Jonathan Moore
Genome edit designer
Research Expertise
Publications
Evidence for Network Evolution in an Arabidopsis Interactome Map
Science / Jul 29, 2011
Dreze, M., Carvunis, A.-R., Charloteaux, B., Galli, M., Pevzner, S. J., Tasan, M., Ahn, Y.-Y., Balumuri, P., Barabási, A.-L., Bautista, V., Braun, P., Byrdsong, D., Chen, H., Chesnut, J. D., Cusick, M. E., Dangl, J. L., de los Reyes, C., Dricot, A., … Yazaki, J. (2011). Evidence for Network Evolution in an Arabidopsis Interactome Map. Science, 333(6042), 601–607. https://doi.org/10.1126/science.1203877
High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation
The Plant Cell / Mar 01, 2011
Breeze, E., Harrison, E., McHattie, S., Hughes, L., Hickman, R., Hill, C., Kiddle, S., Kim, Y., 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., … 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. https://doi.org/10.1105/tpc.111.083345
Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network
Science / Jul 29, 2011
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. (2011). Independently Evolved Virulence Effectors Converge onto Hubs in a Plant Immune System Network. Science, 333(6042), 596–601. https://doi.org/10.1126/science.1203659
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea
Genome Biology / Jan 01, 2014
Parkin, I. A., Koh, C., Tang, H., Robinson, S. J., Kagale, S., Clarke, W. E., Town, C. D., Nixon, J., Krishnakumar, V., Bidwell, S. L., Denoeud, F., Belcram, H., Links, M. G., Just, J., Clarke, C., Bender, T., Huebert, T., Mason, A. S., Pires, J., … Sharpe, A. G. (2014). Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea. Genome Biology, 15(6), R77. https://doi.org/10.1186/gb-2014-15-6-r77
Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice
American Journal of Physiology-Endocrinology and Metabolism / Apr 15, 2014
Rosell, M., Kaforou, M., Frontini, A., Okolo, A., Chan, Y.-W., Nikolopoulou, E., Millership, S., Fenech, M. E., MacIntyre, D., Turner, J. O., Moore, J. D., Blackburn, E., Gullick, W. J., Cinti, S., Montana, G., Parker, M. G., & Christian, M. (2014). Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice. American Journal of Physiology-Endocrinology and Metabolism, 306(8), E945–E964. https://doi.org/10.1152/ajpendo.00473.2013
Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis
The Plant Cell / Sep 01, 2012
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., Kliebenstein, D. J., Kim, Y., Stegle, O., Borgwardt, K., Zhang, C., Tabrett, A., … Denby, K. J. (2012). Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis . The Plant Cell, 24(9), 3530–3557. https://doi.org/10.1105/tpc.112.102046
A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission
PLoS Pathogens / Jun 26, 2014
Ryabov, E. V., Wood, G. R., Fannon, J. M., Moore, J. D., Bull, J. C., Chandler, D., Mead, A., Burroughs, N., & Evans, D. J. (2014). A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission. PLoS Pathogens, 10(6), e1004230. https://doi.org/10.1371/journal.ppat.1004230
Uterine Selection of Human Embryos at Implantation
Scientific Reports / Feb 06, 2014
Brosens, J. J., Salker, M. S., Teklenburg, G., Nautiyal, J., Salter, S., Lucas, E. S., Steel, J. H., Christian, M., Chan, Y.-W., Boomsma, C. M., Moore, J. D., Hartshorne, G. M., Šućurović, S., Mulac-Jericevic, B., Heijnen, C. J., Quenby, S., Groot Koerkamp, M. J., Holstege, F. C. P., Shmygol, A., & Macklon, N. S. (2014). Uterine Selection of Human Embryos at Implantation. Scientific Reports, 4(1). https://doi.org/10.1038/srep03894
A local regulatory network around three
NAC transcription factors in
stress responses and senescence in
A rabidopsis leaves
The Plant Journal / May 11, 2013
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., & Buchanan‐Wollaston, V. (2013). A local regulatory network around three <scp>NAC</scp> transcription factors in stress responses and senescence in <scp>A</scp>rabidopsis leaves. The Plant Journal, 75(1), 26–39. Portico. https://doi.org/10.1111/tpj.12194
