David Studholme
Senior Lecturer / Associate Professor at University of Exeter
Research Expertise
Publications
The Pfam protein families database
Nucleic Acids Research / Jan 01, 2004
Bateman, A. (2004). The Pfam protein families database. Nucleic Acids Research, 32(90001), 138D – 141. https://doi.org/10.1093/nar/gkh121
PREreview of bioRxiv article “Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans”
Authorea
Kamoun, S. (n.d.). PREreview of bioRxiv article “Genome-wide increased copy number is associated with emergence of super-fit clones of the Irish potato famine pathogen Phytophthora infestans.” Authorea. https://doi.org/10.22541/au.156177170.03785716
Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity
Aug 04, 2020
Volz, E., Hill, V., McCrone, J. T., Price, A., Jorgensen, D., O’Toole, Á., Southgate, J., Johnson, R., Jackson, B., Nascimento, F. F., Rey, S. M., Nicholls, S. M., Colquhoun, R. M., da Silva Filipe, A., Shepherd, J., Pascall, D. J., Shah, R., Jesudason, N., Li, K., … Connor, T. R. (2020). Evaluating the effects of SARS-CoV-2 Spike mutation D614G on transmissibility and pathogenicity. https://doi.org/10.1101/2020.07.31.20166082
InterPro, progress and status in 2005
Nucleic Acids Research / Dec 17, 2004
Mulder, N. J. (2004). InterPro, progress and status in 2005. Nucleic Acids Research, 33(Database issue), D201–D205. https://doi.org/10.1093/nar/gki106
Descriptive Epidemiology of SARS-CoV-2 Gamma (P.1/501Y.V3) variant cases in England, August 2021
May 31, 2022
Aziz, N. A., Twohig, K. A., Sinnathamby, M., Zaidi, A., Aliabadi, S., Groves, N., Nash, S., Thelwall, S., & Dabrera, G. (2022). Descriptive Epidemiology of SARS-CoV-2 Gamma (P.1/501Y.V3) variant cases in England, August 2021. https://doi.org/10.1101/2022.05.31.22275827
miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii
Nature / May 30, 2007
Molnár, A., Schwach, F., Studholme, D. J., Thuenemann, E. C., & Baulcombe, D. C. (2007). miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 447(7148), 1126–1129. https://doi.org/10.1038/nature05903
Assessing the performance of the Oxford Nanopore Technologies MinION
Biomolecular Detection and Quantification / Mar 01, 2015
Laver, T., Harrison, J., O’Neill, P. A., Moore, K., Farbos, A., Paszkiewicz, K., & Studholme, D. J. (2015). Assessing the performance of the Oxford Nanopore Technologies MinION. Biomolecular Detection and Quantification, 3, 1–8. https://doi.org/10.1016/j.bdq.2015.02.001
The Bacterial Enhancer-Dependent ς54(ςN) Transcription Factor
Journal of Bacteriology / Aug 01, 2000
Buck, M., Gallegos, M.-T., Studholme, D. J., Guo, Y., & Gralla, J. D. (2000). The Bacterial Enhancer-Dependent ς54(ςN) Transcription Factor. Journal of Bacteriology, 182(15), 4129–4136. https://doi.org/10.1128/jb.182.15.4129-4136.2000
Application of 'next-generation' sequencing technologies to microbial genetics
Nature Reviews Microbiology / Feb 23, 2009
MacLean, D., Jones, J. D. G., & Studholme, D. J. (2009). Application of “next-generation” sequencing technologies to microbial genetics. Nature Reviews Microbiology, 7(4), 96–97. https://doi.org/10.1038/nrmicro2088
Recurrent Emergence and Transmission of a SARS-CoV-2 Spike Deletion H69/V70
SSRN Electronic Journal / Jan 01, 2021
Kemp, S. A., Meng, B., Ferriera, I. A. T. M., Datir, R., Harvey, W. T., Collier, D. A., Lytras, S., Papa, G., Carabelli, A., Kenyon, J., Lever, A., James, L. C., Robertson, D., & Gupta, R. K. (2021). Recurrent Emergence and Transmission of a SARS-CoV-2 Spike Deletion H69/V70. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.3780277
Domain Architectures of σ54-Dependent Transcriptional Activators
Journal of Bacteriology / Mar 15, 2003
Studholme, D. J., & Dixon, R. (2003). Domain Architectures of σ54-Dependent Transcriptional Activators. Journal of Bacteriology, 185(6), 1757–1767. https://doi.org/10.1128/jb.185.6.1757-1767.2003
Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis
Nature / Jun 03, 2009
Mosher, R. A., Melnyk, C. W., Kelly, K. A., Dunn, R. M., Studholme, D. J., & Baulcombe, D. C. (2009). Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature, 460(7252), 283–286. https://doi.org/10.1038/nature08084
Genome Sequence of Azotobacter vinelandii , an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes
Journal of Bacteriology / Jul 15, 2009
Setubal, J. C., dos Santos, P., Goldman, B. S., Ertesvåg, H., Espin, G., Rubio, L. M., Valla, S., Almeida, N. F., Balasubramanian, D., Cromes, L., Curatti, L., Du, Z., Godsy, E., Goodner, B., Hellner-Burris, K., Hernandez, J. A., Houmiel, K., Imperial, J., Kennedy, C., … Wood, D. (2009). Genome Sequence of Azotobacter vinelandii , an Obligate Aerobe Specialized To Support Diverse Anaerobic Metabolic Processes. Journal of Bacteriology, 191(14), 4534–4545. https://doi.org/10.1128/jb.00504-09
Changes in symptomatology, re-infection and transmissibility associated with SARS-CoV-2 variant B.1.1.7: an ecological study
Jan 29, 2021
Graham, M. S., Sudre, C. H., May, A., Antonelli, M., Murray, B., Varsavsky, T., Kläser, K., Canas, L. S., Molteni, E., Modat, M., Drew, D. A., Nguyen, L. H., Polidori, L., Selvachandran, S., Hu, C., Capdevila, J., Hammers, A., Chan, A. T., … Wolf, J. (2021). Changes in symptomatology, re-infection and transmissibility associated with SARS-CoV-2 variant B.1.1.7: an ecological study. https://doi.org/10.1101/2021.01.28.21250680
Chloroplasts play a central role in plant defence and are targeted by pathogen effectors
Nature Plants / Jun 01, 2015
de Torres Zabala, M., Littlejohn, G., Jayaraman, S., Studholme, D., Bailey, T., Lawson, T., Tillich, M., Licht, D., Bölter, B., Delfino, L., Truman, W., Mansfield, J., Smirnoff, N., & Grant, M. (2015). Chloroplasts play a central role in plant defence and are targeted by pathogen effectors. Nature Plants, 1(6). https://doi.org/10.1038/nplants.2015.74
Multidimensional Protein Identification Technology (MudPIT) Analysis of Ubiquitinated Proteins in Plants
Molecular & Cellular Proteomics / Apr 01, 2007
Maor, R., Jones, A., Nühse, T. S., Studholme, D. J., Peck, S. C., & Shirasu, K. (2007). Multidimensional Protein Identification Technology (MudPIT) Analysis of Ubiquitinated Proteins in Plants. Molecular & Cellular Proteomics, 6(4), 601–610. https://doi.org/10.1074/mcp.m600408-mcp200
Genome sequence and genetic diversity of European ash trees
Nature / Dec 26, 2016
Sollars, E. S. A., Harper, A. L., Kelly, L. J., Sambles, C. M., Ramirez-Gonzalez, R. H., Swarbreck, D., Kaithakottil, G., Cooper, E. D., Uauy, C., Havlickova, L., Worswick, G., Studholme, D. J., Zohren, J., Salmon, D. L., Clavijo, B. J., Li, Y., He, Z., Fellgett, A., McKinney, L. V., … Buggs, R. J. A. (2016). Genome sequence and genetic diversity of European ash trees. Nature, 541(7636), 212–216. https://doi.org/10.1038/nature20786
The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences
FEMS Microbiology Letters / May 01, 2000
Studholme, D. J., & Buck, M. (2000). The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. FEMS Microbiology Letters, 186(1), 1–9. https://doi.org/10.1111/j.1574-6968.2000.tb09074.x
A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000
Molecular Plant-Microbe Interactions® / Jan 01, 2009
Almeida, N. F., Yan, S., Lindeberg, M., Studholme, D. J., Schneider, D. J., Condon, B., Liu, H., Viana, C. J., Warren, A., Evans, C., Kemen, E., MacLean, D., Angot, A., Martin, G. B., Jones, J. D., Collmer, A., Setubal, J. C., & Vinatzer, B. A. (2009). A Draft Genome Sequence of Pseudomonas syringae pv. tomato T1 Reveals a Type III Effector Repertoire Significantly Divergent from That of Pseudomonas syringae pv. tomato DC3000. Molecular Plant-Microbe Interactions®, 22(1), 52–62. https://doi.org/10.1094/mpmi-22-1-0052
Mechanism of Action of the Escherichia coli Phage Shock Protein PspA in Repression of the AAA Family Transcription Factor PspF
Journal of Molecular Biology / Jun 01, 2002
Elderkin, S., Jones, S., Schumacher, J., Studholme, D., & Buck, M. (2002). Mechanism of Action of the Escherichia coli Phage Shock Protein PspA in Repression of the AAA Family Transcription Factor PspF. Journal of Molecular Biology, 320(1), 23–37. https://doi.org/10.1016/s0022-2836(02)00404-7
Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora
BMC Genomics / Oct 05, 2015
