springer-Verlag Heidelberg, ISBN 3-540-67167-6.