Loss of Endometrial Plasticity in Recurrent Pregnancy Loss
Stem Cells / Dec 17, 2015
Lucas, E. S., Dyer, N. P., Murakami, K., Hou Lee, Y., Chan, Y.-W., Grimaldi, G., Muter, J., Brighton, P. J., Moore, J. D., Patel, G., Chan, J. K. Y., Takeda, S., Lam, E. W.-F., Quenby, S., Ott, S., & Brosens, J. J. (2015). Loss of Endometrial Plasticity in Recurrent Pregnancy Loss. Stem Cells, 34(2), 346–356. https://doi.org/10.1002/stem.2222
The dynamic architecture of the metabolic switch in Streptomyces coelicolor
BMC Genomics / Jan 01, 2010
Nieselt, K., Battke, F., Herbig, A., Bruheim, P., Wentzel, A., Jakobsen, Ø. M., Sletta, H., Alam, M. T., Merlo, M. E., Moore, J., Omara, W. A., Morrissey, E. R., Juarez-Hermosillo, M. A., Rodríguez-García, A., Nentwich, M., Thomas, L., Iqbal, M., Legaie, R., Gaze, W. H., … Wellington, E. M. (2010). The dynamic architecture of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11(1), 10. https://doi.org/10.1186/1471-2164-11-10
Tracing the ancestry of modern bread wheats
Nature Genetics / May 01, 2019
Pont, C., Leroy, T., Seidel, M., Tondelli, A., Duchemin, W., Armisen, D., Lang, D., Bustos-Korts, D., Goué, N., Balfourier, F., Molnár-Láng, M., Lage, J., Kilian, B., Özkan, H., Waite, D., Dyer, S., Letellier, T., Alaux, M., … Salse, J. (2019). Tracing the ancestry of modern bread wheats. Nature Genetics, 51(5), 905–911. https://doi.org/10.1038/s41588-019-0393-z
Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies
Journal of General Virology / Oct 06, 2010
Moore, J., Jironkin, A., Chandler, D., Burroughs, N., Evans, D. J., & Ryabov, E. V. (2010). Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies. Journal of General Virology, 92(1), 156–161. https://doi.org/10.1099/vir.0.025965-0
Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000
The Plant Cell / Nov 01, 2015
Lewis, L. A., Polanski, K., de Torres-Zabala, M., Jayaraman, S., Bowden, L., Moore, J., Penfold, C. A., Jenkins, D. J., Hill, C., Baxter, L., Kulasekaran, S., Truman, W., Littlejohn, G., Prusinska, J., Mead, A., Steinbrenner, J., Hickman, R., Rand, D., Wild, D. L., … Grant, M. (2015). Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000. The Plant Cell, 27(11), 3038–3064. https://doi.org/10.1105/tpc.15.00471
The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation
The Plant Journal / Dec 01, 2008
Alix, K., Joets, J., Ryder, C. D., Moore, J., Barker, G. C., Bailey, J. P., King, G. J., & (Pat) Heslop‐Harrison, J. S. (2008). The CACTA transposon Bot1 played a major role in Brassica genome divergence and gene proliferation. The Plant Journal, 56(6), 1030–1044. Portico. https://doi.org/10.1111/j.1365-313x.2008.03660.x
Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture
Molecular & Cellular Proteomics / Feb 01, 2012
Thomas, L., Hodgson, D. A., Wentzel, A., Nieselt, K., Ellingsen, T. E., Moore, J., Morrissey, E. R., Legaie, R., The STREAM Consortium, Wohlleben, W., Rodríguez-García, A., Martín, J. F., Burroughs, N. J., Wellington, E. M. H., & Smith, M. C. M. (2012). Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture. Molecular & Cellular Proteomics, 11(2), M111.013797. https://doi.org/10.1074/mcp.m111.013797
Developing genetic resources for pre-breeding in Brassica oleracea L.: an overview of the UK perspective
Journal of Plant Biotechnology / Mar 31, 2012
Walley, P. G., Teakle, G. R., Moore, J. D., Allender, C. J., Pink, D. A. C., Buchanan-Wollaston, V., & Barker, G. C. (2012). Developing genetic resources for pre-breeding in Brassica oleracea L.: an overview of the UK perspective. Journal of Plant Biotechnology, 39(1), 62–68. https://doi.org/10.5010/jpb.2012.39.1.062
CWRIS: an information management system to aid crop wild relative conservation and sustainable use.