Sharma, R., Xia, X., Cano, L. M., Evangelisti, E., Kemen, E., Judelson, H., Oome, S., Sambles, C., van den Hoogen, D. J., Kitner, M., Klein, J., Meijer, H. J. G., Spring, O., Win, J., Zipper, R., Bode, H. B., Govers, F., Kamoun, S., Schornack, S., … Thines, M. (2015). Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics, 16(1). https://doi.org/10.1186/s12864-015-1904-7
Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant
Science / Dec 17, 2021
Elliott, P., Haw, D., Wang, H., Eales, O., Walters, C. E., Ainslie, K. E. C., Atchison, C., Fronterre, C., Diggle, P. J., Page, A. J., Trotter, A. J., Prosolek, S. J., Ashby, D., Donnelly, C. A., Barclay, W., Taylor, G., Cooke, G., Ward, H., … Darzi, A. (2021). Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant. Science, 374(6574). https://doi.org/10.1126/science.abl9551
Pseudomonas syringae Strains Naturally Lacking the Classical P. syringae hrp/hrc Locus Are Common Leaf Colonizers Equipped with an Atypical Type III Secretion System
Molecular Plant-Microbe Interactions® / Feb 01, 2010
Clarke, C. R., Cai, R., Studholme, D. J., Guttman, D. S., & Vinatzer, B. A. (2010). Pseudomonas syringae Strains Naturally Lacking the Classical P. syringae hrp/hrc Locus Are Common Leaf Colonizers Equipped with an Atypical Type III Secretion System. Molecular Plant-Microbe Interactions®, 23(2), 198–210. https://doi.org/10.1094/mpmi-23-2-0198
SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans‐acting endogenous siRNA
The Plant Journal / Mar 09, 2007
Hernandez‐Pinzon, I., Yelina, N. E., Schwach, F., Studholme, D. J., Baulcombe, D., & Dalmay, T. (2007). SDE5, the putative homologue of a human mRNA export factor, is required for transgene silencing and accumulation of trans‐acting endogenous siRNA. The Plant Journal, 50(1), 140–148. Portico. https://doi.org/10.1111/j.1365-313x.2007.03043.x
Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens
Microbial Genomics / Oct 01, 2016
Monteil, C. L., Yahara, K., Studholme, D. J., Mageiros, L., Méric, G., Swingle, B., Morris, C. E., Vinatzer, B. A., & Sheppard, S. K. (2016). Population-genomic insights into emergence, crop adaptation and dissemination of Pseudomonas syringae pathogens. Microbial Genomics, 2(10). https://doi.org/10.1099/mgen.0.000089
DNA Binding Activity of the Escherichia coli Nitric Oxide Sensor NorR Suggests a Conserved Target Sequence in Diverse Proteobacteria
Journal of Bacteriology / Oct 01, 2004
Tucker, N. P., D’Autréaux, B., Studholme, D. J., Spiro, S., & Dixon, R. (2004). DNA Binding Activity of the Escherichia coli Nitric Oxide Sensor NorR Suggests a Conserved Target Sequence in Diverse Proteobacteria. Journal of Bacteriology, 186(19), 6656–6660. https://doi.org/10.1128/jb.186.19.6656-6660.2004
Genome-Enabled Phylogeographic Investigation of the Quarantine Pathogen Ralstonia solanacearum Race 3 Biovar 2 and Screening for Sources of Resistance Against Its Core Effectors
Phytopathology® / May 01, 2015
Clarke, C. R., Studholme, D. J., Hayes, B., Runde, B., Weisberg, A., Cai, R., Wroblewski, T., Daunay, M.-C., Wicker, E., Castillo, J. A., & Vinatzer, B. A. (2015). Genome-Enabled Phylogeographic Investigation of the Quarantine Pathogen Ralstonia solanacearum Race 3 Biovar 2 and Screening for Sources of Resistance Against Its Core Effectors. Phytopathology®, 105(5), 597–607. https://doi.org/10.1094/phyto-12-14-0373-r
Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus
PLOS Pathogens / Jul 24, 2017
Galhano, R., Illana, A., Ryder, L. S., Rodríguez-Romero, J., Demuez, M., Badaruddin, M., Martinez-Rocha, A. L., Soanes, D. M., Studholme, D. J., Talbot, N. J., & Sesma, A. (2017). Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus. PLOS Pathogens, 13(7), e1006516. https://doi.org/10.1371/journal.ppat.1006516
Evidence for Large Complex Networks of Plant Short Silencing RNAs
PLoS ONE / Mar 26, 2010
MacLean, D., Elina, N., Havecker, E. R., Heimstaedt, S. B., Studholme, D. J., & Baulcombe, D. C. (2010). Evidence for Large Complex Networks of Plant Short Silencing RNAs. PLoS ONE, 5(3), e9901. https://doi.org/10.1371/journal.pone.0009901
The Impact of Viral Mutations on Recognition by SARS-CoV-2 Specific T-Cells
SSRN Electronic Journal / Jan 01, 2021
de Silva, T. I., Liu, G., Lindsey, B. B., Dong, D., Shah, D., Mentzer, A. J., Angyal, A., Brown, R., Parker, M. D., Yin, Z., Yao, X., Turtle, L., Dunachie, S., Maini, M., Ogg, G., Knight, J., Peng, Y., Rowland-Jones, S. L., & Dong, T. (2021). The Impact of Viral Mutations on Recognition by SARS-CoV-2 Specific T-Cells. SSRN Electronic Journal. https://doi.org/10.2139/ssrn.3844713
Pain Mapping and Neuropathic Features of Common Shoulder Pathologies
Hong Kong Journal of Orthopaedic Research / Aug 30, 2020
Dunkerley, S., King, A., Batten, T. J., Evans, J. P., Metz, J., Gallacher, S., Davies, K. E., Smith, C., & Kitson, J. (2020). Pain Mapping and Neuropathic Features of Common Shoulder Pathologies. Hong Kong Journal of Orthopaedic Research, 3(2), 41–45. https://doi.org/10.37515/ortho.8231.3205
Phylogenetic analysis of transformable strains of thermophilicBacillusspecies
FEMS Microbiology Letters / Mar 01, 1999
Studholme, D. J., Jackson, R. A., & Leak, D. J. (1999). Phylogenetic analysis of transformable strains of thermophilicBacillusspecies. FEMS Microbiology Letters, 172(1), 85–90. https://doi.org/10.1111/j.1574-6968.1999.tb13454.x
Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius
Biotechnology Letters / Mar 27, 2008
Thompson, A. H., Studholme, D. J., Green, E. M., & Leak, D. J. (2008). Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius. Biotechnology Letters, 30(8), 1359–1365. https://doi.org/10.1007/s10529-008-9698-1
Identification of potential σN-dependent promoters in bacterial genomes
Microbiology / Dec 01, 2000
Studholme, D. J., Buck, M., & Nixon, T. (2000). Identification of potential σN-dependent promoters in bacterial genomes. Microbiology, 146(12), 3021–3023. https://doi.org/10.1099/00221287-146-12-3021
Metagenomic analysis of the complex microbial consortium associated with cultures of the oil‐rich alga Botryococcus braunii
MicrobiologyOpen / Jun 28, 2017
Sambles, C., Moore, K., Lux, T. M., Jones, K., Littlejohn, G. R., Gouveia, J. D., Aves, S. J., Studholme, D. J., Lee, R., & Love, J. (2017). Metagenomic analysis of the complex microbial consortium associated with cultures of the oil‐rich alga Botryococcus braunii. MicrobiologyOpen, 6(4). Portico. https://doi.org/10.1002/mbo3.482
New and Improved Techniques for the Study of Pathogenic Fungi
Trends in Microbiology / Jan 01, 2016
Cairns, T. C., Studholme, D. J., Talbot, Nicholas. J., & Haynes, K. (2016). New and Improved Techniques for the Study of Pathogenic Fungi. Trends in Microbiology, 24(1), 35–50. https://doi.org/10.1016/j.tim.2015.09.008
A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger”
Agronomy / Jan 17, 2014
Harrison, J., Moore, K., Paszkiewicz, K., Jones, T., Grant, M., Ambacheew, D., Muzemil, S., & Studholme, D. (2014). A Draft Genome Sequence for Ensete ventricosum, the Drought-Tolerant “Tree Against Hunger.” Agronomy, 4(1), 13–33. https://doi.org/10.3390/agronomy4010013
Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil
Molecular Plant Pathology / Jul 24, 2016
Shaw, S., Le Cocq, K., Paszkiewicz, K., Moore, K., Winsbury, R., de Torres Zabala, M., Studholme, D. J., Salmon, D., Thornton, C. R., & Grant, M. R. (2016). Transcriptional reprogramming underpins enhanced plant growth promotion by the biocontrol fungus Trichoderma hamatum GD12 during antagonistic interactions with Sclerotinia sclerotiorum in soil. Molecular Plant Pathology, 17(9), 1425–1441. Portico. https://doi.org/10.1111/mpp.12429
Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica
FEMS Microbiology Letters / Jul 01, 2004
Studholme, D. J., Fuerst, J. A., & Bateman, A. (2004). Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica. FEMS Microbiology Letters, 236(2), 333–340. https://doi.org/10.1111/j.1574-6968.2004.tb09666.x
Novel roles of σN in small genomes
Microbiology / Jan 01, 2000
Studholme, D. J., & Buck, M. (2000). Novel roles of σN in small genomes. Microbiology, 146(1), 4–5. https://doi.org/10.1099/00221287-146-1-4
Rapid, specific, simple, in-field detection of Xanthomonas campestris pathovar musacearum by loop-mediated isothermal amplification
Journal of Applied Microbiology / Nov 22, 2015
