Faculty of Health and Life Sciences

Dr David Studholme

Dr David Studholme

Associate Professor in Bioinformatics and Employability Lead

 D.J.Studholme@exeter.ac.uk

 Contact me via email

 Geoffrey Pope 419 ("GP Heights")

 

Geoffrey Pope Building, University of Exeter , Stocker Road, Exeter, EX4 4QD, UK

Overview

My main technical expertise is in bioinformatics, especially in the context of handling data from massively parallel DNA sequencing (a.k.a. next-generation sequencing). I also have experience in laboratory-based molecular microbiology having done my PhD and postdoctoral research at Imperial College, London, in the laboratories of Prof David Leak and Prof Martin Buck, respectively. Whilst at the Wellcome Trust Sanger Institute, I contributed to the widely used Pfam and InterPro databases and developed an interest and expertise in high-throughput sequence analysis and data management. Whilst at The Sainsbury Laboratory, I became interested in exploiting large nucleotide sequence datasets generated from so-called next-generation sequencing technologies.

Qualifications

  • 2012 Postgraduate Certificate in Academic Practice, University of Exeter
  • 1998 PhD Imperial College, London
  • 1994 MSc (with Distinction), University of East Anglia
  • 1993 BSc (Hons), Southampton University

Career

  • 2013-present Associate Professor, University of Exeter
  • 2009-2013 Senior Lecturer, University of Exeter
  • 2004-2009 Head of Bioinformatics, The Sainsbury Laboratory
  • 2002–2004 Computer Biologist, Wellcome Trust Sanger Institute
  • 2000-2002 Postdoctoral Fellow, Southampton University
  • 1997-2000 Postdoctoral Fellow, Imperial College, London

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Research

Research interests

There are two main themes to our research:

  • Understanding the evolution and emergence of infectious disease.
  • Deploying bioinformatics and computational methods to address biological questions (mostly around infectious disease of plants).

Work in our laboratory is mostly computer-based and we collaborate widely with colleagues at Exeter, elsewhere in the UK and worldwide.

Research projects

Microbial Uptakes for Sustainable management of major bananA pests and diseases (MUSA)

My research group is part of the MUSA consortium. The principal outcome of this project will be to achieve sustainable intensification of Musa spp. and ensete crops, through identification, development and implementation of IPM based on beneficial microorganisms. This is a large international collaboration to which we contribute aspects around genomics and bioinformatics.

EuroXanth: Integrating science on Xanthomonadaceae for integrated plant disease management in Europe

We are members of this international consortium (COST Action). Bacteria of the family Xanthomonadaceae, including species of Xanthomonas and Xylella fastidiosa, belong to the most devastating plant pathogens continually challenging food security.

Banana Genetic Resources at Eden Project

Bananas and plantains (Musa species) are vital for food security in many tropical and subtropical countries and the most popular fruit in industrialized countries. Although ‘Cavendish’ bananas dominate the world export trade, hundreds of different banana and plantain cultivars are grown for local consumption. In fact, there are about 1,000 types of banana: sweet, savoury, round, bent, straight, green, yellow, pink, silvery, even spotted and striped. Its health benefits include reducing appetite and sugar craving, fighting obesity, improving muscle endurance, and reducing bad cholesterol in humans. Genome sequencing and resequencing open a window into the genetics of crop plants, for example revealing genetic variation that can be exploited as markers for accelerated breeding, genes potentially encoding traits such as disease resistance, as well as more fundamental insights into the biology. A handful of reference genome sequences are available for representative varieties of Musa acuminata, Musa balbisiana the progenitor species contributing the ‘A’ and ‘B’ genomes found in cultivated hybrids, and also the species Musa itinerans. However, there are many gaps in our knowledge of genetic differences within and among Musa species. Prior to this application, we have also performed genome sequencing on several varieties including Sukali Ndiizi (AAB), Pisang Awak (ABB), Gonja Manjaya (AAB), Cavendish (AAA) and M. balbisana (BB). The Eden Project Musa collection is an important long-term repository of diverse banana germplasm, including 45 accessions from several species representing a diverse range of phenotypes such as fruit morphology. To fully leverage this valuable resource it is important to genetically characterise its content. 

Xanthomonas Threats

Xanthomonas plant diseases: mitigating existing, emerging and future threats to UK agriculture.
 We will utilise extensive Brassica germplasm to investigate the genetics, demography and diagnosis of Xanthomonas spp. This is a collaborative project with the University of Warwick and Fera Science. The Exeter component of the project includes genome sequencing and analysis of > 900 bacterial strains.