Crop wild relative conservation and use / Jan 01, 2007
Kell, S. P., Moore, J. D., Iriondo, J. M., Scholten, M. A., Ford-Lloyd, B. V., & Maxted, N. (2007). CWRIS: an information management system to aid crop wild relative conservation and sustainable use. Crop Wild Relative Conservation and Use, 471–491. https://doi.org/10.1079/9781845930998.0471
Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response
Journal of Integrative Bioinformatics / Dec 01, 2010
Hassani-Pak, K., Legaie, R., Canevet, C., Berg, H. A. van den, Moore, J. D., & Rawlings, C. J. (2010). Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response. Journal of Integrative Bioinformatics, 7(3). https://doi.org/10.1515/jib-2010-121
Biotechnology and Genomics: Exploiting the Potential of CWR
Crop Wild Relatives and Climate Change / Jul 20, 2015
Walley, P. G., & Moore, J. D. (2015). Biotechnology and Genomics: Exploiting the Potential of CWR. Crop Wild Relatives and Climate Change, 212–223. Portico. https://doi.org/10.1002/9781118854396.ch12
Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus
Nature Communications / Feb 16, 2023
Edwards, A., Njaci, I., Sarkar, A., Jiang, Z., Kaithakottil, G. G., Moore, C., Cheema, J., Stevenson, C. E. M., Rejzek, M., Novák, P., Vigouroux, M., Vickers, M., Wouters, R. H. M., Paajanen, P., Steuernagel, B., Moore, J. D., Higgins, J., Swarbreck, D., Martens, S., … Emmrich, P. M. F. (2023). Genomics and biochemical analyses reveal a metabolon key to β-L-ODAP biosynthesis in Lathyrus sativus. Nature Communications, 14(1). https://doi.org/10.1038/s41467-023-36503-2
Evolutionarily related Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate horizontal or vertical transmission of these viruses
Sep 30, 2015
Ryabov, E. V., Fannon, J. M., Moore, J. D., Wood, G. R., & Evans, D. J. (2015). Evolutionarily related Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate horizontal or vertical transmission of these viruses. https://doi.org/10.7287/peerj.preprints.1405v1
Field cancerisation in colorectal cancer: Characterisation of the gene expression profile of the mucosal field around colorectal cancers and polyps
International Journal of Surgery / Nov 01, 2016
Patel, A., Wang, Y., Moore, J., Tripathi, G., Williams, N., & Arasaradnam, R. (2016). Field cancerisation in colorectal cancer: Characterisation of the gene expression profile of the mucosal field around colorectal cancers and polyps. International Journal of Surgery, 36, S33–S34. https://doi.org/10.1016/j.ijsu.2016.08.245
PWE-254 Is the macroscopically normal mucosa (MNM) around colorectal cancer really ‘normal’?: Abstract PWE-254 Table 1
Gut / Jun 01, 2015
Patel, A., Fang, Y., Moore, J., Williams, N., Tripathi, G., & Arasaradnam, R. (2015). PWE-254 Is the macroscopically normal mucosa (MNM) around colorectal cancer really ‘normal’?: Abstract PWE-254 Table 1. Gut, 64(Suppl 1), A324.2-A325. https://doi.org/10.1136/gutjnl-2015-309861.700
Vitamin B12 deficiency alters adipogenesis and associated microRNA's in human adipocytes
Endocrine Abstracts / Oct 12, 2015
Adaikalakoteswari, A., Vatish, M., McTernan, P., Randeva, H., Tripathi, G., & Saravanan, P. (2015). Vitamin B12 deficiency alters adipogenesis and associated microRNA’s in human adipocytes. Endocrine Abstracts. https://doi.org/10.1530/endoabs.38.p209
Vitamin B12 and folate imbalance induces cholesterol synthesis and endoplasmic reticulum stress in human adipocytes
Endocrine Abstracts / Mar 01, 2013
Adaikalakoteswari, A., Moore, J., Ciara, M., Voyais, P., Mcternan, P., Saravanan, P., & Tripathi, G. (2013). Vitamin B12 and folate imbalance induces cholesterol synthesis and endoplasmic reticulum stress in human adipocytes. Endocrine Abstracts, 1–1. https://doi.org/10.1530/endoabs.31.p182
Unified establishment and epigenetic inheritance of DNA methylation through cooperative MET1 activity
Sep 13, 2022