Hodgetts, J., Hall, J., Karamura, G., Grant, M., Studholme, D. J., Boonham, N., Karamura, E., & Smith, J. J. (2015). Rapid, specific, simple, in-field detection of Xanthomonas campestris pathovar musacearum by loop-mediated isothermal amplification. Journal of Applied Microbiology, 119(6), 1651–1658. Portico. https://doi.org/10.1111/jam.12959
Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors
Pathogens / Mar 18, 2014
Wasukira, A., Coulter, M., Al-Sowayeh, N., Thwaites, R., Paszkiewicz, K., Kubiriba, J., Smith, J., Grant, M., & Studholme, D. (2014). Genome Sequencing of Xanthomonas vasicola Pathovar vasculorum Reveals Variation in Plasmids and Genes Encoding Lipopolysaccharide Synthesis, Type-IV Pilus and Type-III Secretion Effectors. Pathogens, 3(1), 211–237. https://doi.org/10.3390/pathogens3010211
Molecular Fingerprinting of Salmonella enterica subsp. enterica Typhimurium and Salmonella enterica subsp. enterica Derby Isolated from Tropical Seafood in South India
Molecular Biotechnology / May 15, 2008
Kumar, R., Surendran, P. K., & Thampuran, N. (2008). Molecular Fingerprinting of Salmonella enterica subsp. enterica Typhimurium and Salmonella enterica subsp. enterica Derby Isolated from Tropical Seafood in South India. Molecular Biotechnology, 40(1), 95–100. https://doi.org/10.1007/s12033-008-9067-2
Farmers’ knowledge and perception of enset Xanthomonas wilt in southern Ethiopia
Agriculture & Food Security / Nov 28, 2017
Yemataw, Z., Mekonen, A., Chala, A., Tesfaye, K., Mekonen, K., Studholme, D. J., & Sharma, K. (2017). Farmers’ knowledge and perception of enset Xanthomonas wilt in southern Ethiopia. Agriculture & Food Security, 6(1). https://doi.org/10.1186/s40066-017-0146-0
Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida
International Journal of Systematic and Evolutionary Microbiology / Sep 01, 2017
Vicente, J. G., Rothwell, S., Holub, E. B., & Studholme, D. J. (2017). Pathogenic, phenotypic and molecular characterisation of Xanthomonas nasturtii sp. nov. and Xanthomonas floridensis sp. nov., new species of Xanthomonas associated with watercress production in Florida. International Journal of Systematic and Evolutionary Microbiology, 67(9), 3645–3654. https://doi.org/10.1099/ijsem.0.002189
Application of high‐throughput genome sequencing to intrapathovar variation in Pseudomonas syringae
Molecular Plant Pathology / Apr 01, 2011
STUDHOLME, D. J. (2011). Application of high‐throughput genome sequencing to intrapathovar variation in Pseudomonas syringae. Molecular Plant Pathology, 12(8), 829–838. Portico. https://doi.org/10.1111/j.1364-3703.2011.00713.x
Brevibacillus laterosporus strains BGSP7, BGSP9 and BGSP11 isolated from silage produce broad spectrum multi-antimicrobials
PLOS ONE / May 10, 2019
Miljkovic, M., Jovanovic, S., O’Connor, P. M., Mirkovic, N., Jovcic, B., Filipic, B., Dinic, M., Studholme, D. J., Fira, D., Cotter, P. D., & Kojic, M. (2019). Brevibacillus laterosporus strains BGSP7, BGSP9 and BGSP11 isolated from silage produce broad spectrum multi-antimicrobials. PLOS ONE, 14(5), e0216773. https://doi.org/10.1371/journal.pone.0216773
Genome Update. Let the consumer beware: Streptomyces genome sequence quality
Microbial Biotechnology / Jan 01, 2016
Studholme, D. J. (2016). Genome Update. Let the consumer beware: Streptomyces genome sequence quality. Microbial Biotechnology, 9(1), 3–7. Portico. https://doi.org/10.1111/1751-7915.12344
Draft Genome Sequence of Pseudomonas fuscovaginae, a Broad-Host-Range Pathogen of Plants
Journal of Bacteriology / Apr 24, 2012
Patel, H. K., Passos da Silva, D., Devescovi, G., Maraite, H., Paszkiewicz, K., Studholme, D. J., & Venturi, V. (2012). Draft Genome Sequence of Pseudomonas fuscovaginae, a Broad-Host-Range Pathogen of Plants. Journal of Bacteriology, 194(10), 2765–2766. https://doi.org/10.1128/jb.00341-12
First Identification of Xanthomonas nasturtii as the Cause of Black Rot of Watercress in Hawaii
Plant Disease / Aug 01, 2023
Vicente, J. G., McHugh, J., Bryning, A., Carroll, S., Harrison, J., & Studholme, D. J. (2023). First Identification of Xanthomonas nasturtii as the Cause of Black Rot of Watercress in Hawaii. Plant Disease, 107(8), 2511. https://doi.org/10.1094/pdis-05-22-1043-pdn
Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance
Access Microbiology / Jul 01, 2023
Harrison, J., Hussain, R. M. F., Greer, S. F., Ntoukakis, V., Aspin, A., Vicente, J. G., Grant, M., & Studholme, D. J. (2023). Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiology, 5(7). https://doi.org/10.1099/acmi.0.000532.v3
De novo genome assembly of Akanthomyces muscarius, a biocontrol agent of insect agricultural pests
Access Microbiology / Jun 01, 2023
Erdos, Z., Studholme, D. J., Raymond, B., & Sharma, M. D. (2023). De novo genome assembly of Akanthomyces muscarius, a biocontrol agent of insect agricultural pests. Access Microbiology, 5(6). https://doi.org/10.1099/acmi.0.000568.v3
Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance
Apr 11, 2023
Harrison, J., Hussain, R. M. F., Greer, S. F., Ntoukakis, V., Aspin, A., Vicente, J. G., Grant, M., & Studholme, D. J. (2023). Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. https://doi.org/10.1099/acmi.0.000532.v2
De-novo genome assembly for Akanthomyces muscarius, a biocontrol agent of insect agricultural pests
Mar 20, 2023
Erdos, Z., Studholme, D. J., Raymond, B., & Sharma, M. (2023). De-novo genome assembly for Akanthomyces muscarius, a biocontrol agent of insect agricultural pests. https://doi.org/10.1099/acmi.0.000568.v2
De-novo genome assembly for Akanthomyces muscarius, a biocontrol agent of insect agricultural pests
Jan 23, 2023
Erdos, Z., Studholme, D. J., Raymond, B., & Sharma, M. (2023). De-novo genome assembly for Akanthomyces muscarius, a biocontrol agent of insect agricultural pests. https://doi.org/10.1099/acmi.0.000568.v1
Data management challenges for artificial intelligence in plant and agricultural research
F1000Research / Jan 17, 2023
Williamson, H. F., Brettschneider, J., Caccamo, M., Davey, R. P., Goble, C., Kersey, P. J., May, S., Morris, R. J., Ostler, R., Pridmore, T., Rawlings, C., Studholme, D., Tsaftaris, S. A., & Leonelli, S. (2023). Data management challenges for artificial intelligence in plant and agricultural research. F1000Research, 10, 324. https://doi.org/10.12688/f1000research.52204.2
Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria
Taxonomy / Jan 06, 2023
Harrison, J., Hussain, R. M. F., Aspin, A., Grant, M. R., Vicente, J. G., & Studholme, D. J. (2023). Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. Taxonomy, 3(1), 29–45. https://doi.org/10.3390/taxonomy3010003
Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America
Phytopathology® / Jan 01, 2023
Reyes-Herrera, P. H., Torres-Bedoya, E., Lopez-Alvarez, D., Burbano-David, D., Carmona, S. L., Bebber, D. P., Studholme, D. J., Betancourt, M., & Soto-Suarez, M. (2023). Genome Sequence Data Reveal at Least Two Distinct Incursions of the Tropical Race 4 Variant of Fusarium Wilt into South America. Phytopathology®, 113(1), 90–97. https://doi.org/10.1094/phyto-01-22-0034-r
Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance
Nov 30, 2022
Harrison, J., Hussain, R. M. F., Greer, S., Ntoukakis, V., Aspin, A., Vicente, J., Grant, M., & Studholme, D. J. (2022). Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. https://doi.org/10.1099/acmi.0.000532.v1
First report of black rot caused by Xanthomonas nasturtii on watercress in Spain and Portugal
New Disease Reports / Oct 01, 2022
Lascelles, D. M., Roberts, M. R., Cruz, L., Cruz, J., Studholme, D. J., Harrison, J., Greer, S. F., Grant, M., Holden, J. M., Carter, B., Bryning, A., Carroll, S., Aspin, A., & Vicente, J. G. (2022). First report of black rot caused by Xanthomonas nasturtii on watercress in Spain and Portugal. New Disease Reports, 46(2). Portico. https://doi.org/10.1002/ndr2.12134
De-novo assembly of Xanthomonas genomes from Illumina NovaSeq reads v1
Aug 19, 2022
J Studholme, D. (2022). De-novo assembly of Xanthomonas genomes from Illumina NovaSeq reads v1. https://doi.org/10.17504/protocols.io.kxygxzrqzv8j/v1
Phylogenomic analysis of Xanthomonas v1
Aug 03, 2022
J Studholme, D. (2022). Phylogenomic analysis of Xanthomonas v1. https://doi.org/10.17504/protocols.io.261geny57g47/v1
Culturing Xanthomonas v1
Aug 03, 2022
Grant, M. (2022). Culturing Xanthomonas v1. https://doi.org/10.17504/protocols.io.ewov1nr92gr2/v1