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Publications

Journal articles

Studholme DJ (In Press). Population-genomic insights into emergence, crop-adaptation, and dissemination of Pseudomonas syringae pathogens. Microbial Genomics
Erdos Z, Studholme DJ, Sharma MD, Chandler D, Bass C, Raymond B (2024). Manipulating multi-level selection in a fungal entomopathogen reveals social conflicts and a method for improving biocontrol traits. PLoS Pathog, 20(3). Abstract.  Author URL.
Bagratee TJ, Studholme DJ (2024). Targeted genome sequencing for tuberculosis drug susceptibility testing in South Africa: a proposed diagnostic pipeline. Access Microbiology, 6(2). Abstract.
Williamson HF, Brettschneider J, Caccamo M, Davey RP, Goble C, Kersey PJ, May S, Morris RJ, Ostler R, Pridmore T, et al (2023). Data management challenges for artificial intelligence in plant and agricultural research. F1000Research, 10, 324-324. Abstract.
Erdos Z, Studholme DJ, Raymond B, Sharma MD (2023). De novo genome assembly of Akanthomyces muscarius, a biocontrol agent of insect agricultural pests. Access Microbiology, 5(6). Abstract.
Harrison J, Hussain RMF, Greer SF, Ntoukakis V, Aspin A, Vicente JG, Grant M, Studholme DJ (2023). Draft genome sequences for ten strains of Xanthomonas species that have phylogenomic importance. Access Microbiology, 5(7). Abstract.
Vicente JG, McHugh J, Bryning A, Carroll S, Harrison J, Studholme D (2023). First identification of Xanthomonas nasturtii as the cause of black rot of watercress in Hawaii. Plant Dis Abstract.  Author URL.
Reyes-Herrera PH, Torres-Bedoya E, Lopez-Alvarez D, Burbano-David D, Carmona SL, Bebber DP, Studholme DJ, 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. Abstract.  Author URL.
Devran Z, Özalp T, Studholme DJ, Tör M (2023). Mapping of the gene in tomato conferring resistance to root-knot nematodes at high soil temperature. Frontiers in Plant Science, 14 Abstract.
Harrison J, Hussain RMF, Aspin A, Grant MR, Vicente JG, Studholme DJ (2023). Phylogenomic Analysis Supports the Transfer of 20 Pathovars from Xanthomonas campestris into Xanthomonas euvesicatoria. Taxonomy, 3(1), 29-45. Abstract.
Wacker T, Helmstetter N, Wilson D, Fisher MC, Studholme DJ, Farrer RA (2023). Two-speed genome evolution drives pathogenicity in fungal pathogens of animals. Proceedings of the National Academy of Sciences, 120(2). Abstract.
Wacker T, Helmstetter N, Wilson D, Fisher MC, Studholme DJ, Farrer RA (2023). Two-speed genome evolution drives pathogenicity in fungal pathogens of animals (vol 120, e2212633120, 2023). PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 120(28).  Author URL.
Sambles C, Suarez-Fernandez M, Lopez-Moya F, Vicente Lopez-Llorca L, Studholme DJ (2022). Chitosan induces differential transcript usage of chitosanase 3 encoding gene (<i>csn3</i>) in the biocontrol fungus <i>Pochonia chlamydosporia</i> 123. BMC GENOMICS, 23(1).  Author URL.
Lebas B, Adams I, Al Rwahnih M, Baeyen S, Bilodeau G, Blouin AG, Boonham N, Candresse T, Chandelier A, De Jonghe K, et al (2022). Facilitating the adoption of high-throughput sequencing technologies as a plant pest diagnostic test in laboratories: A step-by-step description. EPPO Bulletin, 52(2), 394-418. Abstract.
Lascelles DM, Roberts MR, Cruz L, Cruz J, Studholme DJ, Harrison J, Greer SF, Grant M, Holden JM, Carter B, et al (2022). First report of black rot caused by <i>Xanthomonas nasturtii</i> on watercress in Spain and Portugal. New Disease Reports, 46(2).
Twohig KA, Nyberg T, Zaidi A, Thelwall S, Sinnathamby MA, Aliabadi S, Seaman SR, Harris RJ, Hope R, Lopez-Bernal J, et al (2022). Hospital admission and emergency care attendance risk for SARS-CoV-2 delta (B.1.617.2) compared with alpha (B.1.1.7) variants of concern: a cohort study. The Lancet Infectious Diseases, 22(1), 35-42. Abstract.
Mirghasempour SA, Studholme DJ, Chen W, Cui D, Mao B (2022). Identification and Characterization of Fusarium nirenbergiae Associated with Saffron Corm Rot Disease. Plant Dis, 106(2), 486-495. Abstract.  Author URL.
Mirghasempour SA, Studholme DJ, 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).
O'Sullivan DM, Doyle RM, Temisak S, Redshaw N, Whale AS, Logan G, Huang J, Fischer N, Amos GCA, Preston MD, et al (2021). An inter-laboratory study to investigate the impact of the bioinformatics component on microbiome analysis using mock communities. Sci Rep, 11(1). Abstract.  Author URL.
Volz E, Mishra S, Chand M, Barrett JC, Johnson R, Geidelberg L, Hinsley WR, Laydon DJ, Dabrera G, Toole AO, et al (2021). Assessing transmissibility of SARS-CoV-2 lineage B.1.1.7 in England. NATURE, 593(7858), 266-+.  Author URL.
Graham MS, Sudre CH, May A, Antonelli M, Murray B, Varsavsky T, Kläser K, Canas LS, Molteni E, Modat M, et al (2021). Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study. The Lancet Public Health, 6(5), e335-e345.
Suarez‐Fernandez M, Sambles C, Lopez‐Moya F, Nueda MJ, Studholme DJ, Lopez‐Llorca LV (2021). Chitosan modulates <i>Pochonia chlamydosporia</i> gene expression during nematode egg parasitism. Environmental Microbiology, 23(9), 4980-4997. Abstract.
Chen NWG, Ruh M, Darrasse A, Foucher J, Briand M, Costa J, Studholme DJ, Jacques M-A (2021). Common bacterial blight of bean: a model of seed transmission and pathological convergence. Mol Plant Pathol, 22(12), 1464-1480. Abstract.  Author URL.
Williamson HF, Brettschneider J, Caccamo M, Davey RP, Goble C, Kersey PJ, May S, Morris RJ, Ostler R, Pridmore T, et al (2021). Data management challenges for artificial intelligence in plant and agricultural research. F1000Research, 10, 324-324. Abstract.
Williamson HF, Brettschneider J, Caccamo M, Davey RP, Goble C, Kersey PJ, May S, Morris RJ, Ostler R, Pridmore T, et al (2021). Data management challenges for artificial intelligence in plant and agricultural research. F1000Research, 10 Abstract.