Briffa, A., Hollwey, E., Shahzad, Z., Moore, J. D., Lyons, D. B., Howard, M., & Zilberman, D. (2022). Unified establishment and epigenetic inheritance of DNA methylation through cooperative MET1 activity. https://doi.org/10.1101/2022.09.12.507517
Generated Randomly and Selected Functionally? The Nature of Enterovirus Recombination
Viruses / Apr 28, 2022
Alnaji, F. G., Bentley, K., Pearson, A., Woodman, A., Moore, J., Fox, H., Macadam, A. J., & Evans, D. J. (2022). Generated Randomly and Selected Functionally? The Nature of Enterovirus Recombination. Viruses, 14(5), 916. https://doi.org/10.3390/v14050916
The Evolutionary History of Wild, Domesticated, and FeralBrassica oleracea(Brassicaceae)
Apr 06, 2021
Mabry, M. E., Turner-Hissong, S. D., Gallagher, E. Y., McAlvay, A. C., An, H., Edger, P. P., Moore, J. D., Pink, D. A. C., Teakle, G. R., Stevens, C. J., Barker, G., Labate, J., Fuller, D. Q., Allaby, R. G., Beissinger, T., Decker, J. E., Gore, M. A., & Pires, J. C. (2021). The Evolutionary History of Wild, Domesticated, and FeralBrassica oleracea(Brassicaceae). https://doi.org/10.1101/2021.04.06.438638
Epigenetic inheritance mediates phenotypic diversity in natural populations
Mar 15, 2021
Shahzad, Z., Moore, J. D., Choi, J., & Zilberman, D. (2021). Epigenetic inheritance mediates phenotypic diversity in natural populations. https://doi.org/10.1101/2021.03.15.435374
Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale
Microbiome / Jan 22, 2021
Hilton, S., Picot, E., Schreiter, S., Bass, D., Norman, K., Oliver, A. E., Moore, J. D., Mauchline, T. H., Mills, P. R., Teakle, G. R., Clark, I. M., Hirsch, P. R., van der Gast, C. J., & Bending, G. D. (2021). Identification of microbial signatures linked to oilseed rape yield decline at the landscape scale. Microbiome, 9(1). https://doi.org/10.1186/s40168-020-00972-0
The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae)
Molecular Biology and Evolution / Jun 22, 2021
Mabry, M. E., Turner-Hissong, S. D., Gallagher, E. Y., McAlvay, A. C., An, H., Edger, P. P., Moore, J. D., Pink, D. A. C., Teakle, G. R., Stevens, C. J., Barker, G., Labate, J., Fuller, D. Q., Allaby, R. G., Beissinger, T., Decker, J. E., Gore, M. A., & Pires, J. C. (2021). The Evolutionary History of Wild, Domesticated, and Feral Brassica oleracea (Brassicaceae). Molecular Biology and Evolution, 38(10), 4419–4434. https://doi.org/10.1093/molbev/msab183
Time‐series transcriptomics reveals a BBX32‐directed control of acclimation to high light in mature Arabidopsis leaves
The Plant Journal / Aug 06, 2021
Alvarez‐Fernandez, R., Penfold, C. A., Galvez‐Valdivieso, G., Exposito‐Rodriguez, M., Stallard, E. J., Bowden, L., Moore, J. D., Mead, A., Davey, P. A., Matthews, J. S. A., Beynon, J., Buchanan‐Wollaston, V., Wild, D. L., Lawson, T., Bechtold, U., Denby, K. J., & Mullineaux, P. M. (2021). Time‐series transcriptomics reveals a BBX32‐directed control of acclimation to high light in mature Arabidopsis leaves. The Plant Journal, 107(5), 1363–1386. Portico. https://doi.org/10.1111/tpj.15384
Time series transcriptomics reveals aBBX32-directed control of dynamic acclimation to high light in matureArabidopsisleaves
Dec 26, 2020
Alvarez-Fernandez, R., Penfold, C. A., Galvez-Valdivieso, G., Exposito-Rodriguez, M., Stallard, E. J., Bowden, L., Moore, J. D., Mead, A., Davey, P. A., Matthews, J. S. A., Beynon, J., Buchanan-Wollaston, V., Wild, D. L., Lawson, T., Bechtold, U., Denby, K., & Mullineaux, P. M. (2020). Time series transcriptomics reveals aBBX32-directed control of dynamic acclimation to high light in matureArabidopsisleaves. https://doi.org/10.1101/2020.12.23.424212
Generated randomly and selected functionally? The nature of enterovirus recombination
Sep 29, 2020
Alnaji, F. G., Bentley, K., Pearson, A., Woodman, A., Moore, J., Fox, H., MacAdam, A., & Evans, D. J. (2020). Generated randomly and selected functionally? The nature of enterovirus recombination. https://doi.org/10.1101/2020.09.29.319285
