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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Aug 03, 2022

J Studholme, D. (2022). Phylogenomic analysis of Xanthomonas v1. https://doi.org/10.17504/protocols.io.261geny57g47/v1

Aug 03, 2022

Grant, M. (2022). Culturing Xanthomonas v1. https://doi.org/10.17504/protocols.io.ewov1nr92gr2/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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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 &amp; Infectious Diseases, 32(8), 1097–1098. https://doi.org/10.1007/s10096-013-1842-8

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

FEMS Microbiology Letters / Jan 01, 2004

Studholme, D. J., & Dixon, R. (2004). In silico analysis of the σ54-dependent enhancer-binding proteins inPirellulaspecies strain 1. FEMS Microbiology Letters, 230(2), 215–225. https://doi.org/10.1016/s0378-1097(03)00897-8

FEMS Microbiology Letters / Oct 01, 2000

Studholme, D. J., & Buck, M. (2000). The alternative sigma factor σ28of 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

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