Christakis CA, Daskalogiannis G, Chatzaki A, Markakis EA, Mermigka G, Sagia A, Rizzo GF, Catara V, Lagkouvardos I, Studholme DJ, et al (2021). Endophytic Bacterial Isolates from Halophytes Demonstrate Phytopathogen Biocontrol and Plant Growth Promotion Under High Salinity. Front Microbiol, 12 Abstract.  Author URL.
Volz E, Hill V, McCrone JT, Price A, Jorgensen D, O’Toole Á, Southgate J, Johnson R, Jackson B, Nascimento FF, et al (2021). Evaluating the Effects of SARS-CoV-2 Spike Mutation D614G on Transmissibility and Pathogenicity. Cell, 184(1), 64-75.e11.
Muzemil S, Chala A, Tesfaye B, Studholme DJ, Grant M, Yemataw Z, Mekonin S, Olango TM (2021). Evaluation of 20 enset (<i>Ensete ventricosum)</i> landraces for response to <i>Xanthomonas vasicola</i> pv. <i>Musacearum</i> infection. EUROPEAN JOURNAL OF PLANT PATHOLOGY, 161(4), 821-836.  Author URL.
Elliott P, Haw D, Wang H, Eales O, Walters CE, Ainslie KEC, Atchison C, Fronterre C, Diggle PJ, Page AJ, et al (2021). Exponential growth, high prevalence of SARS-CoV-2, and vaccine effectiveness associated with the Delta variant. Science, 374(6574). Abstract.  Author URL.
Kahveci E, Devran Z, oezkaynak E, Hong Y, Studholme DJ, Toer M (2021). Genomic-Assisted Marker Development Suitable for <i>CsCvy</i>-<i>1</i> Selection in Cucumber Breeding. FRONTIERS IN PLANT SCIENCE, 12  Author URL.
Wang S, Vetukuri RR, Kushwaha SK, Hedley PE, Morris J, Studholme DJ, Welsh LRJ, Boevink PC, Birch PRJ, Whisson SC, et al (2021). Haustorium formation and a distinct biotrophic transcriptome characterize infection of <i>Nicotiana benthamiana</i> by the tree pathogen <i>Phytophthora kernoviae</i>. MOLECULAR PLANT PATHOLOGY, 22(8), 954-968.  Author URL.
Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, et al (2021). Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. NATURE, 593(7857), 136-+.  Author URL.
Torres Bedoya E, Bebber DP, Studholme DJ (2021). Taxonomic Revision of the Banana Fusarium Wilt TR4 Pathogen is Premature. Phytopathology, 111(12), 2141-2145. Abstract.  Author URL.
Malesevic M, Stanisavljevic N, Miljkovic M, Jovcic B, Filipic B, Studholme DJ, Kojic M (2021). The large plasmidome of Lactococcus lactis subsp. lactis bv. diacetylactis S50 confers its biotechnological properties. Int J Food Microbiol, 337 Abstract.  Author URL.
Catara V, Cubero J, Pothier JF, Bosis E, Bragard C, Đermić E, Holeva MC, Jacques MA, Petter F, Pruvost O, et al (2021). Trends in molecular diagnosis and diversity studies for phytosanitary regulated xanthomonas. Microorganisms, 9(4). Abstract.
Mirghasempour SA, Huang S, Studholme DJ, Brady CL (2020). A Grain Rot of Rice in Iran Caused by a Xanthomonas Strain Closely Related to X. sacchari. Plant Dis, 104(6), 1581-1583. Abstract.  Author URL.
Lange A, Paris JR, Gharbi K, Cézard T, Miyagawa S, Iguchi T, Studholme DJ, Tyler CR (2020). A newly developed genetic sex marker and its application to understanding chemically induced feminisation in roach (<i>Rutilus rutilus</i>). Molecular Ecology Resources, 20(4), 1007-1022. Abstract.
Bez C, Javvadi SG, Bertani I, Devescovi G, Guarnaccia C, Studholme DJ, Geller AM, Levy A, Venturi V (2020). AzeR, a transcriptional regulator that responds to azelaic acid in Pseudomonas nitroreducens. Microbiology (Reading), 166(1), 73-84. Abstract.  Author URL.
Morcrette H, Kovacs-Simon A, Tennant RK, Love J, Wagley S, Yang ZR, Studholme DJ, Soyer OS, Champion OL, Butler CS, et al (2020). Campylobacter jejuni 11168H Exposed to Penicillin Forms Persister Cells and Cells with Altered Redox Protein Activity. Frontiers in Cellular and Infection Microbiology, 10 Abstract.
Sidda JD, Song L, Parker JL, Studholme DJ, Sambles C, Grant M (2020). Diversity of secoiridoid glycosides in leaves of UK and Danish ash provide new insight for ash dieback management. Scientific Reports, 10(1). Abstract.
Guo Y, Dupont P-Y, Mesarich CH, Yang B, McDougal RL, Panda P, Dijkwel P, Studholme DJ, Sambles C, Win J, et al (2020). Functional analysis of RXLR effectors from the New Zealand kauri dieback pathogen Phytophthora agathidicida. Mol Plant Pathol, 21(9), 1131-1148. Abstract.  Author URL.
Sambles C, Venkatesan L, Shittu OM, Harrison J, Moore K, Tripathi L, Grant M, Warmington R, Studholme DJ (2020). Genome sequencing data for wild and cultivated bananas, plantains and abacá. Data in Brief, 33 Abstract.
Stulberg MJ, Santillana G, Studholme DJ, Kasiborski B, Ortiz-Castro M, Broders K, Arias S, Block C, Munkvold G, Rascoe J, et al (2020). Genomics-Informed Molecular Detection of Xanthomonas vasicola pv. vasculorum Strains Causing Severe Bacterial Leaf Streak of Corn. Phytopathology, 110(6), 1174-1179. Abstract.  Author URL.
Christakis CA, Daskalogiannis G, Chatzakis A, Markakis EA, Sagia A, Rizzo GF, Catara V, Lagkouvardos I, Studholme DJ, Sarris PF, et al (2020). Halophytic bacterial endophytome: a potential source of beneficial microbes for a sustainable agriculture. Abstract.
Kioukis A, Michalopoulou VA, Briers L, Pirintsos S, Studholme DJ, Pavlidis P, Sarris PF (2020). Intraspecific diversification of the crop wild relative Brassica cretica Lam. using demographic model selection. BMC Genomics, 21(1). Abstract.  Author URL.
Hamilton PB, Lockyer AE, Uren Webster TM, Studholme DJ, Paris JR, Baynes A, Nicol E, Dawson DA, Moore K, Farbos A, et al (2020). Investigation into Adaptation in Genes Associated with Response to Estrogenic Pollution in Populations of Roach (Rutilus rutilus) Living in English Rivers. Environ Sci Technol, 54(24), 15935-15945. Abstract.  Author URL.
Kojic M, Jovcic B, Miljkovic M, Novovic K, Begovic J, Studholme DJ (2020). Large-scale chromosome flip-flop reversible inversion mediates phenotypic switching of expression of antibiotic resistance in lactococci. Microbiol Res, 241 Abstract.  Author URL.