DNA extraction using the Qiagen 67563 MagAttract HMW DNA Kit (48) v1
Aug 03, 2022
Grant, M. (2022). DNA extraction using the Qiagen 67563 MagAttract HMW DNA Kit (48) v1. https://doi.org/10.17504/protocols.io.5jyl89428v2w/v1
Molecular and Pathogenic Characterization of Fusarium Species Associated with Corm Rot Disease in Saffron from China
Journal of Fungi / May 17, 2022
Mirghasempour, S. A., Studholme, D. J., Chen, W., Zhu, W., & Mao, B. (2022). Molecular and Pathogenic Characterization of Fusarium Species Associated with Corm Rot Disease in Saffron from China. Journal of Fungi, 8(5), 515. https://doi.org/10.3390/jof8050515
Identification and Characterization of Fusarium nirenbergiae Associated with Saffron Corm Rot Disease
Plant Disease / Feb 01, 2022
Mirghasempour, S. A., Studholme, D. J., Chen, W., Cui, D., & Mao, B. (2022). Identification and Characterization of Fusarium nirenbergiae Associated with Saffron Corm Rot Disease. Plant Disease, 106(2), 486–495. https://doi.org/10.1094/pdis-04-21-0871-re
Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America
Jan 17, 2022
Reyes-Herrera, P. H., Torres-Bedoya, E., Lopez-Alvarez, D., Burbano-David, D., Carmona, S. L., Bebber, D. P., Studholme, D. J., Betancourt, M., & Soto-Suarez, M. (2022). Genome sequence data reveal at least two distinct incursions of the tropical race 4 (TR4) variant of Fusarium wilt into South America. https://doi.org/10.1101/2022.01.17.476647
Common bacterial blight of bean: a model of seed transmission and pathological convergence
Molecular Plant Pathology / May 04, 2021
Chen, N. W. G., Ruh, M., Darrasse, A., Foucher, J., Briand, M., Costa, J., Studholme, D. J., & Jacques, M. (2021). Common bacterial blight of bean: a model of seed transmission and pathological convergence. Molecular Plant Pathology, 22(12), 1464–1480. Portico. https://doi.org/10.1111/mpp.13067
Taxonomic Revision of the Banana Fusarium Wilt TR4 Pathogen Is Premature
Phytopathology® / Dec 01, 2021
Torres Bedoya, E., Bebber, D. P., & Studholme, D. J. (2021). Taxonomic Revision of the Banana Fusarium Wilt TR4 Pathogen Is Premature. Phytopathology®, 111(12), 2141–2145. https://doi.org/10.1094/phyto-03-21-0089-le
Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens
Nov 04, 2021
Wacker, T., Helmstetter, N., Wilson, D., Fisher, M. C., Studholme, D. J., & Farrer, R. A. (2021). Two-speed genome expansion drives the evolution of pathogenicity in animal fungal pathogens. https://doi.org/10.1101/2021.11.03.467166
Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae
Molecular Plant Pathology / May 20, 2021
Wang, S., Vetukuri, R. R., Kushwaha, S. K., Hedley, P. E., Morris, J., Studholme, D. J., Welsh, L. R. J., Boevink, P. C., Birch, P. R. J., & Whisson, S. C. (2021). Haustorium formation and a distinct biotrophic transcriptome characterize infection of Nicotiana benthamiana by the tree pathogen Phytophthora kernoviae. Molecular Plant Pathology, 22(8), 954–968. Portico. https://doi.org/10.1111/mpp.13072
SNP‐based genotyping and whole‐genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin
Plant Pathology / Nov 27, 2020
Nakato, G. V., Studholme, D. J., Blomme, G., Grant, M., Coutinho, T. A., Were, E. M., Wicker, E., & Mahuku, G. (2020). SNP‐based genotyping and whole‐genome sequencing reveal previously unknown genetic diversity in Xanthomonas vasicola pv. musacearum, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin. Plant Pathology, 70(3), 534–543. Portico. https://doi.org/10.1111/ppa.13308
Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas
Microorganisms / Apr 16, 2021
Catara, V., Cubero, J., Pothier, J. F., Bosis, E., Bragard, C., Đermić, E., Holeva, M. C., Jacques, M.-A., Petter, F., Pruvost, O., Robène, I., Studholme, D. J., Tavares, F., Vicente, J. G., Koebnik, R., & Costa, J. (2021). Trends in Molecular Diagnosis and Diversity Studies for Phytosanitary Regulated Xanthomonas. Microorganisms, 9(4), 862. https://doi.org/10.3390/microorganisms9040862
Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture
Jul 29, 2020
Christakis, C. A., Daskalogiannis, G., Chatzakis, A., Markakis, E. A., Sagia, A., Rizzo, G. F., Catara, V., Lagkouvardos, I., Studholme, D. J., & Sarris, P. F. (2020). Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture. https://doi.org/10.1101/2020.07.29.226860
A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus)
Molecular Ecology Resources / Jun 15, 2020
Lange, A., Paris, J. R., Gharbi, K., Cézard, T., Miyagawa, S., Iguchi, T., Studholme, D. J., & Tyler, C. R. (2020). A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (Rutilus rutilus). Molecular Ecology Resources, 20(4), 1007–1022. Portico. https://doi.org/10.1111/1755-0998.13166
A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari
Plant Disease / Jun 01, 2020
Mirghasempour, S. A., Huang, S., Studholme, D. J., & Brady, C. L. (2020). A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari. Plant Disease, 104(6), 1581–1583. https://doi.org/10.1094/pdis-01-20-0179-sc
Genomics-Informed Molecular Detection of Xanthomonas vasicola pv. vasculorum Strains Causing Severe Bacterial Leaf Streak of Corn
Phytopathology® / Jun 01, 2020
Stulberg, M. J., Santillana, G., Studholme, D. J., Kasiborski, B., Ortiz-Castro, M., Broders, K., Arias, S., Block, C., Munkvold, G., & Rascoe, J. (2020). Genomics-Informed Molecular Detection of Xanthomonas vasicola pv. vasculorum Strains Causing Severe Bacterial Leaf Streak of Corn. Phytopathology®, 110(6), 1174–1179. https://doi.org/10.1094/phyto-12-18-0453-r
Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov.
Phytopathology® / Jun 01, 2020
Studholme, D. J., Wicker, E., Abrare, S. M., Aspin, A., Bogdanove, A., Broders, K., Dubrow, Z., Grant, M., Jones, J. B., Karamura, G., Lang, J., Leach, J., Mahuku, G., Nakato, G. V., Coutinho, T., Smith, J., & Bull, C. T. (2020). Transfer of Xanthomonas campestris pv. arecae and X. campestris pv. musacearum to X. vasicola (Vauterin) as X. vasicola pv. arecae comb. nov. and X. vasicola pv. musacearum comb. nov. and Description of X. vasicola pv. vasculorum pv. nov. Phytopathology®, 110(6), 1153–1160. https://doi.org/10.1094/phyto-03-19-0098-le
AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens
Microbiology / Jan 01, 2020
Bez, C., Javvadi, S. G., Bertani, I., Devescovi, G., Guarnaccia, C., Studholme, D. J., Geller, A. M., Levy, A., & Venturi, V. (2020). AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens. Microbiology, 166(1), 73–84. https://doi.org/10.1099/mic.0.000865
High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic
Microbiology Resource Announcements / Sep 05, 2019
Warmington, R. J., Kay, W., Jeffries, A., O’Neill, P., Farbos, A., Moore, K., Bebber, D. P., & Studholme, D. J. (2019). High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic. Microbiology Resource Announcements, 8(36). https://doi.org/10.1128/mra.00904-19
Evaluation of 20 enset (Ensete ventricosum) landraces for response to Xanthomonas vasicola pv. musacearum infection
Aug 15, 2019
Muzemil, S., Chala, A., Tesfaye, B., Studholme, D. J., Grant, M., Yemataw, Z., & Olango, T. M. (2019). Evaluation of 20 enset (Ensete ventricosum) landraces for response to Xanthomonas vasicola pv. musacearum infection. https://doi.org/10.1101/736793
Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA
Parasitology / Apr 12, 2019
Minardi, D., Studholme, D. J., Oidtmann, B., Pretto, T., & van der Giezen, M. (2019). Improved method for genotyping the causative agent of crayfish plague (Aphanomyces astaci) based on mitochondrial DNA. Parasitology, 146(8), 1022–1029. https://doi.org/10.1017/s0031182019000283
The Zymoseptoria tritici ORFeome: a functional genomics community resource
Mar 20, 2019
Chaudhari, Y., Cairns, T. C., Sidhu, Y., Attah, V., Thomas, G., Csukai, M., Talbot, N. J., Studholme, D. J., & Haynes, K. (2019). The Zymoseptoria tritici ORFeome: a functional genomics community resource. https://doi.org/10.1101/582205
Transfer of Xanthomonas campestris pv. arecae, and Xanthomonas campestris pv. musacearum to Xanthomonas vasicola (Vauterin) as Xanthomonas vasicola pv. arecae comb. nov., and Xanthomonas vasicola pv. musacearum comb. nov. and description of Xanthomonas vasicola pv. vasculorum pv. nov
Mar 09, 2019