A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume
Apr 27, 2020
Emmrich, P. M. F., Sarkar, A., Njaci, I., Kaithakottil, G. G., Ellis, N., Moore, C., Edwards, A., Heavens, D., Waite, D., Cheema, J., Trick, M., Moore, J., Webb, A., Caiazzo, R., Thomas, J., Higgins, J., Swarbreck, D., Kumar, S., Mundree, S., … Wang, T. L. (2020). A draft genome of grass pea (Lathyrus sativus), a resilient diploid legume. https://doi.org/10.1101/2020.04.24.058164
DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts
Molecular Cell / Jan 01, 2020
Choi, J., Lyons, D. B., Kim, M. Y., Moore, J. D., & Zilberman, D. (2020). DNA Methylation and Histone H1 Jointly Repress Transposable Elements and Aberrant Intragenic Transcripts. Molecular Cell, 77(2), 310-323.e7. https://doi.org/10.1016/j.molcel.2019.10.011
DNA methylation and histone H1 cooperatively repress transposable elements and aberrant intragenic transcripts
Jan 27, 2019
Choi, J., Lyons, D. B., Yvonne Kim, M., Moore, J. D., & Zilberman, D. (2019). DNA methylation and histone H1 cooperatively repress transposable elements and aberrant intragenic transcripts. https://doi.org/10.1101/527523
Differential expression of Lp-PLA2 in obesity and type 2 diabetes and the influence of lipids
Diabetologia / Feb 09, 2018
Jackisch, L., Kumsaiyai, W., Moore, J. D., Al-Daghri, N., Kyrou, I., Barber, T. M., Randeva, H., Kumar, S., Tripathi, G., & McTernan, P. G. (2018). Differential expression of Lp-PLA2 in obesity and type 2 diabetes and the influence of lipids. Diabetologia, 61(5), 1155–1166. https://doi.org/10.1007/s00125-018-4558-6
Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture
The Plant Cell / Sep 11, 2017
Walker, L., Boddington, C., Jenkins, D., Wang, Y., Grønlund, J. T., Hulsmans, J., Kumar, S., Patel, D., Moore, J. D., Carter, A., Samavedam, S., Bonomo, G., Hersh, D. S., Coruzzi, G. M., Burroughs, N. J., & Gifford, M. L. (2017). Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture. The Plant Cell, 29(10), 2393–2412. https://doi.org/10.1105/tpc.16.00961
The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae
BMC Genomics / Aug 30, 2017
Ingham, V. A., Pignatelli, P., Moore, J. D., Wagstaff, S., & Ranson, H. (2017). The transcription factor Maf-S regulates metabolic resistance to insecticides in the malaria vector Anopheles gambiae. BMC Genomics, 18(1). https://doi.org/10.1186/s12864-017-4086-7
The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low‐pH soils
MicrobiologyOpen / Apr 16, 2017
Lidbury, I. D. E. A., Fraser, T., Murphy, A. R. J., Scanlan, D. J., Bending, G. D., Jones, A. M. E., Moore, J. D., Goodall, A., Tibbett, M., Hammond, J. P., & Wellington, E. M. H. (2017). The ‘known’ genetic potential for microbial communities to degrade organic phosphorus is reduced in low‐pH soils. MicrobiologyOpen, 6(4). Portico. https://doi.org/10.1002/mbo3.474
Identification of extracellular glycerophosphodiesterases in Pseudomonas and their role in soil organic phosphorus remineralisation
Scientific Reports / May 19, 2017
Lidbury, I. D. E. A., Murphy, A. R. J., Fraser, T. D., Bending, G. D., Jones, A. M. E., Moore, J. D., Goodall, A., Tibbett, M., Hammond, J. P., Scanlan, D. J., & Wellington, E. M. H. (2017). Identification of extracellular glycerophosphodiesterases in Pseudomonas and their role in soil organic phosphorus remineralisation. Scientific Reports, 7(1). https://doi.org/10.1038/s41598-017-02327-6
BTB-BACK Domain Protein POB1 Suppresses Immune Cell Death by Targeting Ubiquitin E3 ligase PUB17 for Degradation
PLOS Genetics / Jan 05, 2017
Orosa, B., He, Q., Mesmar, J., Gilroy, E. M., McLellan, H., Yang, C., Craig, A., Bailey, M., Zhang, C., Moore, J. D., Boevink, P. C., Tian, Z., Birch, P. R. J., & Sadanandom, A. (2017). BTB-BACK Domain Protein POB1 Suppresses Immune Cell Death by Targeting Ubiquitin E3 ligase PUB17 for Degradation. PLOS Genetics, 13(1), e1006540. https://doi.org/10.1371/journal.pgen.1006540