Nakato GV, Studholme DJ, Blomme G, Grant M, Coutinho TA, Were EM, Wicker E, Mahuku G (2020). SNP‐based genotyping and whole‐genome sequencing reveal previously unknown genetic diversity in <i>Xanthomonas vasicola</i> pv. <i>musacearum</i>, causal agent of banana xanthomonas wilt, in its presumed Ethiopian origin. Plant Pathology, 70(3), 534-543. Abstract.
Filipic B, Novovic K, Studholme DJ, Malesevic M, Mirkovic N, Kojic M, Jovcic B (2020). Shotgun metagenomics reveals differences in antibiotic resistance genes among bacterial communities in Western Balkans glacial lakes sediments. J Water Health, 18(3), 383-397. Abstract.  Author URL.
Thines M, Sharma R, Rodenburg SYA, Gogleva A, Judelson HS, Xia X, van den Hoogen J, Kitner M, Klein J, Neilen M, et al (2020). The Genome of Peronospora belbahrii Reveals High Heterozygosity, a Low Number of Canonical Effectors, and TC-Rich Promoters. Mol Plant Microbe Interact, 33(5), 742-753. Abstract.  Author URL.
Studholme DJ, Wicker E, Abrare SM, Aspin A, Bogdanove A, Broders K, Dubrow Z, Grant M, Jones JB, Karamura G, et al (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. Abstract.  Author URL.
Miljkovic M, Jovanovic S, O'Connor PM, Mirkovic N, Jovcic B, Filipic B, Dinic M, Studholme DJ, Fira D, Cotter PD, et al (2019). Brevibacillus laterosporus strains BGSP7, BGSP9 and BGSP11 isolated from silage produce broad spectrum multi-antimicrobials. PLoS One, 14(5). Abstract.  Author URL.
Kioukis A, Michalopoulou VA, Briers L, Pirintsos S, Studholme DJ, Pavlidis P, Sarris PF (2019). Draft Genome Sequence and intraspecific diversification of the wild crop relative<i>Brassica cretica</i>Lam. using demographic model selection. Abstract.
Muzemil S, Chala A, Tesfaye B, Studholme DJ, Grant M, Yemataw Z, Olango TM (2019). Evaluation of 20 enset (<i>Ensete ventricosum</i>) landraces for response to <i>Xanthomonas vasicola</i> pv. <i>musacearum</i> infection. Abstract.
Wagley S, Scott AE, Ireland PM, Prior JL, Atkins TP, Bancroft GJ, Studholme DJ, Titball RW (2019). Genome Resequencing of Laboratory Stocks of Burkholderia pseudomallei K96243. Microbiol Resour Announc, 8(9). Abstract.  Author URL.
Studholme DJ, Panda P, Sanfuentes Von Stowasser E, González M, Hill R, Sambles C, Grant M, Williams NM, McDougal RL (2019). Genome sequencing of oomycete isolates from Chile supports the New Zealand origin of Phytophthora kernoviae and makes available the first Nothophytophthora sp. genome. Mol Plant Pathol, 20(3), 423-431. Abstract.  Author URL.
Warmington RJ, Kay W, Jeffries A, O'Neill P, Farbos A, Moore K, Bebber DP, Studholme DJ (2019). High-Quality Draft Genome Sequence of the Causal Agent of the Current Panama Disease Epidemic. Microbiol Resour Announc, 8(36). Abstract.  Author URL.
Minardi D, Studholme DJ, 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. Abstract.  Author URL.
Chaudhari Y, Cairns TC, Sidhu Y, Attah V, Thomas G, Csukai M, Talbot NJ, Studholme DJ, Haynes K (2019). The <i>Zymoseptoria tritici</i> ORFeome: a functional genomics community resource. Abstract.
Chaudhari Y, Cairns TC, Sidhu Y, Attah V, Thomas G, Csukai M, Talbot NJ, Studholme DJ, Haynes K (2019). The Zymoseptoria tritici ORFeome: a Functional Genomics Community Resource. Mol Plant Microbe Interact, 32(12), 1564-1570. Abstract.  Author URL.
Nakato GV, Wicker E, Coutinho TA, Mahuku G, Studholme DJ (2018). A highly specific tool for identification of Xanthomonas vasicola pv. musacearum based on five Xvm-specific coding sequences. Heliyon, 4(12). Abstract.
Woods-Tör A, Studholme DJ, Cevik V, Telli O, Holub EB, Tör M (2018). A suppressor/avirulence gene combination in hyaloperonospora arabidopsidis determines race specificity in Arabidopsis thaliana. Frontiers in Plant Science, 9 Abstract.
Dorati F, Barrett GA, Sanchez-Contreras M, Arseneault T, José MS, Studholme DJ, Murillo J, Caballero P, Waterfield NR, Arnold DL, et al (2018). Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators. Microorganisms, 6(2). Abstract.  Author URL.
Michalopoulou VA, Vicente JG, Studholme DJ, Sarris PF (2018). Draft genome sequences of pathotype strains for three pathovars belonging to three xanthomonas species. Microbiology Resource Announcements, 7(12). Abstract.
Schaum E, Buckling A, Studholme D, Smirnoff N, Yvon-Durocher G (2018). Environmental fluctuations accelerate molecular evolution of thermal tolerance in a marine diatom. Nature Communications
Yemataw Z, Muzemil S, Ambachew D, Tripathi L, Tesfaye K, Chala A, Farbos A, O'Neill P, Moore K, Grant M, et al (2018). Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia. Data in Brief, 18, 285-293. Abstract.
Morcrette H, Morgan MS, Farbos A, O'Neill P, Moore K, Titball RW, Studholme DJ (2018). Genome sequence of Staphylococcus aureus Ex1, isolated from a patient with spinal osteomyelitis. Genome Announcements, 6(26). Abstract.
Devran Z, Kahveci E, Hong Y, Studholme DJ, Tör M (2018). Identifying molecular markers suitable for Frl selection in tomato breeding. Theor Appl Genet, 131(10), 2099-2105. Abstract.  Author URL.
Yemataw Z, Tesfaye K, Grant M, Studholme DJ, Chala A (2018). Multivariate analysis of morphological variation in enset (Ensete ventricosum (Welw.) Cheesman) reveals regional and clinal variation in germplasm from south and south western Ethiopia. Australian Journal of Crop Science, 12(12), 1849-1858. Abstract.
Minardi D, Studholme DJ, 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. Abstract.
Sambles CM, Salmon DL, Florance H, Howard TP, Smirnoff N, Nielsen LR, McKinney LV, Kjær ED, Buggs RJA, Studholme DJ, et al (2017). Ash leaf metabolomes reveal differences between trees tolerant and susceptible to ash dieback disease. Sci Data, 4 Abstract.  Author URL.
Yemataw Z, Mekonen A, Chala A, Tesfaye K, Mekonen K, Studholme DJ, Sharma K (2017). Farmers' knowledge and perception of enset Xanthomonas wilt in southern Ethiopia. Agriculture and Food Security, 6(1). Abstract.