Studholme, D. J., Wicker, E., Abrare, S. M., Aspin, A., Bogdanove, A., Broders, K., Dubrow, Z., Grant, M., Jones, J. B., Karamura, G., Lang, J., Leach, J., Mahuku, G., Nakato, G. V., Coutinho, T., Smith, J., & Bull, C. T. (2019). Transfer of Xanthomonas campestris pv. arecae, and Xanthomonas campestris pv. musacearum to Xanthomonas vasicola (Vauterin) as Xanthomonas vasicola pv. arecae comb. nov., and Xanthomonas vasicola pv. musacearum comb. nov. and description of Xanthomonas vasicola pv. vasculorum pv. nov. https://doi.org/10.1101/571166
Genome Resequencing of Laboratory Stocks of Burkholderia pseudomallei K96243
Microbiology Resource Announcements / Feb 28, 2019
Wagley, S., Scott, A. E., Ireland, P. M., Prior, J. L., Atkins, T. P., Bancroft, G. J., Studholme, D. J., & Titball, R. W. (2019). Genome Resequencing of Laboratory Stocks of Burkholderia pseudomallei K96243. Microbiology Resource Announcements, 8(9). https://doi.org/10.1128/mra.01529-18
Draft Genome Sequence and intraspecific diversification of the wild crop relativeBrassica creticaLam. using demographic model selection
Jan 16, 2019
Kioukis, A., Michalopoulou, V. A., Briers, L., Pirintsos, S., Studholme, D. J., Pavlidis, P., & Sarris, P. F. (2019). Draft Genome Sequence and intraspecific diversification of the wild crop relativeBrassica creticaLam. using demographic model selection. https://doi.org/10.1101/521138
A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences
Heliyon / Dec 01, 2018
Nakato, G. V., Wicker, E., Coutinho, T. A., Mahuku, G., & Studholme, D. J. (2018). A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences. Heliyon, 4(12), e01080. https://doi.org/10.1016/j.heliyon.2018.e01080
Identifying molecular markers suitable for Frl selection in tomato breeding
Theoretical and Applied Genetics / Jul 07, 2018
Devran, Z., Kahveci, E., Hong, Y., Studholme, D. J., & Tör, M. (2018). Identifying molecular markers suitable for Frl selection in tomato breeding. Theoretical and Applied Genetics, 131(10), 2099–2105. https://doi.org/10.1007/s00122-018-3136-0
Draft Genome Sequences of Pathotype Strains for Three Pathovars Belonging to Three Xanthomonas Species
Microbiology Resource Announcements / Sep 27, 2018
Michalopoulou, V. A., Vicente, J. G., Studholme, D. J., & Sarris, P. F. (2018). Draft Genome Sequences of Pathotype Strains for Three Pathovars Belonging to Three Xanthomonas Species. Microbiology Resource Announcements, 7(12). https://doi.org/10.1128/mra.00923-18
Publisher Correction: Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom
Nature Communications / Jul 13, 2018
Schaum, C.-E., Buckling, A., Smirnoff, N., Studholme, D. J., & Yvon-Durocher, G. (2018). Publisher Correction: Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-05353-8
Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis
Genome Announcements / Jun 28, 2018
Morcrette, H., Morgan, M. S., Farbos, A., O’Neill, P., Moore, K., Titball, R. W., & Studholme, D. J. (2018). Genome Sequence of Staphylococcus aureus Ex1, Isolated from a Patient with Spinal Osteomyelitis. Genome Announcements, 6(26). https://doi.org/10.1128/genomea.00623-18
New genotyping method for the causative agent of crayfish plague (Aphanomyces astaci) based on whole genome data
Journal of Invertebrate Pathology / Jul 01, 2018
Minardi, D., Studholme, D. J., van der Giezen, M., Pretto, T., & Oidtmann, B. (2018). New genotyping method for the causative agent of crayfish plague (Aphanomyces astaci) based on whole genome data. Journal of Invertebrate Pathology, 156, 6–13. https://doi.org/10.1016/j.jip.2018.06.002
Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom
Nature Communications / Apr 30, 2018
Schaum, C.-E., Buckling, A., Smirnoff, N., Studholme, D. J., & Yvon-Durocher, G. (2018). Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom. Nature Communications, 9(1). https://doi.org/10.1038/s41467-018-03906-5
Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators
Microorganisms / Apr 21, 2018
Dorati, F., Barrett, G., Sanchez-Contreras, M., Arseneault, T., José, M., Studholme, D., Murillo, J., Caballero, P., Waterfield, N., Arnold, D., Shaw, L., & Jackson, R. (2018). Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators. Microorganisms, 6(2), 32. https://doi.org/10.3390/microorganisms6020032
Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease
Scientific Data / Dec 19, 2017
Sambles, C. M., Salmon, D. L., Florance, H., Howard, T. P., Smirnoff, N., Nielsen, L. R., McKinney, L. V., Kjær, E. D., Buggs, R. J. A., Studholme, D. J., & Grant, M. (2017). Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease. Scientific Data, 4(1). https://doi.org/10.1038/sdata.2017.190
Morphological Variation and Inter-Relationships of Quantitative Traits in Enset (Ensete ventricosum (welw.) Cheesman) Germplasm from South and South-Western Ethiopia
Plants / Dec 06, 2017
Yemataw, Z., Chala, A., Ambachew, D., Studholme, D., Grant, M., & Tesfaye, K. (2017). Morphological Variation and Inter-Relationships of Quantitative Traits in Enset (Ensete ventricosum (welw.) Cheesman) Germplasm from South and South-Western Ethiopia. Plants, 6(4), 56. https://doi.org/10.3390/plants6040056
Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum , a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants
Genomics Data / Jun 01, 2017
Turner, J., O’Neill, P., Grant, M., Mumford, R. A., Thwaites, R., & Studholme, D. J. (2017). Genome sequences of 12 isolates of the EU1 lineage of Phytophthora ramorum , a fungus-like pathogen that causes extensive damage and mortality to a wide range of trees and other plants. Genomics Data, 12, 17–21. https://doi.org/10.1016/j.gdata.2017.02.006
Genome sequences of six Phytophthora species associated with forests in New Zealand
Genomics Data / Mar 01, 2016
Studholme, D. J., McDougal, R. L., Sambles, C., Hansen, E., Hardy, G., Grant, M., Ganley, R. J., & Williams, N. M. (2016). Genome sequences of six Phytophthora species associated with forests in New Zealand. Genomics Data, 7, 54–56. https://doi.org/10.1016/j.gdata.2015.11.015
Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa
Genome Announcements / Feb 25, 2016
Harrison, J., Dornbusch, M. R., Samac, D., & Studholme, D. J. (2016). Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa. Genome Announcements, 4(1). https://doi.org/10.1128/genomea.01722-15
Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii
Genome Announcements / Feb 25, 2016
Jones, K. J., Moore, K., Sambles, C., Love, J., Studholme, D. J., & Aves, S. J. (2016). Draft Genome Sequences of Achromobacter piechaudii GCS2, Agrobacterium sp. Strain SUL3, Microbacterium sp. Strain GCS4, Shinella sp. Strain GWS1, and Shinella sp. Strain SUS2 Isolated from Consortium with the Hydrocarbon-Producing Alga Botryococcus braunii. Genome Announcements, 4(1). https://doi.org/10.1128/genomea.01527-15
Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants
Genome Announcements / Feb 25, 2016
Harrison, J., Grant, M. R., & Studholme, D. J. (2016). Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants. Genome Announcements, 4(1). https://doi.org/10.1128/genomea.01705-15
Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255
Genome Announcements / Oct 29, 2015
Siddiqui, F. M., Ibrahim, M., Noureen, N., Noreen, Z., Titball, R. W., Champion, O. L., Wren, B. W., Studholme, D., & Bokhari, H. (2015). Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255. Genome Announcements, 3(5). https://doi.org/10.1128/genomea.01223-15
A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici
Fungal Genetics and Biology / Jun 01, 2015
Kilaru, S., Schuster, M., Studholme, D., Soanes, D., Lin, C., Talbot, N. J., & Steinberg, G. (2015). A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici. Fungal Genetics and Biology, 79, 125–131. https://doi.org/10.1016/j.fgb.2015.03.022
Construction and high-throughput phenotypic screening of Zymoseptoria tritici over-expression strains
Fungal Genetics and Biology / Jun 01, 2015
Cairns, T. C., Sidhu, Y. S., Chaudhari, Y. K., Talbot, N. J., Studholme, D. J., & Haynes, K. (2015). Construction and high-throughput phenotypic screening of Zymoseptoria tritici over-expression strains. Fungal Genetics and Biology, 79, 110–117. https://doi.org/10.1016/j.fgb.2015.04.013
Development of a lateral flow device for
in‐field detection and evaluation of
PCR ‐based diagnostic methods
for Xanthomonas campestris pv.