Towards new sources of resistance to the currant-lettuce aphid (Nasonovia ribisnigri)
Molecular Breeding / Jan 01, 2017
Walley, P. G., Hough, G., Moore, J. D., Carder, J., Elliott, M., Mead, A., Jones, J., Teakle, G., Barker, G., Buchanan-Wollaston, V., Hand, P., Pink, D., & Collier, R. (2017). Towards new sources of resistance to the currant-lettuce aphid (Nasonovia ribisnigri). Molecular Breeding, 37(1). https://doi.org/10.1007/s11032-016-0606-4
Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis
Nature Communications / Aug 23, 2016
Sieberts, S. K., Zhu, F., García-García, J., Stahl, E., Pratap, A., Pandey, G., Pappas, D., Aguilar, D., Anton, B., Bonet, J., Eksi, R., Fornés, O., Guney, E., Li, H., Marín, M. A., Panwar, B., Planas-Iglesias, J., Poglayen, D., … Cui, J. (2016). Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis. Nature Communications, 7(1). https://doi.org/10.1038/ncomms12460
Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria
Environmental Microbiology / Jul 07, 2016
Lidbury, I. D. E. A., Murphy, A. R. J., Scanlan, D. J., Bending, G. D., Jones, A. M. E., Moore, J. D., Goodall, A., Hammond, J. P., & Wellington, E. M. H. (2016). Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria. Environmental Microbiology, 18(10), 3535–3549. Portico. https://doi.org/10.1111/1462-2920.13390
The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission
PeerJ / Jan 18, 2016
Ryabov, E. V., Fannon, J. M., Moore, J. D., Wood, G. R., & Evans, D. J. (2016). The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate their horizontal or vertical transmission. PeerJ, 4, e1591. Portico. https://doi.org/10.7717/peerj.1591
Prediction of human population responses to toxic compounds by a collaborative competition
Nature Biotechnology / Sep 01, 2015
Eduati, F., Mangravite, L. M., Wang, T., Tang, H., Bare, J. C., Huang, R., Norman, T., Kellen, M., Menden, M. P., Yang, J., Zhan, X., Zhong, R., Xiao, G., Xia, M., Abdo, N., Kosyk, O., Friend, S., Dearry, A., … Saez-Rodriguez, J. (2015). Prediction of human population responses to toxic compounds by a collaborative competition. Nature Biotechnology, 33(9), 933–940. https://doi.org/10.1038/nbt.3299
A Randomized Trial of Progesterone in Women with Recurrent Miscarriages
New England Journal of Medicine / Nov 26, 2015
Coomarasamy, A., Williams, H., Truchanowicz, E., Seed, P. T., Small, R., Quenby, S., Gupta, P., Dawood, F., Koot, Y. E. M., Bender Atik, R., Bloemenkamp, K. W. M., Brady, R., Briley, A. L., Cavallaro, R., Cheong, Y. C., Chu, J. J., Eapen, A., Ewies, A., Hoek, A., … Rai, R. (2015). A Randomized Trial of Progesterone in Women with Recurrent Miscarriages. New England Journal of Medicine, 373(22), 2141–2148. https://doi.org/10.1056/nejmoa1504927
The clock protein period 2 synchronizes mitotic expansion and decidual transformation of human endometrial stromal cells
The FASEB Journal / Jan 08, 2015
Muter, J., Lucas, E. S., Chan, Y., Brighton, P. J., Moore, J. D., Lacey, L., Quenby, S., Lam, E. W. ‐F., & Brosens, J. J. (2015). The clock protein period 2 synchronizes mitotic expansion and decidual transformation of human endometrial stromal cells. The FASEB Journal, 29(4), 1603–1614. Portico. https://doi.org/10.1096/fj.14-267195
Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis
The Plant Cell / Feb 01, 2016
Bechtold, U., Penfold, C. A., Jenkins, D. J., Legaie, R., Moore, J. D., Lawson, T., Matthews, J. S. A., Vialet-Chabrand, S. R. M., Baxter, L., Subramaniam, S., Hickman, R., Florance, H., Sambles, C., Salmon, D. L., Feil, R., Bowden, L., Hill, C., Baker, N. R., Lunn, J. E., … Mullineaux, P. M. (2016). Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis. The Plant Cell, 28(2), 345–366. https://doi.org/10.1105/tpc.15.00910
Vitamin B12 insufficiency induces cholesterol biosynthesis by limiting s-adenosylmethionine and modulating the methylation of SREBF1 and LDLR genes