Sollars ESA, Harper AL, Kelly LJ, Sambles CM, Ramirez-Gonzalez RH, Swarbreck D, Kaithakottil G, Cooper ED, Uauy C, Havlickova L, et al (2017). Genome sequence and genetic diversity of European ash trees. Nature, 541(7636), 212-216. Abstract.  Author URL.
Turner J, O'Neill P, Grant M, Mumford RA, Thwaites R, Studholme DJ (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.
Sambles C, Moore K, Lux TM, Jones K, Littlejohn GR, Gouveia JD, Aves SJ, Studholme DJ, Lee R, Love J, et al (2017). Metagenomic analysis of the complex microbial consortium associated with cultures of the oil‐rich alga <i>Botryococcus braunii</i>. MicrobiologyOpen, 6(4). Abstract.
Yemataw Z, Chala A, Ambachew D, Studholme DJ, Grant MR, 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 (Basel), 6(4). Abstract.  Author URL.
Vicente JG, Rothwell S, Holub EB, Studholme DJ (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. Int J Syst Evol Microbiol, 67(9), 3645-3654. Abstract.  Author URL.
Galhano R, Illana A, Ryder LS, Rodríguez-Romero J, Demuez M, Badaruddin M, Martinez-Rocha AL, Soanes DM, Studholme DJ, Talbot NJ, et al (2017). Tpc1 is an important Zn(II)2Cys6 transcriptional regulator required for polarized growth and virulence in the rice blast fungus. PLoS Pathog, 13(7). Abstract.  Author URL.
Asif H, Studholme DJ, Khan A, Aurongzeb M, Khan IA, Azim MK (2016). Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard. Genet Mol Biol, 39(3), 465-473. Abstract.  Author URL.
Asif H, Studholme DJ, Khan A, Aurongzeb M, Khan IA, Azim MK (2016). Comparative genomics of an endophytic Pseudomonas putida isolated from mango orchard. Genet Mol Biol, 0 Abstract.  Author URL.
Harrison J, Dornbusch MR, Samac D, Studholme DJ (2016). Draft Genome Sequence of Pseudomonas syringae pv. syringae ALF3 Isolated from Alfalfa. Genome Announc, 4(1). Abstract.  Author URL.
Jones KJ, Moore K, Sambles C, Love J, Studholme DJ, Aves SJ (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 Announc, 4(1). Abstract.  Author URL.
Harrison J, Grant MR, Studholme DJ (2016). Draft Genome Sequences of Two Strains of Xanthomonas arboricola pv. celebensis Isolated from Banana Plants. Genome Announc, 4(1). Abstract.  Author URL.
Studholme DJ (2016). Genome Update. Let the consumer beware: Streptomyces genome sequence quality. Microbial Biotechnology, 9(1), 3-7. Abstract.
Studholme DJ, McDougal RL, Sambles C, Hansen E, Hardy G, Grant M, Ganley RJ, Williams NM (2016). Genome sequences of six Phytophthora species associated with forests in New Zealand. Genomics Data, 7, 54-56. Abstract.
Cairns TC, Studholme DJ, Talbot NJ, Haynes K (2016). New and Improved Techniques for the Study of Pathogenic Fungi. Trends in Microbiology, 24(1), 35-50. Abstract.
Cairns TC, Studholme DJ, Talbot NJ, Haynes K (2016). New and Improved Techniques for the Study of Pathogenic Fungi. Trends Microbiol, 24(1), 35-50. Abstract.  Author URL.
Kilaru S, Schuster M, Studholme D, Soanes D, Lin C, Talbot NJ, Steinberg G (2015). A codon-optimized green fluorescent protein for live cell imaging in Zymoseptoria tritici. Fungal Genet Biol, 79, 125-131. Abstract.  Author URL.
Laver T, Harrison J, O'Neill PA, Moore K, Farbos A, Paszkiewicz K, Studholme DJ (2015). Assessing the performance of the Oxford Nanopore Technologies MinION. Biomolecular Detection and Quantification, 3, 1-8. Abstract.
Nandi T, Holden MTG, Didelot X, Mehershahi K, Boddey JA, Beacham I, Peak I, Harting J, Baybayan P, Guo Y, et al (2015). Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles. Genome Res, 25(1), 129-141. Abstract.  Author URL.
de Torres M, Littlejohn G, Jayaraman S, Studholme D, Bailey TC, Lawson T, Delfino L, Licht D, Truman W, Bölter B, et al (2015). Chloroplasts play a central role in plant defence and are targeted by pathogen effectors. Nature Plants, 1, n/a-n/a.
Karamura G, Smith J, Studholme D, Kubiriba J, Karamura E (2015). Comparative pathogenicity studies of the Xanthomonas vasicola species on maize, sugarcane and banana. African Journal of Plant Science, 9(9), 385-400.
Cairns TC, Sidhu YS, Chaudhari YK, Talbot NJ, Studholme DJ, Haynes K (2015). Construction and high-throughput phenotypic screening ofZymoseptoria tritici over-expression strains. Fungal Genet Biol, 79, 110-117. Abstract.  Author URL.
Hodgetts J, Karamura G, Johnson G, Hall J, Perkins K, Beed F, Nakato V, Grant M, Studholme DJ, Boonham N, et al (2015). 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, 64(3), 559-567. Abstract.
Devran Z, Kahveci E, Özkaynak E, Studholme DJ, Tör M (2015). Development of molecular markers tightly linked to Pvr4 gene in pepper using next-generation sequencing. Mol Breed, 35(4). Abstract.  Author URL.
Siddiqui FM, Ibrahim M, Noureen N, Noreen Z, Titball RW, Champion OL, Wren BW, Studholme D, Bokhari H (2015). Draft Genome Sequence of the Enteropathogenic Bacterium Campylobacter jejuni Strain cj255. Genome Announc, 3(5). Abstract.  Author URL.
Sambles C, Schlenzig A, O'Neill P, Grant M, Studholme DJ (2015). Draft genome sequences of Phytophthora kernoviae and Phytophthora ramorum lineage EU2 from Scotland. Genomics Data, 6, 193-194.
Mata Saez LDL, McCracken AR, Cooke LR, O'Neill P, Grant M, Studholme DJ (2015). Draft genome sequences of seven isolates of Phytophthora ramorum EU2 from Northern Ireland. Genomics Data, 6, 191-192. Abstract.
Taylor TB, Mulley G, Dills AH, Alsohim AS, McGuffin LJ, Studholme DJ, Silby MW, Brockhurst MA, Johnson LJ, Jackson RW, et al (2015). Evolution. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science, 347(6225), 1014-1017. Abstract.  Author URL.
Sidhu YS, Cairns TC, Chaudhari YK, Usher J, Talbot NJ, Studholme DJ, Csukai M, Haynes K (2015). Exploitation of sulfonylurea resistance marker and non-homologous end joining mutants for functional analysis in Zymoseptoria tritici. Fungal Genet Biol, 79, 102-109. Abstract.  Author URL.
