Jonathan Moore

Genome edit designer

Norwich

Research Interests

Data science
Genome editing
Bioinformatics
Evolution
Biodiversity
Cell Biology
Plant Science
Physiology (medical)
Physiology
Endocrinology, Diabetes and Metabolism
Virology
Genetics
Molecular Biology
Immunology
Microbiology
Parasitology
Developmental Biology
Molecular Medicine
Biotechnology
Biomedical Engineering
Applied Microbiology and Biotechnology
Bioengineering
Nutrition and Dietetics
Genetics (clinical)
Ecology, Evolution, Behavior and Systematics
Agronomy and Crop Science
Computational Mathematics
Computational Theory and Mathematics
Computer Science Applications
Statistics and Probability
Applied Mathematics
Structural Biology
Infectious Diseases

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 Arabidopsis 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 &amp; 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

BAI3, CDX2 and VIL1: 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

Coventry

University of Birmingham

MSc Conservation and Utilisation of Plant Genetic Resources, Biology / June, 2003

Birmingham

Sheffield Hallam University Sheffield Business School

PGCert Enterprise and Network Management / June, 1996

Sheffield

University of Sheffield

B.eng Electronic and Electrical Engineering, Engineering / June, 1985

Sheffield

Experience

Tropic Biosciences

Bioinformatician / July, 2021Present

John Innes Centre

Research Bioinformatics Specialist / September, 2017June, 2021

Earlham Institute

Bioinformatics Manager / November, 2015August, 2017

University of Warwick

Senior Research Fellow in Bioinformatics / March, 2008October, 2015

PDRA Ancient DNA Bioinformatics / 2006March, 2008

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