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

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

Related outputs

The complete genome assemblies of 19 insect pests of worldwide importance to agriculture

A - Papers appearing in refereed journals

King, R., Buer, B., Davies, T. G. E., Ganko, E., Guest, M., Hassani-Pak, K., Hughes, D. J., Raming, K., Rawlings, C. J., Williamson, M. S., Crossthwaite, A., Nauen, R. and Field, L. M. 2023. The complete genome assemblies of 19 insect pests of worldwide importance to agriculture. Pesticide Biochemistry and Physiology. 191, p. 105339. https://doi.org/10.1016/j.pestbp.2023.105339

Proanthocyanidin Biosynthesis in the Developing Wheat Seed Coat Investigated by Chemical and RNA-seq Analysis

A - Papers appearing in refereed journals

Phillips, A. L., Vaughan, S., Baker, J., Primavesi, L. F., Patil, A., King, R., Hassani-Pak, K., Kulasekaran, S., Coghill, J., Ward, J. L. and Huttly, A. K. 2022. Proanthocyanidin Biosynthesis in the Developing Wheat Seed Coat Investigated by Chemical and RNA-seq Analysis. Plant Direct. 6 (10), p. e453. https://doi.org/10.1002/pld3.453

Novel molecules and target genes for vegetative heat tolerance in wheat

A - Papers appearing in refereed journals

Rose, T., Wilkinson, M. D., Lowe, C., Xu, J., Hughes, D. J., Hassall, K. L., Hassani-Pak, K., Amberkar, S., Noleto-Dias, C., Ward, J. L. and Heuer, S. 2022. Novel molecules and target genes for vegetative heat tolerance in wheat. Plant Environmental Interactions. 3 (6), pp. 264-289. https://doi.org/10.1002/pei3.10096

A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators

A - Papers appearing in refereed journals

Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mohareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A Near-Chromosome Level Genome Assembly of the European Hoverfly, Sphaerophoria Rueppellii (Diptera: Syrphidae), and a Comparative Analysis of Insecticide Resistance-Related Gene Families in Hemipteran Crop Pests and Pollinators. BMC Genomics. 23 (1), p. 198. https://doi.org/10.1186/s12864-022-08436-5

A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests

A - Papers appearing in refereed journals

Bailey, E., Field, L. M., Rawlings, C. J., King, R., Mahareb, F., Hassani-Pak, K., Hughes, D. J., Williamson, M. S., Ganko, E., Buer, B. and Nauen, R. 2022. A scaffold-level genome assembly of a minute pirate bug, Orius laevigatus, and a comparative analysis of insecticide resistance-related gene families with hemipteran crop pests. BMC Genomics. 23, p. 45. https://doi.org/10.1186/s12864-021-08249-y

Daisychain Search and Interactive Visualisation of Homologs in Genome Assemblies

A - Papers appearing in refereed journals

Schliebs, O., Chan, C-K. K., Bayer, P. E., Petereit, J., Singh, A., Hassani-Pak, K., Batley, J. and Edwards, D. 2021. Daisychain Search and Interactive Visualisation of Homologs in Genome Assemblies. Agronomy. 11 (12), p. 2587. https://doi.org/10.3390/agronomy11122587

High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding

C1 - Edited contributions to conferences/learned societies

Usai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bosi, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Solorzano, L. S., Cavallini, A. and Natali, L. 2021. High-quality, haplotype-phased de novo assembly of the highly heterozygous fig genome, a major genetic resource for fig breeding. International Society of Horticultural Science (ISHS). https://doi.org/10.17660/ActaHortic.2021.1310.4

Harmonic radar tracking reveals that honeybee drones navigate between multiple aerial leks

A - Papers appearing in refereed journals

Woodgate, J. L., Makinson, J. C., Rossi, N., Reynolds, A. M., Rawlings, C. J. and Chittka, L. 2021. Harmonic radar tracking reveals that honeybee drones navigate between multiple aerial leks. iScience. 24 (6), p. 102499. https://doi.org/10.1016/j.isci.2021.102499

Cerebrospinal fluid proteome shows disrupted neuronal development in multiple sclerosis