Sharma R, Xia X, Cano LM, Evangelisti E, Kemen E, Judelson H, Oome S, Sambles C, van den Hoogen DJ, Kitner M, et al (2015). Genome analyses of the sunflower pathogen Plasmopara halstedii provide insights into effector evolution in downy mildews and Phytophthora. BMC Genomics, 16 Abstract.  Author URL.
Aritua V, Harrison J, Sapp M, Buruchara R, Smith J, Studholme DJ (2015). Genome sequencing reveals a new lineage associated with lablab bean and genetic exchange between Xanthomonas axonopodis pv. phaseoli and Xanthomonas fuscans subsp. fuscans. Front Microbiol, 6 Abstract.  Author URL.
Clarke CR, Studholme DJ, Hayes B, Runde B, Weisberg A, Cai R, Wroblewski T, Daunay M-C, Wicker E, Castillo JA, et al (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. Abstract.  Author URL.
Siddiqui F, Champion O, Akram M, Studholme D, Eqani SAMAS, Wren BW, Titball R, Bokhari H (2015). Molecular detection identified a type six secretion system in Campylobacter jejuni from various sources but not from human cases. J Appl Microbiol, 118(5), 1191-1198. Abstract.  Author URL.
Hodgetts J, Hall J, Karamura G, Grant M, Studholme DJ, Boonham N, Karamura E, Smith JJ (2015). Rapid, specific, simple, in-field detection of Xanthomonas campestris pathovar musacearum by loop-mediated isothermal amplification. J Appl Microbiol, 119(6), 1651-1658. Abstract.  Author URL.
Studholme DJ (2015). Some (bacilli) like it hot: Genomics of Geobacillus species. Microbial Biotechnology, 8(1), 40-48.
Aritua V, Musoni A, Kabeja A, Butare L, Mukamuhirwa F, Gahakwa D, Kato F, Abang MM, Buruchara R, Sapp M, et al (2015). The draft genome sequence of Xanthomonas species strain Nyagatare, isolated from diseased bean in Rwanda. FEMS Microbiol Lett, 362(4). Abstract.  Author URL.
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, 13-33. Abstract.
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, 13-33. Abstract.
O'Sullivan DM, Laver T, Temisak S, Redshaw N, Harris KA, Foy CA, Studholme DJ, Huggett JF (2014). Assessing the accuracy of quantitative molecular microbial profiling. Int J Mol Sci, 15(11), 21476-21491. Abstract.  Author URL.
Wagley S, Newcombe J, Laing E, Yusuf E, Sambles CM, Studholme DJ, La Ragione RM, Titball RW, Champion OL (2014). Differences in carbon source utilisation distinguish Campylobacter jejuni from Campylobacter coli. BMC Microbiol, 14 Abstract.  Author URL.
Uzelac G, Bertani I, Kojic M, Paszkiewicz KH, Studholme DJ, Passos da Silva D, Venturi V (2014). Draft Genome Sequence of Beneficial Rice Rhizosphere Isolate Pseudomonas aeruginosa PUPa3. Genome Announc, 2(4). Abstract.  Author URL.
Harrison J, Studholme DJ (2014). Draft genome sequence of Xanthomonas axonopodis pathovar vasculorum NCPPB 900. FEMS Microbiology Letters, 360(2), 113-116. Abstract.
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, 211-237. Abstract.
Harrison JW, Dung TTN, Siddiqui F, Korbrisate S, Bukhari H, Tra MPV, Hoang NVM, Carrique-Mas J, Bryant J, Campbell JI, et al (2014). Identification of possible virulence marker from Campylobacter jejuni isolates. Emerg Infect Dis, 20(6), 1026-1029. Abstract.  Author URL.
Harrison J, Studholme DJ (2014). Recently published Streptomyces genome sequences. Microb Biotechnol, 7(5), 373-380.  Author URL.
Rhodes G, Bosma H, Studholme D, Arnold DL, Jackson RW, Pickup RW (2014). The rulB gene of plasmid pWW0 is a hotspot for the site-specific insertion of integron-like elements found in the chromosomes of environmental Pseudomonas fluorescens group bacteria. Environmental Microbiology, 16(8), 2374-2388. Abstract.
Huggett JF, Laver T, Tamisak S, Nixon G, O'Sullivan DM, Elaswarapu R, Studholme DJ, Foy CA (2013). Considerations for the development and application of control materials to improve metagenomic microbial community profiling. Accreditation and Quality Assurance, 18(2), 77-83. Abstract.
Passos da Silva D, Devescovi G, Paszkiewicz K, Moretti C, Buonaurio R, Studholme DJ, Venturi V (2013). Draft Genome Sequence of Erwinia toletana, a Bacterium Associated with Olive Knots Caused by Pseudomonas savastanoi pv. Savastanoi. Genome Announc, 1(3). Abstract.  Author URL.
Khan A, Asif H, Studholme DJ, Khan IA, Azim MK (2013). Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards. World J Microbiol Biotechnol, 29(11), 2033-2044. Abstract.  Author URL.
Quinn L, O'Neill PA, Harrison J, Paskiewicz KH, Mccracken AR, Cooke LR, Grant MR, Studholme DJ (2013). Genome-wide sequencing of Phytophthora lateralis reveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland. FEMS Microbiology Letters, 344(2), 179-185. Abstract.
Quinn L, O'Neill PA, Harrison J, Paskiewicz KH, McCracken AR, Cooke LR, Grant MR, Studholme DJ (2013). Genome-wide sequencing of Phytophthora lateralis reveals genetic variation among isolates from Lawson cypress (Chamaecyparis lawsoniana) in Northern Ireland. FEMS Microbiol Lett, 344(2), 179-185. Abstract.  Author URL.
Studholme D, Harris B, Le Cocq K, Winsbury R, Perera V, Ryder L, Beale M, Ward J, Thornton CR, Grant M, et al (2013). Investigating the Beneficial Traits of Trichoderma hamatum GD12 for Sustainable Agriculture - Insights from Genomics. Frontiers in Plant-Microbe Interactions, 4, 1-13. Abstract.
Martinez-Argudo I, Veenendaal AKJ, Liu X, Roehrich AD, Ronessen MC, Franzoni G, van Rietschoten KN, Morimoto YV, Saijo-Hamano Y, Avison MB, et al (2013). Isolation of Salmonella mutants resistant to the inhibitory effect of Salicylidene acylhydrazides on flagella-mediated motility. PLoS One, 8(1). Abstract.  Author URL.
Monteil CL, Cai R, Liu H, Llontop MEM, Leman S, Studholme DJ, Morris CE, Vinatzer BA (2013). Nonagricultural reservoirs contribute to emergence and evolution of Pseudomonas syringae crop pathogens. New Phytol, 199(3), 800-811. Abstract.  Author URL.
