Jay Moore

Dr. Jonathan D. Moore
Senior Research Fellow in Bioinformatics

Tel: +44 777 625 3051
Email: jonathan dot moore at warwick dot ac dot uk

Research interests

I specialise in data integration, palaeointeractomics and evolutionary systems biology. I am working on analysis of deep-sequencing and protein interaction data and am interested in developing integrations of pre/historical, geographical, biodiversity, and omics data. I lead Warwick Systems Biology's bioinformatics engineering group, supporting research projects acorss the University and our collaborators.

I am developing bioinformatic approaches to understanding evolution of response to environmental stress in Arabidopsis and metabolic switching in Streptomyces coelicolor. I am collaborating on genome assembly and development of a SNP platform for Brassica oleracea analysing genome resequencing and transcriptome sequence data. I am on the PALS group of the SYSMO programme, developing common approaches to bioinformatics for the systems biology of microorganisms. I am an honorary member of the Allaby Research Group which specialises in plant evolution and crop domestication, with whom I developed the TreeMos application to identify and visualise phylogenetic mosaicism, and collaborate on plant archaeogenomics. I maintain an ongoing interest in developing comparative models of genome organisation in Brassicaceae.

I'm a review editor for Frontiers in Bioinformatics and Computational Biology.

Biography

Ph.D. Plant and Environmental Science, University of Warwick: Constraints on sequence evolution in the segmentally duplicated Brassica oleracea genome
M.Sc. Conservation and Utilisation of Plant Genetic Resources (Distinction), University of Birmingham
P.G.Cert. Enterprise and Network Management, Sheffield Hallam University Business School
B.Eng. (Hons.) Electronic Engineering, University of Sheffield

I have provided leadership in a variety of collaborative online projects, currently including curation of the ScoCyc database of Streptomyces metabolic pathways, and in the past managing the development of the online Journal of International Wildlife Law and Policy, and working for the Open University as an Associate Lecturer and Team Leader in piloting their first online course. I also provided technical leadership to the European Crop Wild Relative Diversity Assessment and Conservation Forum, and was responsible for database design and development of the forum's Crop Wild Relative Information System CWRIS, an online database of the Crop Wild Relatives of Europe and the Mediterranean.

I have worked as a consultant for a variety of international management consultancy companies and public sector organisations through my own consultancy business, providing technical leadership in large-scale data integration projects.

External profiles

NCBI
Google Scholar
http://orcid.org/0000-0002-5486-0407
ResearcherID
ResearchGate
Academia.edu