musacearum, the causal agent of
banana xanthomonas wilt
Plant Pathology / Oct 02, 2014
Hodgetts, J., Karamura, G., Johnson, G., Hall, J., Perkins, K., Beed, F., Nakato, V., Grant, M., Studholme, D. J., Boonham, N., & Smith, J. (2014). Development of a lateral flow device for in‐field detection and evaluation of <scp>PCR</scp>‐based diagnostic methods for Xanthomonas campestris pv. musacearum, the causal agent of banana xanthomonas wilt. Plant Pathology, 64(3), 559–567. Portico. https://doi.org/10.1111/ppa.12289
Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing
Molecular Breeding / Mar 17, 2015
Devran, Z., Kahveci, E., Özkaynak, E., Studholme, D. J., & Tör, M. (2015). Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing. Molecular Breeding, 35(4). https://doi.org/10.1007/s11032-015-0294-5
Draft genome sequences of Phytophthora kernoviae and Phytophthora ramorum lineage EU2 from Scotland
Genomics Data / Dec 01, 2015
Sambles, C., Schlenzig, A., O’Neill, P., Grant, M., & Studholme, D. J. (2015). Draft genome sequences of Phytophthora kernoviae and Phytophthora ramorum lineage EU2 from Scotland. Genomics Data, 6, 193–194. https://doi.org/10.1016/j.gdata.2015.09.010
Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland
Genomics Data / Dec 01, 2015
Mata Saez, L. de la, McCracken, A. R., Cooke, L. R., O’Neill, P., Grant, M., & Studholme, D. J. (2015). Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland. Genomics Data, 6, 191–192. https://doi.org/10.1016/j.gdata.2015.09.009
Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system
Science / Feb 27, 2015
Taylor, T. B., Mulley, G., Dills, A. H., Alsohim, A. S., McGuffin, L. J., Studholme, D. J., Silby, M. W., Brockhurst, M. A., Johnson, L. J., & Jackson, R. W. (2015). Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science, 347(6225), 1014–1017. https://doi.org/10.1126/science.1259145
Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici
Fungal Genetics and Biology / Jun 01, 2015
Sidhu, Y. S., Cairns, T. C., Chaudhari, Y. K., Usher, J., Talbot, N. J., Studholme, D. J., Csukai, M., & Haynes, K. (2015). Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici. Fungal Genetics and Biology, 79, 102–109. https://doi.org/10.1016/j.fgb.2015.04.015
Differences in carbon source utilisation distinguish Campylobacter jejuni from Campylobacter coli
BMC Microbiology / Oct 28, 2014
Wagley, S., Newcombe, J., Laing, E., Yusuf, E., Sambles, C. M., Studholme, D. J., La Ragione, R. M., Titball, R. W., & Champion, O. L. (2014). Differences in carbon source utilisation distinguish Campylobacter jejuni from Campylobacter coli. BMC Microbiology, 14(1). https://doi.org/10.1186/s12866-014-0262-y
Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles
Genome Research / Sep 18, 2014
Nandi, T., Holden, M. T. G., Didelot, X., Mehershahi, K., Boddey, J. A., Beacham, I., Peak, I., Harting, J., Baybayan, P., Guo, Y., Wang, S., How, L. C., Sim, B., Essex-Lopresti, A., Sarkar-Tyson, M., Nelson, M., Smither, S., Ong, C., Aw, L. T., … Tan, P. (2014). Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles. Genome Research, 25(1), 129–141. https://doi.org/10.1101/gr.177543.114
Draft genome sequence ofXanthomonas axonopodispathovarvasculorumNCPPB 900
FEMS Microbiology Letters / Oct 13, 2014
Harrison, J., & Studholme, D. J. (2014). Draft genome sequence ofXanthomonas axonopodispathovarvasculorumNCPPB 900. FEMS Microbiology Letters, 360(2), 113–116. https://doi.org/10.1111/1574-6968.12607
Recently published S treptomyces genome sequences
Microbial Biotechnology / Aug 07, 2014
Harrison, J., & Studholme, D. J. (2014). Recently published <scp>S</scp>treptomyces genome sequences. Microbial Biotechnology, 7(5), 373–380. Portico. https://doi.org/10.1111/1751-7915.12143
Some (bacilli) like it hot: genomics of
G eobacillus species
Microbial Biotechnology / Sep 05, 2014
Studholme, D. J. (2014). Some (bacilli) like it hot: genomics of <scp>G</scp>eobacillus species. Microbial Biotechnology, 8(1), 40–48. Portico. https://doi.org/10.1111/1751-7915.12161
The rulB gene of plasmid
pWW 0 is a hotspot for the
site‐specific insertion of integron‐like
elements found in the chromosomes of
environmental P seudomonas fluorescens group
bacteria
Environmental Microbiology / Jan 07, 2014
Rhodes, G., Bosma, H., Studholme, D., Arnold, D. L., Jackson, R. W., & Pickup, R. W. (2014). The <scp>rulB</scp> gene of plasmid <scp>pWW</scp>0 is a hotspot for the site‐specific insertion of integron‐like elements found in the chromosomes of environmental <scp>P</scp>seudomonas fluorescens group bacteria. Environmental Microbiology, 16(8), 2374–2388. Portico. https://doi.org/10.1111/1462-2920.12345
Identification of Possible Virulence Marker fromCampylobacter jejuniIsolates
Emerging Infectious Diseases / Jun 01, 2014
Harrison, J. W., Dung, T. T. N., Siddiqui, F., Korbrisate, S., Bukhari, H., Tra, M. P. V., Hoang, N. V. M., Carrique-Mas, J., Bryant, J., Campbell, J. I., Studholme, D. J., Wren, B. W., Baker, S., Titball, R. W., & Champion, O. L. (2014). Identification of Possible Virulence Marker fromCampylobacter jejuniIsolates. Emerging Infectious Diseases, 20(6), 1026–1029. https://doi.org/10.3201/eid2006.130635
Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3
Genome Announcements / Aug 28, 2014
Uzelac, G., Bertani, I., Kojic, M., Paszkiewicz, K. H., Studholme, D. J., Passos da Silva, D., & Venturi, V. (2014). Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3. Genome Announcements, 2(4). https://doi.org/10.1128/genomea.00654-14
Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards
World Journal of Microbiology and Biotechnology / May 08, 2013
Khan, A., Asif, H., Studholme, D. J., Khan, I. A., & Azim, M. K. (2013). Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards. World Journal of Microbiology and Biotechnology, 29(11), 2033–2044. https://doi.org/10.1007/s11274-013-1366-5
Salmonella Gallinarum field isolates from laying hens are related to the vaccine strain SG9R
Vaccine / Oct 01, 2013
Van Immerseel, F., Studholme, D. J., Eeckhaut, V., Heyndrickx, M., Dewulf, J., Dewaele, I., Van Hoorebeke, S., Haesebrouck, F., Van Meirhaeghe, H., Ducatelle, R., Paszkiewicz, K., & Titball, R. W. (2013). Salmonella Gallinarum field isolates from laying hens are related to the vaccine strain SG9R. Vaccine, 31(43), 4940–4945. https://doi.org/10.1016/j.vaccine.2013.08.033
Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens
New Phytologist / May 21, 2013
Monteil, C. L., Cai, R., Liu, H., Mechan Llontop, M. E., Leman, S., Studholme, D. J., Morris, C. E., & Vinatzer, B. A. (2013). Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytologist, 199(3), 800–811. Portico. https://doi.org/10.1111/nph.12316
Progress in metagenomics requires a balanced appraisal of the available technologies
European Journal of Clinical Microbiology & Infectious Diseases / Feb 23, 2013
Huggett, J. F., Studholme, D. J., Laver, T., & Foy, C. A. (2013). Progress in metagenomics requires a balanced appraisal of the available technologies. European Journal of Clinical Microbiology & Infectious Diseases, 32(8), 1097–1098. https://doi.org/10.1007/s10096-013-1842-8
Genome-wide sequencing ofPhytophthora lateralisreveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland
FEMS Microbiology Letters / Jun 05, 2013
Quinn, L., O’Neill, P. A., Harrison, J., Paskiewicz, K. H., McCracken, A. R., Cooke, L. R., Grant, M. R., & Studholme, D. J. (2013). Genome-wide sequencing ofPhytophthora lateralisreveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland. FEMS Microbiology Letters, 344(2), 179–185. https://doi.org/10.1111/1574-6968.12179
Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator
The ISME Journal / Feb 21, 2013
Burlinson, P., Studholme, D., Cambray-Young, J., Heavens, D., Rathjen, J., Hodgkin, J., & Preston, G. M. (2013). Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator. The ISME Journal, 7(6), 1126–1138. https://doi.org/10.1038/ismej.2013.9
Considerations for the development and application of control materials to improve metagenomic microbial community profiling
Accreditation and Quality Assurance / Dec 28, 2012
Huggett, J. F., Laver, T., Tamisak, S., Nixon, G., O’Sullivan, D. M., Elaswarapu, R., Studholme, D. J., & Foy, C. A. (2012). Considerations for the development and application of control materials to improve metagenomic microbial community profiling. Accreditation and Quality Assurance, 18(2), 77–83. https://doi.org/10.1007/s00769-012-0941-z
Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi
Genome Announcements / Jun 27, 2013
Passos da Silva, D., Devescovi, G., Paszkiewicz, K., Moretti, C., Buonaurio, R., Studholme, D. J., & Venturi, V. (2013). Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi. Genome Announcements, 1(3). https://doi.org/10.1128/genomea.00205-13
Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics
Frontiers in Plant Science / Jan 01, 2013
Studholme, D. J., Harris, B., Le Cocq, K., Winsbury, R., Perera, V., Ryder, L., Ward, J. L., Beale, M. H., Thornton, C. R., & Grant, M. (2013). Investigating the beneficial traits of Trichoderma hamatum GD12 for sustainable agriculture—insights from genomics. Frontiers in Plant Science, 4. https://doi.org/10.3389/fpls.2013.00258
Isolation of Salmonella Mutants Resistant to the Inhibitory Effect of Salicylidene acylhydrazides on Flagella-Mediated Motility
PLoS ONE / Jan 02, 2013
Martinez-Argudo, I., Veenendaal, A. K. J., Liu, X., Roehrich, A. D., Ronessen, M. C., Franzoni, G., van Rietschoten, K. N., Morimoto, Y. V., Saijo-Hamano, Y., Avison, M. B., Studholme, D. J., Namba, K., Minamino, T., & Blocker, A. J. (2013). Isolation of Salmonella Mutants Resistant to the Inhibitory Effect of Salicylidene acylhydrazides on Flagella-Mediated Motility. PLoS ONE, 8(1), e52179. https://doi.org/10.1371/journal.pone.0052179
Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects
Scientific Reports / Mar 21, 2013
Farrer, R. A., Henk, D. A., MacLean, D., Studholme, D. J., & Fisher, M. C. (2013). Using False Discovery Rates to Benchmark SNP-callers in next-generation sequencing projects. Scientific Reports, 3(1). https://doi.org/10.1038/srep01512
Draft Genome Sequence of Pseudomonas syringae Pathovar Syringae Strain FF5, Causal Agent of Stem Tip Dieback Disease on Ornamental Pear
Journal of Bacteriology / Jul 15, 2012
Sohn, K. H., Jones, J. D. G., & Studholme, D. J. (2012). Draft Genome Sequence of Pseudomonas syringae Pathovar Syringae Strain FF5, Causal Agent of Stem Tip Dieback Disease on Ornamental Pear. Journal of Bacteriology, 194(14), 3733–3734. https://doi.org/10.1128/jb.00567-12
Coverage‐based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome
American Journal of Botany / Feb 01, 2012
Azam, S., Thakur, V., Ruperao, P., Shah, T., Balaji, J., Amindala, B., Farmer, A. D., Studholme, D. J., May, G. D., Edwards, D., Jones, J. D. G., & Varshney, R. K. (2012). Coverage‐based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum; Fabaceae), a crop species without a reference genome. American Journal of Botany, 99(2), 186–192. Portico. https://doi.org/10.3732/ajb.1100419
Deep sequencing of small RNAs in plants: applied bioinformatics
Briefings in Functional Genomics / Dec 19, 2011
Studholme, D. J. (2011). Deep sequencing of small RNAs in plants: applied bioinformatics. Briefings in Functional Genomics, 11(1), 71–85. https://doi.org/10.1093/bfgp/elr039
Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050–1065.
