Ondex Web: web-based visualization and exploration of heterogeneous biological networks

Taubert, J., Hassani-Pak, K., Castells-Brooke, N. I. D. and Rawlings, C. J. 2014. Ondex Web: web-based visualization and exploration of heterogeneous biological networks. Bioinformatics. 30, pp. 1034-1035. https://doi.org/10.1093/bioinformatics/btt740

Authors	Taubert, J., Hassani-Pak, K., Castells-Brooke, N. I. D. and Rawlings, C. J.
Year of Publication	2014
Journal	Bioinformatics
Journal citation	30, pp. 1034-1035
Digital Object Identifier (DOI)	https://doi.org/10.1093/bioinformatics/btt740
Open access	Published as ‘gold’ (paid) open access
Funder project or code	Wheat
	QTLNetMiner: Mining Candidate Gene Networks From Genetic Studies of Crops and Animals
	Project: 4918
Publisher's version	Taubert-2014-Ondex-web-web-based-visualization-a (1).pdf
Publisher	Oxford University Press (OUP) Oxford
	Oxford University Press (OUP)
ISSN	1367-4803

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Wan, Y., Gritsch, C., Tryfona, T., Ray, M. J., Andongabo, A. E., Hassani-Pak, K., Jones, H. D., Dupree, P., Karp, A., Shewry, P. R. and Mitchell, R. A. C. 2014. Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems. Planta. 239, pp. 1041-1053. https://doi.org/10.1007/s00425-014-2034-1

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Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach

A - Papers appearing in refereed journals

Sternberg, M. J. E., Tamaddoni-Nezhad, A., Lesk, V. I., Kay, E., Hitchen, P. G., Cootes, A., Van Alphen, L. B., Lamoureux, M. P., Jarrell, H. C., Rawlings, C. J., Soo, E. C., Szymanski, C. M., Dell, A., Wren, B. W. and Muggleton, S. H. 2013. Gene function hypotheses for the Campylobacter jejuni glycome generated by a logic-based approach. Journal of Molecular Biology. 425 (1), pp. 186-197. https://doi.org/10.1016/j.jmb.2012.10.014

Detection of multi-clustered genes and community structure for the plant pathogenic fungus Fusarium graminearum

B - Book chapters etc edited externally

Bennett, L., Lysenko, A., Papageorgiou, L. G., Urban, M., Hammond-Kosack, K. E., Rawlings, C. J., Saqi, M. and Tsoka, S. 2012. Detection of multi-clustered genes and community structure for the plant pathogenic fungus Fusarium graminearum. in: Gilbert, D. and Heiner, M. (ed.) Computational Methods in Systems Biology Springer-Verlag Berlin Heidelberg.

InterStoreDB: a generic integration resource for genetic and genomic data

A - Papers appearing in refereed journals

Love, C. G., Andongabo, A. E., Wang, J., Carion, P. W. C., Rawlings, C. J. and King, G. J. 2012. InterStoreDB: a generic integration resource for genetic and genomic data. Journal of Integrative Plant Biology. 54 (5), pp. 345-355. https://doi.org/10.1111/j.1744-7909.2012.01120.x

Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits

C1 - Edited contributions to conferences/learned societies

Defoin-Platel, M., Hassani-Pak, K. and Rawlings, C. J. 2011. Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits. Systems Approaches to Crop Improvement. Aspects of Applied Biology 107 . Association of Applied Biologists (AAB) Wellesbourne Warwick . pp. 79-87

Lost in translation: data integration tools meet the Semantic Web

C1 - Edited contributions to conferences/learned societies

Splendiani, A., Rawlings, C. J., Kuo, S-C., Stevens, R. and Lord, P. 2011. Lost in translation: data integration tools meet the Semantic Web. Proceedings 1st IRAST International Conference on Data Engineering and Internet Technology (DEIT), Bali, 15-17 March 2011 . IEEE. pp. 621-625

AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations

A - Papers appearing in refereed journals

Defoin-Platel, M., Hindle, M. M., Lysenko, A., Powers, S. J., Habash, D. Z., Rawlings, C. J. and Saqi, M. 2011. AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations. BMC Bioinformatics. 12, p. 431 (13pp). https://doi.org/10.1186/1471-2105-12-431

Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis

A - Papers appearing in refereed journals

Lysenko, A., Defoin-Platel, M., Hassani-Pak, K., Taubert, J., Hodgman, C., Rawlings, C. J. and Saqi, M. 2011. Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis. BMC Bioinformatics. 12, p. 203 (14pp). https://doi.org/10.1186/1471-2105-12-203