A - Papers appearing in refereed journals

Mosleth, E. F., Vedeler, C. A., Liland, K. H., Mcleod, A., Bringeland, G. H., Kroondijk, L., Berven, F. S., Lysenko, A., Rawlings, C. J., Eid, K. E-H., Opsahl, J. A., Gjertsen, B. T., Myhr, K-M. and Gavasso, S. 2021. Cerebrospinal fluid proteome shows disrupted neuronal development in multiple sclerosis. Scientific Reports. 11, p. 4087. https://doi.org/10.1038/s41598-021-82388-w

KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species

A - Papers appearing in refereed journals

Hassani-Pak, K., Singh, A., Brandizi, M., Hearnshaw, J., Parsons, J. D., Amberkar, S., Phillips, A. L., Doonan, J. H. and Rawlings, C. J. 2021. KnetMiner: a comprehensive approach for supporting evidence-based gene discovery and complex trait analysis across species. Plant Biotechnology Journal. https://doi.org/10.1111/pbi.13583

Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel

A - Papers appearing in refereed journals

Lyra, D. H., Griffiths, C. A., Watson, A., Joynson, R., Molero, G., Igna, A. A., Hassani-Pak, K., Reynolds, M. P., Hall, A. and Paul, M. J. 2021. Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel. Food and Energy Security. p. e292. https://doi.org/10.1002/fes3.292

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

A - Papers appearing in refereed journals

Harrington, S. A., Backhaus, A. E., Singh, A., Hassani-Pak, K. and Uauy, C. 2020. The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat. G3: Genes, Genomes, Genetics. 10 (10), pp. 3675-3686. https://doi.org/10.1534/g3.120.401436

A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat

A - Papers appearing in refereed journals

Adamski, N. M., Borril, P., Brinton, J., Harrington​, S. A., Marchal, C., Bentley, A. R., Bovill, W. D., Cattivelli, L., Cockram, J., Contreras-Moreira, B., Ford, B., Ghosh, S., Harwood, W., Hassani-Pak, K., Hayta, S., Hickey, L. T., Kanyuka, K., King, J., Maccaferri, M., Naamati, G., Pozniak, C. J., Ramirez-Gonzalez, R. H., Sansaloni, C., Trevaskis, B., Wingen, L. U., Wulff, B. B. H. and Uauy​, C. 2020. A roadmap for gene functional characterisation in crops with large genomes: Lessons from polyploid wheat. eLife. 9, p. e55646. https://doi.org/10.7554/eLife.55646

Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome

A - Papers appearing in refereed journals

Usai, G., Mascagni, F., Giordani, T., Vangelisti, A., Bose, E., Zuccolo, A., Ceccarelli, M., King, R., Hassani-Pak, K., Zambrano, L. S., Cavallini, A. and Natali, L. 2020. Epigenetic patterns within the haplotype phased fig (Ficus carica L.) genome. The Plant Journal. https://doi.org/10.1111/tpj.14635

PHI-base - the Pathogen–Host Interactions database

A - Papers appearing in refereed journals

Urban, M., Cuzick, A., Seager, J., Wood, V., Rutherford, K., De Silva, N., Venkatesh, S. Y, Martinez, M. C., Pedro, H., Yates, A. D., Hassani-Pak, K. and Hammond-Kosack, K. E. 2020. PHI-base - the Pathogen–Host Interactions database . Nucleic Acids Research. 48 (Database issue D1), pp. D613-D620. https://doi.org/10.1093/nar/gkz904

A roadmap for gene functional characterisation in wheat

A - Papers appearing in refereed journals

Adamski, N. M., Borril, P., Brinton, J., Harrington​, S. A., Marchal, C., Bentley, A. R., Bovill, W. D., Cattivelli, L., Cockram, J., Contreras-Moreira, B., Ford, B., Ghosh, S., Harwood, W., Hassani-Pak, K., Hayta, S., Hickey, L. T., Kanyuka, K., King, J., Maccaferri, M., Naamati, G., Pozniak, C. J., Ramirez-Gonzalez, R. H., Sansaloni, C., Trevaskis, B., Wingen, L. U., Wulff, B. B. H. and Uauy​, C. 2019. A roadmap for gene functional characterisation in wheat. PeerJ. 7, p. e26877v2. https://doi.org/10.7287/peerj.preprints.26877v2