Recent publications Web of Science h-index: 9

  • Brown, P., Baxter, L., Hickman, R., Beynon, J., Moore, J.D. and Ott, S. (2013) MEME-LaB: motif analysis in clusters. Bioinformatics, doi: 10.1093/bioinformatics/btt248.
  • Hickman, R., Hill, C., Penfold, C.A., Breeze, E., Bowden, L., Moore, J.D., Zhang, P., Jackson, A., Cooke, E., Bewicke-Copley, F., Mead, A., Beynon, J., Wild, D.L., Denby, K.J., Ott, S. and Buchanan-Wollaston, V. (2013). A Local Regulatory Network Around Three NAC Transcription Factors in Stress Responses and Senescence in Arabidopsis leaves. The Plant Journal, 04/2013.
  • Traka, M. H., Saha, S., Huseby, S., Kopriva, S., Walley, P. G., Barker, G., Moore, J., Mero, G., van den Bosch, F., Constant, H., Kelly, L., Schepers, H., Boddupalli, S., and Mithen, R. F. (2013). Genetic regulation of glucoraphanin accumulation in Beneforté® broccoli. New Phytologist, doi: 10.1111/nph.12232.
  • Baxter, L., Jironkin, A., Hickman, R., Moore, J., Barrington, C., Krusche, P., Dyer, N.P., Buchanan-Wollaston, V., Tiskin, A., Beynon, J., Denby, K. and Ott, S. (2012) Conserved noncoding sequences highlight shared components of regulatory networks in dicotyledonous plants. The Plant Cell, 24(10): 3949-3965.
  • Kitchen, J.L., Moore, J.D., Palmer, S.A. and Allaby, R.G. (2012) MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling. BMC Bioinformatics, 13:287
  • Windram, O., Madhou, P., McHattie, S., Hill, C., Hickman, R., Cooke, E., Jenkins, D.J., Penfold, C.A., Baxter, L., Breeze, E., Kiddle, S.J., Rhodes, J., Atwell, S., Klieberstein, D.J., Kim Y-S., Stegle, O., Borgwardt, K., Zhang, C., Tabrett, A., Legaie, R., Moore, J., Finkenstadt, B., Wild, D.L., Mead, A., Rand, D., Beynon, J., Ott, S, Buchanan-Wollaston, V. and Denby, K. (2012) Arabidopsis defense against Botrytis cinerea: chronology and regulation deciphered by high-resolution temporal transcriptomic analysis. The Plant Cell, 24(9): 3530-3557
  • Palmer, S.A., Clapham, A.J., Rose, P., Freitas, F.O., Owen, B.D., Beresford-Jones, D., Moore, J.D., Kitchen, J.L. and Allaby, R.G. (2012) Archaeogenomic evidence of punctuated genome evolution in Gossypium. Molecular Biology and Evolution 29 (8). [citations 6]
  • Thomas, L., Hodgson, D.A., Wentzel, A., Nieselt, K., Ellingsen, T.E., Moore. J., Morrissey, E.R., Legaie, R; The STREAM Consortium, Wohleben, W., Rodriguez-Garcia, A., Martin, J.F., Burroughs, N.J., Wellington, E.M., Smith, M.C. (2012) Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture, Mol. Cell Proteomics, 11(2): M111.013797. [citations 5]
  • Mukhtar, M.S., Carvunis, A-R., Dreze, M., Epple, P., Steinbrenner, J., Moore, J., Tasan, M., Galli, M., Hao, T., Nishimura, M.T., Pevzner, S.J., Donovan, S.E., Ghamsari, L., Santhanam, B., Romero, V., Poulin, M.M., Gebreab, F., Gutierrez, B.J., Tam, S., Monachello, D., Boxem, M., Harbort, C.J., McDonald, N., Gai, L., Chen, H., He, Y., European Union Effectoromics Consortium, Vandenhaute, J., Roth, F.P., Hill, D.E., Ecker, J.R., Vidal, M., Beynon, J., Braun, P., Dangl, J.L. (2011) Independently evolved virulence effectors converge onto hubs in a plant immune system network. Science 333(6042): 596-601. [citations 66]
  • Arabidopsis Interactome Mapping Consortium (2011) Evidence for network evolution in an Arabidopsis interactome map. Science 333(6042): 601-607. [citations 82]
  • Breeze, E., Harrison, E., McHattie, S., Hughes, L., Hickman, R., Hill, C., Kiddle, S., Kim, Y-S., Penfold, C.A., Jenkins, D., Zhang, C., Morris, K., Jenner, C., Jackson, S., Thomas, B., Tabrett, A., Legaie, R., Moore, J.D., Wild, D.L., Ott, S., Rand, D., Beynon, J., Denby, K., Mead, A. and Buchanan-Wollaston, V. (2011) High-Resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation. The Plant Cell 23(3): 873-894. [citations 43]
  • Moore, J., Jironkin, A., Chandler, D., Burroughs, N., Evans, D.J. and Ryabov, E.V. (2011) Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies. Journal of General Virology 92, 156-161. [citations 16]
  • Hassani-Pak, K., Legaie, R., Canevet, C., van den Berg, H.A., Moore, J.D. and Rawlings, C. (2010) Enhancing data integration with text analysis to find proteins implicated in plant stress response. Journal of Integrative Bioinformatics 7:3. [citations 2]
  • Alam, M.T., Merlo, M.E., The STREAM Consortium, Hodgson, D.A., Wellington, E.M.H., Takano, E., Breitling, R. (2010) Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor BMC Genomics 11:202. [citations 8]
  • Nieselt, K., Battke, F., Herbig, A., Bruheim, P., Wentzel, A., Jakobsen, O.M., Sletta, H., Alam, M.T., Merlo, M.E., Moore, J., Omara,W., Morrissey, E.R., Juarez-Hermosillo, M., Rodríguez-García, A., Nentwich, M., Thomas, L., Legaie, R., Gaze, W.H., Challis, G.L., Jansen, R.C., Dijkhuizen, L., Rand, D.A., Wild, D.L., Bonin, M., Reuther, J., Wohlleben, W., Smith, M.C.M., Burroughs, N.J., Martín, J.F., Hodgson, D.A., Takano, E., Breitling, R., Ellingsen, T.E., Elizabeth M. H. Wellington, E.M.H. (2010) The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics 11:10. Highly Accessed. [citations 48]
  • Palmer, S.A., Moore, J.D., Clapham, A.J., Rose, P. and Allaby, R.G. (2009) Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation. PLoS ONE 4(7): e6301. [citations 10]
  • Alix, K., Joets, J., Ryder, C.D., Moore, J., Barker, G.C., Bailey, J.P., King, G.J. and Heslop-Harrison, J.S. (2008) The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. The Plant Journal 56: 1030-1044. [citations 31]
  • Moore, J.D., Kell, S.P., Iriondo J, Ford-Lloyd, B. and Maxted, N. (2008) CWRML: representing crop wild relative conservation and use data in XML. BMC Bioinformatics 9:116. [citations 7]
  • Moore, J.D. and Allaby, R.G. (2008) TreeMos: a high-throughput phylogenomic approach to find and visualise phylogenetic mosaicism. Bioinformatics 24(5):717-718.
  • Kell, S.P., Moore, J.D., Iriondo, J.M., Scholten, M.A., Ford-Lloyd, B.V. and Maxted, N. (2008) CWRIS: an information management system to aid crop wild relative conservation and sustainable use. In: Maxted, N., Ford-Lloyd, B.V., Kell, S.P., Iriondo, J., Dulloo, E. and Turok, J. (eds.) Crop Wild Relative Conservation and Use. CABI Publishing, Wallingford. Pp. 469-489. [citations 6]
  • Alix, K., Ryder, C.D., Moore, J., King, G.J., and Heslop-Harrison, P.J.S. (2005). The Genomic Organization of Retrotransposons in Brassica oleracea. Plant Molecular Biology 59:6 839-851. [citations 19]
  • Kell, S.P., and Moore, J. (2005). The PGR Forum crop wild relative information system (CWRIS): an introduction. Crop Wild Relative 4: 4-5.
  • Moore, J.D. and Kell, S.P. (eds.) (2005). PGR Forum CD ROM. University of Birmingham, UK.