Clinical Epigenetics / Feb 27, 2015
Adaikalakoteswari, A., Finer, S., Voyias, P. D., McCarthy, C. M., Vatish, M., Moore, J., Smart-Halajko, M., Bawazeer, N., Al-Daghri, N. M., McTernan, P. G., Kumar, S., Hitman, G. A., Saravanan, P., & Tripathi, G. (2015). Vitamin B12 insufficiency induces cholesterol biosynthesis by limiting s-adenosylmethionine and modulating the methylation of SREBF1 and LDLR genes. Clinical Epigenetics, 7(1). https://doi.org/10.1186/s13148-015-0046-8
Decidualization Induces a Secretome Switch in Perivascular Niche Cells of the Human Endometrium
Endocrinology / Nov 01, 2014
Murakami, K., Lee, Y. H., Lucas, E. S., Chan, Y.-W., Durairaj, R. P., Takeda, S., Moore, J. D., Tan, B. K., Quenby, S., Chan, J. K. Y., Gargett, C. E., & Brosens, J. J. (2014). Decidualization Induces a Secretome Switch in Perivascular Niche Cells of the Human Endometrium. Endocrinology, 155(11), 4542–4553. https://doi.org/10.1210/en.2014-1370
MosaicSolver: a tool for determining recombinants of viral genomes from pileup data
Nucleic Acids Research / Aug 12, 2014
Wood, G. R., Ryabov, E. V., Fannon, J. M., Moore, J. D., Evans, D. J., & Burroughs, N. (2014). MosaicSolver: a tool for determining recombinants of viral genomes from pileup data. Nucleic Acids Research, 42(16), e123–e123. https://doi.org/10.1093/nar/gku524
Assessment of myometrial transcriptome changes associated with spontaneous human labour by high‐throughput RNA‐seq
Experimental Physiology / Jan 09, 2014
Chan, Y., van den Berg, H. A., Moore, J. D., Quenby, S., & Blanks, A. M. (2014). Assessment of myometrial transcriptome changes associated with spontaneous human labour by high‐throughput RNA‐seq. Experimental Physiology, 99(3), 510–524. Portico. https://doi.org/10.1113/expphysiol.2013.072868
Dissecting the organ specificity of insecticide resistance candidate genes in Anopheles gambiae: known and novel candidate genes
BMC Genomics / Jan 01, 2014
Ingham, V. A., Jones, C. M., Pignatelli, P., Balabanidou, V., Vontas, J., Wagstaff, S. C., Moore, J. D., & Ranson, H. (2014). Dissecting the organ specificity of insecticide resistance candidate genes in Anopheles gambiae: known and novel candidate genes. BMC Genomics, 15(1), 1018. https://doi.org/10.1186/1471-2164-15-1018
BAI 3, CDX 2 and
VIL 1: a panel of three
antibodies to distinguish small cell from
large cell neuroendocrine lung carcinomas
Histopathology / Nov 25, 2013
Bari, M. F., Brown, H., Nicholson, A. G., Kerr, K. M., Gosney, J. R., Wallace, W. A., Soomro, I., Muller, S., Peat, D., Moore, J. D., Ward, L. A., Freidin, M. B., Lim, E., Vatish, M., & Snead, D. R. J. (2013). <scp>BAI</scp>3, <scp>CDX</scp>2 and <scp>VIL</scp>1: a panel of three antibodies to distinguish small cell from large cell neuroendocrine lung carcinomas. Histopathology, 64(4), 547–556. Portico. https://doi.org/10.1111/his.12278
Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad‐spectrum virus resistance
The Plant Journal / Dec 30, 2013
Nellist, C. F., Qian, W., Jenner, C. E., Moore, J. D., Zhang, S., Wang, X., Briggs, W. H., Barker, G. C., Sun, R., & Walsh, J. A. (2013). Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad‐spectrum virus resistance. The Plant Journal, 77(2), 261–268. Portico. https://doi.org/10.1111/tpj.12389
Genetic regulation of glucoraphanin accumulation in Beneforté® broccoli
New Phytologist / Apr 08, 2013
Traka, M. H., Saha, S., Huseby, S., Kopriva, S., Walley, P. G., Barker, G. C., Moore, J., Mero, G., van den Bosch, F., Constant, H., Kelly, L., Schepers, H., Boddupalli, S., & Mithen, R. F. (2013). Genetic regulation of glucoraphanin accumulation in Beneforté® broccoli. New Phytologist, 198(4), 1085–1095. Portico. https://doi.org/10.1111/nph.12232
MEME-LaB: motif analysis in clusters
Bioinformatics / May 14, 2013