A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization

A - Papers appearing in refereed journals

Alabdullah AK., Borrill, P., Martin, AC., Ramirez-Gonzalez, RH., Hassani-Pak, K., Uauy, C., Shaw, P. and Moore, G. 2019. A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization. Frontiers in Plant Science. 10 (1325), p. 24pp. https://doi.org/10.3389/fpls.2019.01325

PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets

A - Papers appearing in refereed journals

Janowska-Seja, E. I., Lysenko, A., Urban, M., Rawlings, C. J., Toska, S. and Hammond-Kosack, K. E. 2019. PHI-Nets: A Network Resource for Ascomycete Fungal Pathogens to Annotate and Identify Putative Virulence Interacting Proteins and siRNA Targets. Frontiers in Microbiology. 10 (2721). https://doi.org/10.3389/fmicb.2019.02721

Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis

A - Papers appearing in refereed journals

Bryant, F. M., Hughes, D. J., Hassani-Pak, K. and Eastmond, P. J. 2019. Basic LEUCINE ZIPPER TRANSCRIPTION FACTOR 67 transactivates DELAY OF GERMINATION 1 to establish primary seed dormancy in Arabidopsis. The Plant Cell. https://doi.org/10.1105/tpc.18.00892

The challenges of using satellite data sets to assess historical land use change and associated greenhouse gas emissions: a case study of three Indonesian provinces

A - Papers appearing in refereed journals

van Beijma, S., Chatterton, J., Page, S., Rawlings, C. J., Tiffin, R. and King. H. 2018. The challenges of using satellite data sets to assess historical land use change and associated greenhouse gas emissions: a case study of three Indonesian provinces. Carbon Management. 9, pp. 399-413. https://doi.org/10.1080/17583004.2018.1511383

Natural variation in acyl editing is a determinant of seed storage oil composition

A - Papers appearing in refereed journals

Menard, G. N., Bryant, F. M., Kelly, A. A., Craddock, C. P., Lavagi, I., Hassani-Pak, K., Kurup, S. and Eastmond, P. J. 2018. Natural variation in acyl editing is a determinant of seed storage oil composition. Scientific Reports. 8, p. 17346. https://doi.org/10.1038/s41598-018-35136-6

KnetMaps: a BioJS component to visualize biological knowledge networks

A - Papers appearing in refereed journals

Singh, A., Rawlings, C. J. and Hassani-Pak, K. 2018. KnetMaps: a BioJS component to visualize biological knowledge networks. F1000Research. 7, p. 1651. https://doi.org/10.12688/f1000research.16605.1

Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach

A - Papers appearing in refereed journals

Brandizi, M., Singh, A., Rawlings, C. J. and Hassani-Pak, K. 2018. Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach. Journal of Integrative Bioinformatics. 15 (3), pp. 1-10. https://doi.org/10.1515/jib-2018-0023

The Role of Trehalose 6-Phosphate in Crop Yield and Resilience

A - Papers appearing in refereed journals

Paul, M. J., Gonzalez-Uriarte, A., Griffiths, C. A. and Hassani-Pak, K. 2018. The Role of Trehalose 6-Phosphate in Crop Yield and Resilience. Plant Physiology. 177, pp. 12-23. https://doi.org/10.1104/pp.17.01634

Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots

A - Papers appearing in refereed journals

Vangelisti, A., Natali, L., Bernardi, R., Sbrana, C., Turrini, A., Hassani-Pak, K., Hughes, D. J., Cavallini, A., Giovannetti, M. and Giordani, T. 2018. Transcriptome changes induced by arbuscular mycorrhizal fungi in sunflower (Helianthus annuus L.) roots. Scientific Reports. 8 (4), pp. 1-14. https://doi.org/10.1038/s41598-017-18445-0

The electronic Rothamsted Archive (e-RA): an online resource for data from the Rothamsted long-term experiments

A - Papers appearing in refereed journals

Perryman, S. A. M., Castells-Brooke, N. I. D., Glendining, M. J., Goulding, K. W. T., Hawkesford, M. J., Macdonald, A. J., Ostler, R. J., Poulton, P. R., Rawlings, C. J., Scott, T. and Verrier, P. J. 2018. The electronic Rothamsted Archive (e-RA): an online resource for data from the Rothamsted long-term experiments. Scientific Data. 5, p. 180072. https://doi.org/10.1038/sdata.2018.72