Huggett JF, Studholme DJ, Laver T, Foy CA (2013). Progress in metagenomics requires a balanced appraisal of the available technologies. European Journal of Clinical Microbiology and Infectious Diseases, 32(8), 1097-1098.
Huggett JF, Studholme DJ, Laver T, Foy CA (2013). Progress in metagenomics requires a balanced appraisal of the available technologies. Eur J Clin Microbiol Infect Dis, 32(8), 1097-1098.  Author URL.
Burlinson P, Studholme D, Cambray-Young J, Heavens D, Rathjen J, Hodgkin J, Preston GM (2013). Pseudomonas fluorescens NZI7 repels grazing by C. elegans, a natural predator. ISME J, 7(6), 1126-1138. Abstract.  Author URL.
Van Immerseel F, Studholme DJ, Eeckhaut V, Heyndrickx M, Dewulf J, Dewaele I, Van Hoorebeke S, Haesebrouck F, Van Meirhaeghe H, Ducatelle R, et al (2013). Salmonella Gallinarum field isolates from laying hens are related to the vaccine strain SG9R. Vaccine, 31(43), 4940-4945. Abstract.  Author URL.
Farrer RA, Henk DA, MacLean D, Studholme DJ, Fisher MC (2013). Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects. Sci Rep, 3 Abstract.  Author URL.
Azam S, Thakur V, Ruperao P, Shah T, Balaji J, Amindala B, Farmer AD, Studholme DJ, May GD, Edwards D, et al (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. Am J Bot, 99(2), 186-192. Abstract.  Author URL.
Studholme DJ (2012). Deep sequencing of small RNAs in plants: applied bioinformatics. Brief Funct Genomics, 11(1), 71-85. Abstract.  Author URL.
Patel HK, da Silva DP, Devescovi G, Maraite H, Paszkiewicz K, Studholme DJ, Venturi V (2012). Draft genome sequence of Pseudomonas fuscovaginae, a broad-host-range pathogen of plants. J Bacteriol, 194(10), 2765-2766. Abstract.  Author URL.
Sohn KH, Jones JDG, Studholme DJ (2012). Draft genome sequence of Pseudomonas syringae pathovar syringae strain FF5, causal agent of stem tip dieback disease on ornamental pear. J Bacteriol, 194(14), 3733-3734. Abstract.  Author URL.
Wasukira A, Tayebwa J, Thwaites R, Paszkiewicz K, Aritua V, Kubiriba J, Smith J, Grant M, Studholme DJ (2012). Genome-wide sequencing reveals two major sub-lineages in the genetically monomorphic pathogen Xanthomonas campestris pathovar musacearum. Genes, 3(3), 361-377. Abstract.
Mazzaglia A, Studholme DJ, Taratufolo MC, Cai R, Almeida NF, Goodman T, Guttman DS, Vinatzer BA, Balestra GM (2012). Pseudomonas syringae pv. actinidiae (PSA) isolates from recent bacterial canker of kiwifruit outbreaks belong to the same genetic lineage. PLoS One, 7(5). Abstract.  Author URL.
Punta M, Coggill PC, Eberhardt RY, Mistry J, Tate J, Boursnell C, Pang N, Forslund K, Ceric G, Clements J, et al (2012). The Pfam protein families database. NUCLEIC ACIDS RESEARCH, 40(D1), D290-D301.  Author URL.
Studholme DJ, Glover RH, Boonham N (2011). Application of high-throughput DNA sequencing in phytopathology. Annu Rev Phytopathol, 49, 87-105. Abstract.  Author URL.
Studholme DJ (2011). Application of high-throughput genome sequencing to intrapathovar variation in Pseudomonas syringae. Mol Plant Pathol, 12(8), 829-838. Abstract.  Author URL.
Studholme DJ, 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. Abstract.
Kemen E, Gardiner A, Schultz-Larsen T, Kemen AC, Balmuth AL, Robert-Seilaniantz A, Bailey K, Holub E, Studholme DJ, Maclean D, et al (2011). Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol, 9(7). Abstract.  Author URL.
Fabro G, Steinbrenner J, Coates M, Ishaque N, Baxter L, Studholme DJ, Körner E, Allen RL, Piquerez SJM, Rougon-Cardoso A, et al (2011). Multiple candidate effectors from the oomycete pathogen Hyaloperonospora arabidopsidis suppress host plant immunity. PLoS Pathog, 7(11). Abstract.  Author URL.
Cai R, Lewis J, Yan S, Liu H, Clarke CR, Campanile F, Almeida NF, Studholme DJ, Lindeberg M, Schneider D, et al (2011). The plant pathogen Pseudomonas syringae pv. tomato is genetically monomorphic and under strong selection to evade tomato immunity. PLoS Pathog, 7(8). Abstract.  Author URL.
MacLean D, Studholme DJ (2010). A Boolean model of the Pseudomonas syringae hrp regulon predicts a tightly regulated system. PLoS One, 5(2). Abstract.  Author URL.
Green S, Studholme DJ, Laue BE, Dorati F, Lovell H, Arnold D, Cottrell JE, Bridgett S, Blaxter M, Huitema E, et al (2010). Comparative genome analysis provides insights into the evolution and adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum. PLoS One, 5(4). Abstract.  Author URL.
Paszkiewicz K, Studholme DJ (2010). De novo assembly of short sequence reads. Brief Bioinform, 11(5), 457-472. Abstract.  Author URL.
MacLean D, Elina N, Havecker ER, Heimstaedt SB, Studholme DJ, Baulcombe DC (2010). Evidence for large complex networks of plant short silencing RNAs. PLoS One, 5(3). Abstract.  Author URL.
MacLean D, Moulton V, Studholme DJ (2010). Finding sRNA generative locales from high-throughput sequencing data with NiBLS. BMC Bioinformatics, 11 Abstract.  Author URL.
Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RHY, Zody MC, Kunjeti SG, Donofrio NM, et al (2010). Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science (New York, N.Y.), 330(6010), 1540-1543. Abstract.
Studholme DJ, Kemen E, MacLean D, Schornack S, Aritua V, Thwaites R, Grant M, Smith J, Jones JDG (2010). Genome-wide sequencing data reveals virulence factors implicated in banana Xanthomonas wilt. FEMS Microbiol Lett, 310(2), 182-192. Abstract.  Author URL.
Nemri A, Atwell S, Tarone AM, Huang YS, Zhao K, Studholme DJ, Nordborg M, Jones JDG (2010). Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping. Proc Natl Acad Sci U S A, 107(22), 10302-10307. Abstract.  Author URL.
Clarke CR, Cai R, Studholme DJ, Guttman DS, Vinatzer BA (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. Mol Plant Microbe Interact, 23(2), 198-210. Abstract.  Author URL.