Conference presentations

  • Moore, J.D. (2013). Brassica C genome transcript diversity. Oral presentation. UK Brassica Research Community 2013. Rothamsted, UK.
  • Moore, J.D., Walley, P.G., Edger, P., Arias, T., Mayfield, D.R.F., Teakle, G.R., Allaby, R.G., Pires, J.C. and Barker, G. (2013). Insights Into Evolutionary Relationships Among Brassica C Genome Wild Species and Crops. Oral presentation. Plant and Animal Genome XXI. San Diego, USA.
  • Moore, J.D. (2012). From bench to web via spreadsheets: practical data sharing in research groups. Invited oral presentation. Making data accessible to all conference, Exeter, UK.
  • Bari, M. F.; Nicholson, A. G.; Kerr, K. M.; et al. (2012). Biomarkers for the classification of highly malignant neuroendocrine lung carcinoma. Histopathology 61: 202.
  • Boddington, C., Jenkins, D. and Moore, J.D. (2012) The Arabidopsis IDEAs database: integrating and visualising Interactions, Domains, Experiments and Annotations. Oral and poster presentations. UK Plant Systems Biology 2012, Norwich, UK.
  • Teakle, G., Walley, P., Moore, J., Astley, D., King, G., Buchanan-Wollaston, V., Hand, P., Pink, D. and Barker, G. (2012). Genetic diversity in C genome diploid Brassicas. Poster presentation. Plant and Animal Genome XX.
  • Adaikalakoteswari, A., Moore, J., McTernan, P.G., Kumar, S., Saravanan, P., Tripathi, G. (2011). Low B12 and high folate: a novel regulator of cholesterol biosynthesis in human adipocytes. Poster presentation. European Association for the Study of Diabetes 2011, Lisbon, Portugal.
  • Moore, J. (2011). Palaeointeractomics. Poster presentation. An inter-disciplinary forum on the subject of 'Time', University of Warwick, UK.
  • Hill, C., Jenkins, D., Moore, J.D. and Penfold, C. (2011). Transcriptional networks in plant stress responses. Oral presentation. UK Plant Systems Biology Workshop 2011, CSBE Edinburgh, UK.
  • Bari, M.F., Moore, J., Zehnder, D., Bird, H., and Snead, D. (2010). Analysis of gene expression array data to identify biomarkers specific to small cell lung cancer. Poster Presentation. AACR-IASLC Joint Conference on Molecular Origins of Lung Cancer 2010, Coronado, USA.
  • Bari, M.F., Moore, J., Zehnder, D., Bird, H., and Snead, D. (2010). Molecular Characteristics of Small Cell Lung Carcinoma. Pathological Society of Great Britain and Ireland Winter Meeting, London, UK.
  • Moore, J.D. and Allaby R.G. (2008). TreeMos: a high-throughput phylogenomic approach to identifying and visualising phylogenetic mosaicism. Poster Presentation. Genetics 2008, Berlin, Germany.
  • Alix, K., Ryder, C.D., Moore, J., King, G.J. and Heslop-Harrison, P.J.S. (2006). The Diversity And Organization Of Retrotransposons In Brassica: Understanding Their Phylogeny And Evolution. Poster presentation. In: Plant and Animal Genome XIV Conference Abstracts.
  • Moore, J.D., King, G.J., Lynn, J. (2006). Data integration for Brassica comparative genomics. Oral presentation. 2006 UK Brassica Research Community Annual Meeting, John Innes Centre, UK.
  • Barker, G., Ryder, C., Moore, J., Weaver, G., Naylor, R., Edwards, R., Sharpe, A., Durkin, J., Lydiate, D., and King, G. (2005). EST Sequencing of Brassica oleracea. Poster presentation. In: Plant and Animal Genome XIII Conference Abstracts.
  • Kell, S.P., Moore, J., Iriondo, J.M., Scholten, M.A. and Maxted, N. (2005). Creation and development of the PGR Forum CWR Information System (CWRIS). Oral presentation. In: First International Conference on Crop Wild Relative Conservation and Use: Book of abstracts (Kell, S., Scholten, M. eds.).
  • Barker, G., Ryder, C., Moore, J., Naylor, R., Edwards, R., Sharpe, A., Durkin, J., Lydiate, D., and King, G. (2004). A public EST sequencing programme for Brassica oleracea. Poster presentation. Brassica 2004, Daejeon, Korea.