EpiGeNet : A graph database of interdependencies between genetic and epigenetic events in colorectal cancer

A - Papers appearing in refereed journals

Balaur, I., Saqi, M., Barat, A., Lysenko, A., Mazein, A., Ruskin, H. J., Auffray, C. and Rawlings, C. J. 2017. EpiGeNet : A graph database of interdependencies between genetic and epigenetic events in colorectal cancer. Journal of Computational Biology. 24 (10), pp. 969-980. https://doi.org/10.1089/cmb.2016.0095

Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes

A - Papers appearing in refereed journals

Hassani-Pak, K. and Rawlings, C. J. 2017. Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes. Journal of Integrative Bioinformatics. 14 (1), pp. 1-9. https://doi.org/10.1515/jib-2016-0002

Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress

A - Papers appearing in refereed journals

Wan, Y., King, R., Mitchell, R. A. C., Hassani-Pak, K. and Hawkesford, M. J. 2017. Spatiotemporal expression patterns of wheat amino acid transporters reveal their putative roles in nitrogen transport and responses to abiotic stress. Scientific Reports. 7 (1), p. 5461. https://doi.org/10.1038/s41598-017-04473-3

Genome wide analysis of fatty acid desaturation and its response to temperature

A - Papers appearing in refereed journals

Menard, G. N., Martin-Moreno, J., Bryant, F. M., Munoz-Azcarate, O., Kelly, A. A., Hassani-Pak, K., Kurup, S. and Eastmond, P. J. 2017. Genome wide analysis of fatty acid desaturation and its response to temperature. Plant Physiology. 173 (3), pp. 1594-1605. https://doi.org/10.1104/pp.16.01907

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

A - Papers appearing in refereed journals

Balaur, I., Mazein, A., Saqi, M., Lysenko, A., Rawlings, C. J. and Auffray, C. 2017. Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks. Bioinformatics. 33 (7), pp. 1096-1098. https://doi.org/10.1093/bioinformatics/btw731

KnetMiner - An integrated data platform for gene mining and biological knowledge discovery

F - Theses

Hassani-Pak, K. 2017. KnetMiner - An integrated data platform for gene mining and biological knowledge discovery. F - Theses Rothamsted Research Computational and Analytical Sciences

Developing integrated crop knowledge networks to advance candidate gene discovery

A - Papers appearing in refereed journals

Hassani-Pak, K., Castellote, M., Esch, M., Hindle, M. M., Lysenko, A., Taubert, J. and Rawlings, C. J. 2016. Developing integrated crop knowledge networks to advance candidate gene discovery. Applied and Translational Genomics. 11 (December), pp. 18-26. https://doi.org/10.1016/j.atg.2016.10.003

Insecticide resistance mediated by an exon skipping event.

A - Papers appearing in refereed journals

Berger, M., Puinean, A. M., Randall, E., Zimmer, C. T., Silva, W. M., Bielza, P., Field, L. M., Hughes, D. J., Mellor, I., Hassani-Pak, K., Siqueira, H. A. A., Williamson, M. S. and Bass, C. 2016. Insecticide resistance mediated by an exon skipping event. Molecular Ecology. 25 (22), pp. 5692-5704. https://doi.org/10.1111/mec.13882

Representing and querying disease networks using graph databases

A - Papers appearing in refereed journals

Lysenko, A., Roznovat, I. A., Saqi, M., Mazein, A., Rawlings, C. J. and Auffray, C. 2016. Representing and querying disease networks using graph databases. BioData Mining. 9 (23), pp. 1-19. https://doi.org/10.1186/s13040-016-0102-8

The North Wyke Farm Platform: effect of temperate grassland farming systems on soil moisture contents, runoff and associated water quality dynamics