Genes / Jan 11, 2012
Studholme, D. J., Wasukira, A., Paszkiewicz, K., Aritua, V., Thwaites, R., Smith, J., & Grant, M. (2012). Correction: Studholme et al., Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 clade. Genes 2011, 2, 1050–1065. Genes, 3(1), 88–89. https://doi.org/10.3390/genes3010088
Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas Campestris Pathovar Musacearum
Genes / Jul 04, 2012
Wasukira, A., Tayebwa, J., Thwaites, R., Paszkiewicz, K., Aritua, V., Kubiriba, J., Smith, J., Grant, M., & Studholme, D. J. (2012). Genome-Wide Sequencing Reveals Two Major Sub-Lineages in the Genetically Monomorphic Pathogen Xanthomonas Campestris Pathovar Musacearum. Genes, 3(3), 361–377. https://doi.org/10.3390/genes3030361
Pseudomonas syringae pv. actinidiae (PSA) Isolates from Recent Bacterial Canker of Kiwifruit Outbreaks Belong to the Same Genetic Lineage
PLoS ONE / May 09, 2012
Mazzaglia, A., Studholme, D. J., Taratufolo, M. C., Cai, R., Almeida, N. F., Goodman, T., Guttman, D. S., Vinatzer, B. A., & Balestra, G. M. (2012). Pseudomonas syringae pv. actinidiae (PSA) Isolates from Recent Bacterial Canker of Kiwifruit Outbreaks Belong to the Same Genetic Lineage. PLoS ONE, 7(5), e36518. https://doi.org/10.1371/journal.pone.0036518
Multiple Candidate Effectors from the Oomycete Pathogen Hyaloperonospora arabidopsidis Suppress Host Plant Immunity
PLoS Pathogens / Nov 03, 2011
Fabro, G., Steinbrenner, J., Coates, M., Ishaque, N., Baxter, L., Studholme, D. J., Körner, E., Allen, R. L., Piquerez, S. J. M., Rougon-Cardoso, A., Greenshields, D., Lei, R., Badel, J. L., Caillaud, M.-C., Sohn, K.-H., Van den Ackerveken, G., Parker, J. E., Beynon, J., & Jones, J. D. G. (2011). Multiple Candidate Effectors from the Oomycete Pathogen Hyaloperonospora arabidopsidis Suppress Host Plant Immunity. PLoS Pathogens, 7(11), e1002348. https://doi.org/10.1371/journal.ppat.1002348
Application of High-Throughput DNA Sequencing in Phytopathology
Annual Review of Phytopathology / Sep 08, 2011
Studholme, D. J., Glover, R. H., & Boonham, N. (2011). Application of High-Throughput DNA Sequencing in Phytopathology. Annual Review of Phytopathology, 49(1), 87–105. https://doi.org/10.1146/annurev-phyto-072910-095408
Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade
Genes / Dec 02, 2011
Studholme, D. J., Wasukira, A., Paszkiewicz, K., Aritua, V., Thwaites, R., Smith, J., & Grant, M. (2011). Draft Genome Sequences of Xanthomonas sacchari and Two Banana-Associated Xanthomonads Reveal Insights into the Xanthomonas Group 1 Clade. Genes, 2(4), 1050–1065. https://doi.org/10.3390/genes2041050
Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana
PLoS Biology / Jul 05, 2011
Kemen, E., Gardiner, A., Schultz-Larsen, T., Kemen, A. C., Balmuth, A. L., Robert-Seilaniantz, A., Bailey, K., Holub, E., Studholme, D. J., MacLean, D., & Jones, J. D. G. (2011). Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana. PLoS Biology, 9(7), e1001094. https://doi.org/10.1371/journal.pbio.1001094
The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity
PLoS Pathogens / Aug 25, 2011
Cai, R., Lewis, J., Yan, S., Liu, H., Clarke, C. R., Campanile, F., Almeida, N. F., Studholme, D. J., Lindeberg, M., Schneider, D., Zaccardelli, M., Setubal, J. C., Morales-Lizcano, N. P., Bernal, A., Coaker, G., Baker, C., Bender, C. L., Leman, S., & Vinatzer, B. A. (2011). The Plant Pathogen Pseudomonas syringae pv. tomato Is Genetically Monomorphic and under Strong Selection to Evade Tomato Immunity. PLoS Pathogens, 7(8), e1002130. https://doi.org/10.1371/journal.ppat.1002130
A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated System
PLoS ONE / Feb 15, 2010
MacLean, D., & Studholme, D. J. (2010). A Boolean Model of the Pseudomonas syringae hrp Regulon Predicts a Tightly Regulated System. PLoS ONE, 5(2), e9101. https://doi.org/10.1371/journal.pone.0009101
Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum
PLoS ONE / Apr 19, 2010
Green, S., Studholme, D. J., Laue, B. E., Dorati, F., Lovell, H., Arnold, D., Cottrell, J. E., Bridgett, S., Blaxter, M., Huitema, E., Thwaites, R., Sharp, P. M., Jackson, R. W., & Kamoun, S. (2010). Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum. PLoS ONE, 5(4), e10224. https://doi.org/10.1371/journal.pone.0010224
De novo assembly of short sequence reads
Briefings in Bioinformatics / Aug 19, 2010
Paszkiewicz, K., & Studholme, D. J. (2010). De novo assembly of short sequence reads. Briefings in Bioinformatics, 11(5), 457–472. https://doi.org/10.1093/bib/bbq020
Finding sRNA generative locales from high-throughput sequencing data with NiBLS
BMC Bioinformatics / Feb 18, 2010
MacLean, D., Moulton, V., & Studholme, D. J. (2010). Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11(1). https://doi.org/10.1186/1471-2105-11-93
Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage
Science / Dec 10, 2010
Raffaele, S., Farrer, R. A., Cano, L. M., Studholme, D. J., MacLean, D., Thines, M., Jiang, R. H. Y., Zody, M. C., Kunjeti, S. G., Donofrio, N. M., Meyers, B. C., Nusbaum, C., & Kamoun, S. (2010). Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage. Science, 330(6010), 1540–1543. https://doi.org/10.1126/science.1193070
Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt
FEMS Microbiology Letters / Aug 23, 2010
Studholme, D. J., Kemen, E., MacLean, D., Schornack, S., Aritua, V., Thwaites, R., Grant, M., Smith, J., & Jones, J. D. G. (2010). Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt. FEMS Microbiology Letters, 310(2), 182–192. https://doi.org/10.1111/j.1574-6968.2010.02065.x
Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping
Proceedings of the National Academy of Sciences / May 17, 2010
Nemri, A., Atwell, S., Tarone, A. M., Huang, Y. S., Zhao, K., Studholme, D. J., Nordborg, M., & Jones, J. D. G. (2010). Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proceedings of the National Academy of Sciences, 107(22), 10302–10307. https://doi.org/10.1073/pnas.0913160107
Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome
Science / Dec 10, 2010
Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E., Thines, M., Ah-Fong, A., Anderson, R., Badejoko, W., Bittner-Eddy, P., Boore, J. L., Chibucos, M. C., Coates, M., Dehal, P., Delehaunty, K., Dong, S., Downton, P., Dumas, B., … Tyler, B. M. (2010). Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome. Science, 330(6010), 1549–1551. https://doi.org/10.1126/science.1195203
A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528
BMC Genomics / Jan 01, 2009
Studholme, D. J., Ibanez, S., MacLean, D., Dangl, J. L., Chang, J. H., & Rathjen, J. P. (2009). A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. BMC Genomics, 10(1), 569. https://doi.org/10.1186/1471-2164-10-569
A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528
BMC Genomics / Jan 01, 2009
Studholme, D. J., Ibanez, S., MacLean, D., Dangl, J. L., Chang, J. H., & Rathjen, J. P. (2009). A draft genome sequence and functional screen reveals the repertoire of type III secreted proteins of Pseudomonas syringae pathovar tabaci 11528. BMC Genomics, 10(1), 395. https://doi.org/10.1186/1471-2164-10-395
De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads
FEMS Microbiology Letters / Feb 01, 2009
Farrer, R. A., Kemen, E., Jones, J. D. G., & Studholme, D. J. (2009). De novoassembly of thePseudomonas syringaepv.syringaeB728a genome using Illumina/Solexa short sequence reads. FEMS Microbiology Letters, 291(1), 103–111. https://doi.org/10.1111/j.1574-6968.2008.01441.x
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans
Nature / Sep 01, 2009
Haas, B. J., Kamoun, S., Zody, M. C., Jiang, R. H. Y., Handsaker, R. E., Cano, L. M., Grabherr, M., Kodira, C. D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T. O., Ah-Fong, A. M. V., Alvarado, L., Anderson, V. L., Armstrong, M. R., Avrova, A., Baxter, L., Beynon, J., Boevink, P. C., … Nusbaum, C. (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262), 393–398. https://doi.org/10.1038/nature08358
Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana
Journal of Proteomics / Apr 01, 2009
Jones, A. M. E., MacLean, D., Studholme, D. J., Serna-Sanz, A., Andreasson, E., Rathjen, J. P., & Peck, S. C. (2009). Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. Journal of Proteomics, 72(3), 439–451. https://doi.org/10.1016/j.jprot.2009.02.004
A toolkit for analysing large-scale plant small RNA datasets
Bioinformatics / Aug 19, 2008
Moxon, S., Schwach, F., Dalmay, T., MacLean, D., Studholme, D. J., & Moulton, V. (2008). A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24(19), 2252–2253. https://doi.org/10.1093/bioinformatics/btn428
PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data
BMC Research Notes / Jun 23, 2008
MacLean, D., Burrell, M. A., Studholme, D. J., & Jones, A. M. (2008). PhosCalc: A tool for evaluating the sites of peptide phosphorylation from Mass Spectrometer data. BMC Research Notes, 1(1). https://doi.org/10.1186/1756-0500-1-30
PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis
Proceedings of the National Academy of Sciences / Feb 26, 2008
Mosher, R. A., Schwach, F., Studholme, D., & Baulcombe, D. C. (2008). PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proceedings of the National Academy of Sciences, 105(8), 3145–3150. https://doi.org/10.1073/pnas.0709632105
Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the σ 54-dependent regulon in Campylobacter jejuni
Microbiology / Sep 01, 2007
Kamal, N., Dorrell, N., Jagannathan, A., Turner, S. M., Constantinidou, C., Studholme, D. J., Marsden, G., Hinds, J., Laing, K. G., Wren, B. W., & Penn, C. W. (2007). Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the σ 54-dependent regulon in Campylobacter jejuni. Microbiology, 153(9), 3099–3111. https://doi.org/10.1099/mic.0.2007/007401-0
Integrated bioinformatic and phenotypic analysis of RpoN‐dependent traits in the plant growth‐promoting bacterium Pseudomonas fluorescens SBW25
Environmental Microbiology / Aug 15, 2007
Jones, J., Studholme, D. J., Knight, C. G., & Preston, G. M. (2007). Integrated bioinformatic and phenotypic analysis of RpoN‐dependent traits in the plant growth‐promoting bacterium Pseudomonas fluorescens SBW25. Environmental Microbiology, 9(12), 3046–3064. Portico. https://doi.org/10.1111/j.1462-2920.2007.01416.x
Marker development for the genetic study of natural variation inArabidopsis thaliana
Bioinformatics / Nov 15, 2007
Nemri, A., Neff, M. M., Burrell, M., Jones, J. D. G., & Studholme, D. J. (2007). Marker development for the genetic study of natural variation inArabidopsis thaliana. Bioinformatics, 23(22), 3108–3109. https://doi.org/10.1093/bioinformatics/btm501
G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss
Bioinformatics / Apr 21, 2006
He, Q., Liu, X., Li, Q., Studholme, D. J., Li, X., & Liang, S. (2006). G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss. Bioinformatics, 22(18), 2189–2191. https://doi.org/10.1093/bioinformatics/btl123
Profiling the secretomes of plant pathogenic Proteobacteria
FEMS Microbiology Reviews / Apr 01, 2005
PRESTON, G., STUDHOLME, D., & CALDELARI, I. (2005). Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiology Reviews, 29(2), 331–360. https://doi.org/10.1016/j.femsre.2004.12.004
Transcriptomic analyses support the similarity of gene expression between brain and testis in human as well as mouse
Cytogenetic and Genome Research / Jan 01, 2005
Guo, J. H., Huang, Q., Studholme, D. J., Wu, C. Q., & Zhao, Z. (2005). Transcriptomic analyses support the similarity of gene expression between brain and testis in human as well as mouse. Cytogenetic and Genome Research, 111(2), 107–109. Portico. https://doi.org/10.1159/000086378
NCD3G: a novel nine-cysteine domain in family 3 GPCRs
Trends in Biochemical Sciences / Nov 01, 2004
Liu, X., He, Q., Studholme, D. J., Wu, Q., Liang, S., & Yu, L. (2004). NCD3G: a novel nine-cysteine domain in family 3 GPCRs. Trends in Biochemical Sciences, 29(11), 571. https://doi.org/10.1016/j.tibs.2004.09.007
MANSC: a seven-cysteine-containing domain present in animal membrane and extracellular proteins
Trends in Biochemical Sciences / Apr 01, 2004
Guo, J., Chen, S., Huang, C., Chen, L., Studholme, D. J., Zhao, S., & Yu, L. (2004). MANSC: a seven-cysteine-containing domain present in animal membrane and extracellular proteins. Trends in Biochemical Sciences, 29(4), 172–174. https://doi.org/10.1016/j.tibs.2004.02.007
NCD3G: a novel nine-cysteine domain in family 3 GPCRs
Trends in Biochemical Sciences / Sep 01, 2004
Liu, X., He, Q., Studholme, D. J., Wu, Q., Liang, S., & Yu, L. (2004). NCD3G: a novel nine-cysteine domain in family 3 GPCRs. Trends in Biochemical Sciences, 29(9), 458–461. https://doi.org/10.1016/j.tibs.2004.07.009
Functionality of Purified ς N (ς 54 ) and a NifA-Like Protein from the Hyperthermophile Aquifex aeolicus
Journal of Bacteriology / Mar 15, 2000
Studholme, D. J., Wigneshwereraraj, S. R., Gallegos, M.-T., & Buck, M. (2000). Functionality of Purified ς N (ς 54 ) and a NifA-Like Protein from the Hyperthermophile Aquifex aeolicus. Journal of Bacteriology, 182(6), 1616–1623. https://doi.org/10.1128/jb.182.6.1616-1623.2000
The alternative sigma factor σ28 of the extreme thermophile Aquifex aeolicus restores motility to an Escherichia coli fliA mutant
FEMS Microbiology Letters / Oct 01, 2000
Studholme, D. (2000). The alternative sigma factor σ28 of the extreme thermophile Aquifex aeolicus restores motility to an Escherichia coli fliA mutant. FEMS Microbiology Letters, 191(1), 103–107. https://doi.org/10.1016/s0378-1097(00)00378-5
The C-Terminal 12 Amino Acids of ςN Are Required for Structure and Function
Archives of Biochemistry and Biophysics / Nov 01, 1999
Studholme, D. J., Finn, R. D., Chaney, M. K., & Buck, M. (1999). The C-Terminal 12 Amino Acids of ςN Are Required for Structure and Function. Archives of Biochemistry and Biophysics, 371(2), 234–240. https://doi.org/10.1006/abbi.1999.1426
Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans
Frontiers in Microbiology / Oct 07, 2015
Aritua, V., Harrison, J., Sapp, M., Buruchara, R., Smith, J., & Studholme, D. J. (2015). Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.01080
High-Throughput Sequencing Data Analysis Software: Current State and Future Developments
Bioinformatics for High Throughput Sequencing / Sep 22, 2011
Paszkiewicz, K., & Studholme, D. J. (2011). High-Throughput Sequencing Data Analysis Software: Current State and Future Developments. Bioinformatics for High Throughput Sequencing, 231–248. https://doi.org/10.1007/978-1-4614-0782-9_14
In silico analysis of the Ï54-dependent enhancer-binding proteins inPirellulaspecies strain 1
FEMS Microbiology Letters / Jan 01, 2004
Studholme, D. J., & Dixon, R. (2004). In silico analysis of the Ï54-dependent enhancer-binding proteins inPirellulaspecies strain 1. FEMS Microbiology Letters, 230(2), 215–225. https://doi.org/10.1016/s0378-1097(03)00897-8
The alternative sigma factor Ï28of the extreme thermophileAquifex aeolicusrestores motility to anEscherichia coli fliAmutant
FEMS Microbiology Letters / Oct 01, 2000
Studholme, D. J., & Buck, M. (2000). The alternative sigma factor Ï28of the extreme thermophileAquifex aeolicusrestores motility to anEscherichia coli fliAmutant. FEMS Microbiology Letters, 191(1), 103–107. https://doi.org/10.1111/j.1574-6968.2000.tb09325.x
Protein domains and architectural innovation in plant-associated Proteobacteria
BMC Genomics / Feb 16, 2005
Studholme, D. J., Downie, J. A., & Preston, G. M. (2005). Protein domains and architectural innovation in plant-associated Proteobacteria. BMC Genomics, 6(1). https://doi.org/10.1186/1471-2164-6-17
Education
Imperial College London
PhD in Biochemistry / August, 1998
Imperial College London
PhD in Biochemistry / August, 1998
Experience
University of Exeter
Senior Lecturer / Associate Professor / November, 2009 — Present
University of Exeter
Senior Lecturer / Associate Professor / November, 2009 — Present
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