Brown, P., Baxter, L., Hickman, R., Beynon, J., Moore, J. D., & Ott, S. (2013). MEME-LaB: motif analysis in clusters. Bioinformatics, 29(13), 1696–1697. https://doi.org/10.1093/bioinformatics/btt248
Making open data work for plant scientists
Journal of Experimental Botany / Sep 16, 2013
Leonelli, S., Smirnoff, N., Moore, J., Cook, C., & Bastow, R. (2013). Making open data work for plant scientists. Journal of Experimental Botany, 64(14), 4109–4117. https://doi.org/10.1093/jxb/ert273
Archaeogenomic Evidence of Punctuated Genome Evolution in Gossypium
Molecular Biology and Evolution / Feb 14, 2012
Palmer, S. A., Clapham, A. J., Rose, P., Freitas, F. O., Owen, B. D., Beresford-Jones, D., Moore, J. D., Kitchen, J. L., & Allaby, R. G. (2012). Archaeogenomic Evidence of Punctuated Genome Evolution in Gossypium. Molecular Biology and Evolution, 29(8), 2031–2038. https://doi.org/10.1093/molbev/mss070
Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants
The Plant Cell / Oct 01, 2012
Baxter, L., Jironkin, A., Hickman, R., Moore, J., Barrington, C., Krusche, P., Dyer, N. P., Buchanan-Wollaston, V., Tiskin, A., Beynon, J., Denby, K., & Ott, S. (2012). Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants. The Plant Cell, 24(10), 3949–3965. https://doi.org/10.1105/tpc.112.103010
MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling
BMC Bioinformatics / Nov 05, 2012
Kitchen, J. L., Moore, J. D., Palmer, S. A., & Allaby, R. G. (2012). MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling. BMC Bioinformatics, 13(1). https://doi.org/10.1186/1471-2105-13-287
Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor
BMC Genomics / Mar 26, 2010
Alam, M. T., Merlo, M. E., Hodgson, D. A., Wellington, E. M., Takano, E., & Breitling, R. (2010). Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor. BMC Genomics, 11(1). https://doi.org/10.1186/1471-2164-11-202
Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation
PLoS ONE / Jul 22, 2009
Palmer, S. A., Moore, J. D., Clapham, A. J., Rose, P., & Allaby, R. G. (2009). Archaeogenetic Evidence of Ancient Nubian Barley Evolution from Six to Two-Row Indicates Local Adaptation. PLoS ONE, 4(7), e6301. https://doi.org/10.1371/journal.pone.0006301
CWRML: representing crop wild relative conservation and use data in XML
BMC Bioinformatics / Feb 25, 2008
Moore, J. D., Kell, S. P., Iriondo, J. M., Ford-Lloyd, B. V., & Maxted, N. (2008). CWRML: representing crop wild relative conservation and use data in XML. BMC Bioinformatics, 9(1). https://doi.org/10.1186/1471-2105-9-116
TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism
Bioinformatics / Jan 19, 2008
Moore, J. D., & Allaby, R. G. (2008). TreeMos: a high-throughput phylogenomic approach to find and visualize phylogenetic mosaicism. Bioinformatics, 24(5), 717–718. https://doi.org/10.1093/bioinformatics/btn027
The Genomic Organization of Retrotransposons in Brassica oleracea
Plant Molecular Biology / Dec 01, 2005
Alix, K., Ryder, C. D., Moore, J., King, G. J., & (Pat) Heslop-Harrison, J. S. (2005). The Genomic Organization of Retrotransposons in Brassica oleracea. Plant Molecular Biology, 59(6), 839–851. https://doi.org/10.1007/s11103-005-1510-1
Education
University of Warwick
PhD Bioinformatics, Wellesbourne / June, 2007
University of Birmingham
MSc Conservation and Utilisation of Plant Genetic Resources, Biology / June, 2003
Sheffield Hallam University Sheffield Business School
PGCert Enterprise and Network Management / June, 1996
University of Sheffield
B.eng Electronic and Electrical Engineering, Engineering / June, 1985
Experience
Tropic Biosciences
Bioinformatician / July, 2021 — Present
John Innes Centre
Research Bioinformatics Specialist / September, 2017 — June, 2021
Earlham Institute
Bioinformatics Manager / November, 2015 — August, 2017
University of Warwick
Senior Research Fellow in Bioinformatics / March, 2008 — October, 2015
PDRA Ancient DNA Bioinformatics / 2006 — March, 2008
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