A - Papers appearing in refereed journals

Orr, R. J., Murray, P. J., Eyles, C. J., Blackwell, M. S. A., Cardenas, L. M., Collins, A. L., Dungait, J. A. J., Goulding, K. W. T., Griffith, B. A., Gurr, S. J., Harris, P., Hawkins, J. M. B., Misselbrook, T. H., Rawlings, C. J., Shepherd, A., Sint, H. M., Takahashi, T., Tozer, K. N., Whitmore, A. P., Wu, L. and Lee, M. R. F. 2016. The North Wyke Farm Platform: effect of temperate grassland farming systems on soil moisture contents, runoff and associated water quality dynamics. European Journal of Soil Science. 67 (4), pp. 374-385. https://doi.org/10.1111/ejss.12350

Mutation scanning in wheat by exon capture and next-generation sequencing

A - Papers appearing in refereed journals

King, R., Bird, N., Ramirez-Gonzalez, R., Coghill, J. A., Patil, A., Hassani-Pak, K., Uauy, C. and Phillips, A. L. 2015. Mutation scanning in wheat by exon capture and next-generation sequencing. PLOS ONE. 10, p. e0137549. https://doi.org/10.1371/journal.pone.0137549

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

A - Papers appearing in refereed journals

King, R., Urban, M., Hammond-Kosack, M. C. U., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum. BMC Genomics. 16, p. 544. https://doi.org/10.1186/s12864-015-1756-1

e-RA, the electronic Rothamsted Archive: long-term data for modern-day agroecological research

A - Papers appearing in refereed journals

Glendining, M. J., Perryman, S. A. M., Castells-Brooke, N. I. D. and Rawlings, C. J. 2015. e-RA, the electronic Rothamsted Archive: long-term data for modern-day agroecological research. Aspects of Applied Biology. 128.

Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions

A - Papers appearing in refereed journals

Urban, M., King, R., Hassani-Pak, K. and Hammond-Kosack, K. E. 2015. Whole-genome analysis of Fusarium graminearum insertional mutants identifies virulence associated genes and unmasks untagged chromosomal deletions. BMC Genomics. 16, p. 261. https://doi.org/10.1186/s12864-015-1412-9

Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition

A - Papers appearing in refereed journals

Rudd, J. J., Kanyuka, K., Hassani-Pak, K., Derbyshire, M., Andongabo, A. E., Devonshire, J., Lysenko, A., Saqi, M., Desai, N. M., Powers, S. J., Hooper, J., Ambroso, L., Bharti, A., Farmer, A., Hammond-Kosack, K. E., Dietrich, R. A. and Courbot, M. 2015. Transcriptome and metabolite profiling of the infection cycle of Zymoseptoria tritici on wheat reveals a biphasic interaction with plant immunity involving differential pathogen chromosomal contributions and a variation on the hemibiotrophic lifestyle definition. Plant Physiology. 167 (3), pp. 1158-1185. https://doi.org/10.1104/pp.114.255927

A framework for mining life sciences data on the semantic web in an interactive, graph-based environment

B - Book chapters etc edited externally

Lysenko, A., Grzebyta, J., Hindle, M. M., Rawlings, C. J. and Splendiani, A. 2014. A framework for mining life sciences data on the semantic web in an interactive, graph-based environment. in: Formenti, E., Wit, E. and Tagliaferri, R. (ed.) Computational intelligence methods for bioinformatics and biostatistics. Lecture Notes in Computer Science, Vol. 8452 Springer, Dordrecht. pp. 225-237

Interactive exploration of integrated biological datasets using context-sensitive workflows

A - Papers appearing in refereed journals

Horn, F., Rittweger, M., Taubert, J., Lysenko, A., Rawlings, C. J. and Guthke, R. 2014. Interactive exploration of integrated biological datasets using context-sensitive workflows. Frontiers in Genetics. 5, p. 21. https://doi.org/10.3389/fgene.2014.00021

Systems responses to progressive water stress in durum wheat

A - Papers appearing in refereed journals

Habash, D. Z., Baudo, M., Hindle, M. M., Powers, S. J., Defoin-Platel, M., Mitchell, R. A. C., Saqi, M., Rawlings, C. J., Latiri, K., Araus, J. L., Abdulkader, A., Tuberosa, R., Lawlor, D. W. and Nachit, M. M. 2014. Systems responses to progressive water stress in durum wheat. PLOS ONE. 9, p. e108431. https://doi.org/10.1371/journal.pone.0108431

Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs

A - Papers appearing in refereed journals

Graham, N. S., Hammond, J. P., Lysenko, A., Mayes, S., O Lochlainn, S., Blasco, B., Bowen, H. C., Rawlings, C. J., Rios, J. J., Welham, S. J., Carion, P. W. C., Dupuy, L. X., King, G. J., White, P. J. and Broadley, M. R. 2014. Genetical and comparative genomics of Brassica under altered Ca supply identifies Arabidopsis Ca-transporter orthologs. The Plant Cell. 26, pp. 2818-2830. https://doi.org/10.1105/tpc.114.128603

A tale of one fungal pathogen of wheat: how it evades host surveillance and then hijacks host defences

C2 - Non-edited contributions to conferences

Kanyuka, K., Lysenko, A., Saqi, M., Derbyshire, M., Andongabo, A. E., Hassani-Pak, K., Hammond-Kosack, K. E., Courbot, M. and Rudd, J. J. 2014. A tale of one fungal pathogen of wheat: how it evades host surveillance and then hijacks host defences. Abstracts 16th International Congress on Molecular Plant-Microbe Interactions (IS-MPMI 2014), Rhodes, 6-10 July 2014 . pp. P069

Identification and analysis of differentially expressed genes in the wheat- Zymoseptoria tritici interaction

C2 - Non-edited contributions to conferences

Kanyuka, K., Andongabo, A. E., Hassani-Pak, K., Powers, S. J., Lysenko, A., Saqi, M., Derbyshire, M., Lee, W-S., Hammond-Kosack, K. E., Courbot, M. and Rudd, J. J. 2014. Identification and analysis of differentially expressed genes in the wheat- Zymoseptoria tritici interaction. Abstracts Plant Genomics Congress, London, 12-13 May 2014 .

A query suggestion workflow for life science IR-systems

A - Papers appearing in refereed journals

Esch, M., Chen, J., Weise, S., Hassani-Pak, K., Scholz, U. and Lange, M. 2014. A query suggestion workflow for life science IR-systems. Journal of Integrative Bioinformatics. 11, p. 237. https://doi.org/10.2390/biecoll-jib-2014-237

Secondary cell wall composition and candidate gene expression in developing willow (Salix purpurea) stems

A - Papers appearing in refereed journals

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

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

A - Papers appearing in refereed journals

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

Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum

A - Papers appearing in refereed journals

Lysenko, A., Urban, M., Bennett, L., Tsoka, S., Janowska-Sejda, E., Rawlings, C. J., Hammond-Kosack, K. E. and Saqi, M. 2013. Network-based data integration for selecting candidate virulence associated proteins in the cereal infecting fungus Fusarium graminearum. PLOS ONE. 8, p. e67926. https://doi.org/10.1371/journal.pone.0067926

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

Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses

A - Papers appearing in refereed journals

Anders, N., Wilkinson, M. D., Lovegrove, A., Freeman, J., Tryfona, T., Pellny, T. K., Weimar, T., Mortimer, J. C., Stott, K., Baker, J. M., Defoin-Platel, M., Shewry, P. R., Dupree, P. and Mitchell, R. A. C. 2012. Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses. Proceedings of the National Academy of Sciences. 109 (3), pp. 989-993. https://doi.org/10.1073/pnas.1115858109

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

New perspectives on glutamine synthetase in grasses

A - Papers appearing in refereed journals

Swarbreck, S. M., Defoin-Platel, M., Hindle, M. M., Saqi, M. and Habash, D. M. 2011. New perspectives on glutamine synthetase in grasses. Journal of Experimental Botany. 62, pp. 1511-1522. https://doi.org/10.1093/jxb/erq356

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.

Integrated feature and parameter optimization for an evolving spiking neural network: exploring heterogeneous probabilistic models

A - Papers appearing in refereed journals

Schliebs, S., Defoin-Platel, M., Worner, S. and Kasabov, N. 2009. Integrated feature and parameter optimization for an evolving spiking neural network: exploring heterogeneous probabilistic models. Neural Networks. 22, pp. 623-632. https://doi.org/10.1016/j.neunet.2009.06.038

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.