WIBL: Workbench for Integrative Biological Learning

A - Papers appearing in refereed journals

Lesk, V., Taubert, J., Rawlings, C. J., Dunbar, S. and Muggleton, S. 2011. WIBL: Workbench for Integrative Biological Learning. Journal of Integrative Bioinformatics. 8, p. 156 (9pp). https://doi.org/10.2390/biecoll-jib-2011-156

Analysis and visualisation of RDF resources in Ondex

G - Articles in popular magazines and other technical publications

Canevet, C., Lysenko, A., Splendiani, A., Pocock, M. J. O. and Rawlings, C. J. 2010. Analysis and visualisation of RDF resources in Ondex. Nature Precedings. https://doi.org/10.1038/npre.2010.5430

Enhancing data integration with text analysis to find proteins implicated in plant stress response

A - Papers appearing in refereed journals

Hassani-Pak, K., Legaie, R., Canevet, C., Van Den Berg, H. A., Moore, J. D. and Rawlings, C. J. 2010. Enhancing data integration with text analysis to find proteins implicated in plant stress response. Journal of Integrative Bioinformatics. 7, p. 121 (13pp). https://doi.org/10.2390/biecoll-jib-2010-121

Ondex: Data integration and visualisation for the Semantic Web

C2 - Non-edited contributions to conferences

Canevet, C., Splendiani, A., Kuo, S-C., Stevens, R., Lord, P. and Rawlings, C. J. 2009. Ondex: Data integration and visualisation for the Semantic Web. In: CEUR Workshop Proceedings vol. 559, CEUR-WS.org, Workshop on Semantic Web Applications and Tools for Life Sciences, SWAT4LS 2009, Amsterdam, 1/07/2009. . CEUR-WS.org.

Toward a new paradigm for user interaction on the semantic web to support life sciences investigation

C2 - Non-edited contributions to conferences

Splendiani, A., Kuiper, M. and Rawlings, C. J. 2009. Toward a new paradigm for user interaction on the semantic web to support life sciences investigation. Proceedings Workshop on Semantic Web User Interaction: Sharing Ideas for Complex Problems in User Interaction (SWUI2009), Washington DC, 25 October 2009 .

Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases

A - Papers appearing in refereed journals

Lysenko, A., Hindle, M. M., Taubert, J., Saqi, M. and Rawlings, C. J. 2009. Data integration for plant genomics - exemplars from the integration of Arabidopsis thaliana databases. Briefings in Bioinformatics. 10, pp. 676-693. https://doi.org/10.1093/bib/bbp047

Linking life sciences data using graph-based mapping

B - Book chapters etc edited externally

Taubert, J., Hindle, M. M., Lysenko, A., Weile, J., Kohler, J. and Rawlings, C. J. 2009. Linking life sciences data using graph-based mapping. in: Paton, N. W., Hedeler, C. and Missier, P. (ed.) Data Integration in the Life Sciences. DILS 2009. Lecture Notes in Computer Science Volume 564 Springer, Berlin. pp. 16-30

Analysis of the newly sequenced Fusarium genomes using PHI-Base and ONDEX

C2 - Non-edited contributions to conferences

Beacham, A. M., Cavenet, C., Taubert, J., Urban, M., Antoniw, J. F., Rawlings, C. J. and Hammond-Kosack, K. E. 2008. Analysis of the newly sequenced Fusarium genomes using PHI-Base and ONDEX.

Graph-based sequence annotation using a data integration approach

A - Papers appearing in refereed journals

Pesch, R., Lysenko, A., Hindle, M. M., Hassani-Pak, K., Thiele, R., Rawlings, C. J., Kohler, J. and Taubert, J. 2008. Graph-based sequence annotation using a data integration approach. Journal of Integrative Bioinformatics. 5(2):94, p. 15pp. https://doi.org/10.2390/biecoll-jib-2008-94

PHI-base update: additions to the pathogen-host interaction database

A - Papers appearing in refereed journals

Winnenburg, R., Urban, M., Beacham, A., Baldwin, T. K., Holland, S., Lindeberg, M., Hansen, H., Rawlings, C. J., Hammond-Kosack, K. E. and Kohler, J. 2008. PHI-base update: additions to the pathogen-host interaction database. Nucleic Acids Research. 36, pp. D572-D576. https://doi.org/10.1093/nar/gkm858

PHI-base: a database of experimentally verified pathogenicity, virulence and effector genes in fungal, oomycete and bacterial pathogens of animals and plants

C2 - Non-edited contributions to conferences

Baldwin, T. K., Winnenburg, R., Beacham, A., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2007. PHI-base: a database of experimentally verified pathogenicity, virulence and effector genes in fungal, oomycete and bacterial pathogens of animals and plants. Abstracts 13th International Congress on Molecular Plant-Microbe Interactions, Sorrento, 21-27 July 2007 .

Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence

A - Papers appearing in refereed journals

Mitchell, R. A. C., Castells-Brooke, N. I. D., Taubert, J., Verrier, P. J., Leader, D. J. and Rawlings, C. J. 2007. Wheat Estimated Transcript Server (WhETS): a tool to provide best estimate of hexaploid wheat transcript sequence. Nucleic Acids Research. 35(Web Server issue), pp. W148-W151. https://doi.org/10.1093/nar/gkm220

The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity

A - Papers appearing in refereed journals

Baldwin, T. K., Winnenburg, R., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2006. The Pathogen-Host Interactions database (PHI-base) provides insights into generic and novel themes of pathogenicity. Molecular Plant-Microbe Interactions - MPMI. 19 (12), pp. 1451-1462. https://doi.org/10.1094/MPMI-19-1451

Graph-based analysis and visualization of experimental results with ONDEX

A - Papers appearing in refereed journals

Koehler, J., Baumbach, J., Taubert, J., Specht, M., Skusa, A., Ruegg, A., Rawlings, C. J., Verrier, P. J. and Philippi, S. 2006. Graph-based analysis and visualization of experimental results with ONDEX. Bioinformatics. 22 (11), pp. 1383-1390. https://doi.org/10.1093/bioinformatics/btl081

PHI-base: a new database for pathogen host interactions

A - Papers appearing in refereed journals

Winnenburg, R., Baldwin, T. K., Urban, M., Rawlings, C. J., Koehler, J. and Hammond-Kosack, K. E. 2006. PHI-base: a new database for pathogen host interactions. Nucleic Acids Research. 34 (1), pp. D459-D464. https://doi.org/10.1093/nar/gkj047

Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures

A - Papers appearing in refereed journals

Koehler, J., Rawlings, C. J., Verrier, P. J., Mitchell, R. A. C., Skusa, A., Ruegg, A. and Philippi, S. 2004. Linking experimental results, biological networks and sequence analysis methods using Ontologies and Generalised Data Structures. In Silico Biology. 5 (1), pp. 33-44.

Forecasting light leaf spot (Pyrenopeziza brassicae ) of winter oilseed rape (Brassica napus ) on the Internet

A - Papers appearing in refereed journals

Souter, S. D., Castells-Brooke, N. I. D., Antoniw, J. F., Welham, S. J., Fitt, B. D. L., Evans, N., Gladders, P., Turner, J. A. and Sutherland, K. 1999. Forecasting light leaf spot (Pyrenopeziza brassicae ) of winter oilseed rape (Brassica napus ) on the Internet. Aspects of Applied Biology. 55, pp. 37-42.

The Molecular Biology Notebook (CD-ROM)

J - Computer programs

Antoniw, J. F., Castells-Brooke, N. I. D., Moore, W. J. and Verrier, P. J. 1999. The Molecular Biology Notebook (CD-ROM). Association of Applied Biologists, Wellesbourne.

The Molecular Biology Notebook on CD-ROM - a step toward the virtual laboratory

G - Articles in popular magazines and other technical publications

Castells-Brooke, N. I. D., Mullins, R., Antoniw, J. F. and Verrier, P. J. 1999. The Molecular Biology Notebook on CD-ROM - a step toward the virtual laboratory. Journal Of Biological Education. 33 (4), pp. 223-225. https://doi.org/10.1080/00219266.1999.9655672

Analysis of sodium channel gene sequences in pyrethroid-resistant houseflies. Progress toward a molecular diagnostic for knockdown resistance (kdr )

C1 - Edited contributions to conferences/learned societies

Williamson, M. S., Martinez-Torres, D., Hick, C. A., Castells-Brooke, N. I. D. and Devonshire, A. L. 1996. Analysis of sodium channel gene sequences in pyrethroid-resistant houseflies. Progress toward a molecular diagnostic for knockdown resistance (kdr ). Brown, T. M. (ed.) Molecular Genetics and Evolution of Pesticide Resistance. ACS Symposium Series 645 . American Chemical Society (ACS). pp. 52-61

Transcription analysis of a voltage-sensitive sodium channel gene by in situ hybridization and immunological characterization of its expression product in Musca domestica

C2 - Non-edited contributions to conferences

Pauron, D., Castells-Brooke, N. I. D., Williamson, M. S., Devonshire, A. L. and Berge, J. B. 1993. Transcription analysis of a voltage-sensitive sodium channel gene by in situ hybridization and immunological characterization of its expression product in Musca domestica. Abstracts 2nd International Symposium on Molecular Insect Science, Flagstaff Arizona, July 1993 . pp. 124