Studholme DJ, Ibanez SG, MacLean D, Dangl JL, Chang JH, Rathjen JP (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 Abstract.  Author URL.
Almeida NF, Yan S, Lindeberg M, Studholme DJ, Schneider DJ, Condon B, Liu H, Viana CJ, Warren A, Evans C, et al (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. Mol Plant Microbe Interact, 22(1), 52-62. Abstract.  Author URL.
MacLean D, Jones JDG, Studholme DJ (2009). Application of 'next-generation' sequencing technologies to microbial genetics. NATURE REVIEWS MICROBIOLOGY, 7(4), 287-296.  Author URL.
MacLean D, Jones JDG, Studholme DJ (2009). Application of 'next-generation' sequencing technologies to microbial genetics. Nat Rev Microbiol, 7(4), 287-296. Abstract.  Author URL.
Studholme DJ, Gimenez Ibanez S, Maclean D, Dangl JL, Chang JH, Rathjen JP (2009). Correction: 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), 569-569. Abstract.
Farrer RA, Kemen E, Jones JDG, Studholme DJ (2009). De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads. FEMS Microbiol Lett, 291(1), 103-111. Abstract.  Author URL.
Haas BJ, Kamoun S, Zody MC, Jiang RHY, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, et al (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262), 393-398. Abstract.  Author URL.
Setubal JC, dos Santos P, Goldman BS, Ertesvåg H, Espin G, Rubio LM, Valla S, Almeida NF, Balasubramanian D, Cromes L, et al (2009). Genome sequence of Azotobacter vinelandii, an obligate aerobe specialized to support diverse anaerobic metabolic processes. J Bacteriol, 191(14), 4534-4545. Abstract.  Author URL.
Jones AME, MacLean D, Studholme DJ, Serna-Sanz A, Andreasson E, Rathjen JP, Peck SC (2009). Phosphoproteomic analysis of nuclei-enriched fractions from Arabidopsis thaliana. J Proteomics, 72(3), 439-451. Abstract.  Author URL.
Mosher RA, Melnyk CW, Kelly KA, Dunn RM, Studholme DJ, Baulcombe DC (2009). Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis. Nature, 460(7252), 283-286. Abstract.  Author URL.
Moxon S, Schwach F, Dalmay T, Maclean D, Studholme DJ, Moulton V (2008). A toolkit for analysing large-scale plant small RNA datasets. Bioinformatics, 24(19), 2252-2253. Abstract.  Author URL.
Thompson AH, Studholme DJ, Green EM, Leak DJ (2008). Heterologous expression of pyruvate decarboxylase in Geobacillus thermoglucosidasius. Biotechnol Lett, 30(8), 1359-1365. Abstract.  Author URL.
MacLean D, Burrell MA, Studholme DJ, Jones AM (2008). PhosCalc: a tool for evaluating the sites of peptide phosphorylation from mass spectrometer data. BMC Res Notes, 1 Abstract.  Author URL.
Mosher RA, Schwach F, Studholme D, Baulcombe DC (2008). PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc Natl Acad Sci U S A, 105(8), 3145-3150. Abstract.  Author URL.
Bagnall A, Moxon S, Studholme D, Moulton V (2008). Time series data mining algorithms for identifying short RNA in Arabidopsis thaliana. Proceedings of the 2008 International Conference on Bioinformatics and Computational Biology, BIOCOMP 2008, 182-188. Abstract.
Kamal N, Dorrell N, Jagannathan A, Turner SM, Constantinidou C, Studholme DJ, Marsden G, Hinds J, Laing KG, Wren BW, et al (2007). Deletion of a previously uncharacterized flagellar-hook-length control gene fliK modulates the sigma54-dependent regulon in Campylobacter jejuni. Microbiology (Reading), 153(Pt 9), 3099-3111. Abstract.  Author URL.
Jones J, Studholme DJ, Knight CG, Preston GM (2007). Integrated bioinformatic and phenotypic analysis of RpoN-dependent traits in the plant growth-promoting bacterium Pseudomonas fluorescens SBW25. Environ Microbiol, 9(12), 3046-3064. Abstract.  Author URL.
Nemri A, Neff MM, Burrell M, Jones JDG, Studholme DJ (2007). Marker development for the genetic study of natural variation in Arabidopsis thaliana. Bioinformatics, 23(22), 3108-3109. Abstract.  Author URL.
Maor R, Jones A, Nühse TS, Studholme DJ, Peck SC, Shirasu K (2007). Multidimensional protein identification technology (MudPIT) analysis of ubiquitinated proteins in plants. Mol Cell Proteomics, 6(4), 601-610. Abstract.  Author URL.
Hernandez-Pinzon I, Yelina NE, Schwach F, Studholme DJ, 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. Plant J, 50(1), 140-148. Abstract.  Author URL.
Molnár A, Schwach F, Studholme DJ, Thuenemann EC, Baulcombe DC (2007). miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature, 447(7148), 1126-1129. Abstract.  Author URL.
He Q-Y, Liu X-H, Li Q, Studholme DJ, Li X-W, Liang S-P (2006). G8: a novel domain associated with polycystic kidney disease and non-syndromic hearing loss. Bioinformatics, 22(18), 2189-2191. Abstract.  Author URL.
Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bork P, Bucher P, Cerutti L, et al (2005). InterPro, progress and status in 2005. Nucleic Acids Res, 33(Database issue), D201-D205. Abstract.  Author URL.
Fleck SC, Andreasson E, Merkouropolous G, Nuehse TS, Serna-Sanz A, Studholme D (2005). Phosphoproteomics in <i>Arabidopsis</i> from databases to signalling networks. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY, 141(3), S250-S250.  Author URL.
Preston GM, Studholme DJ, Caldelari I (2005). Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiology Reviews, 29(2), 331-360.
Preston GM, Studholme DJ, Caldelari I (2005). Profiling the secretomes of plant pathogenic Proteobacteria. FEMS Microbiol Rev, 29(2), 331-360. Abstract.  Author URL.
Studholme DJ, Downie JA, Preston GM (2005). Protein domains and architectural innovation in plant-associated Proteobacteria. BMC Genomics, 6 Abstract.  Author URL.
Guo JH, Huang Q, Studholme DJ, Wu CQ, Zhao Z (2005). Transcriptomic analyses support the similarity of gene expression between brain and testis in human as well as mouse. Cytogenet Genome Res, 111(2), 107-109. Abstract.  Author URL.
Studholme DJ, Bentley SD, Kormanec J (2004). Bioinformatic identification of novel regulatory DNA sequence motifs in Streptomyces coelicolor. BMC Microbiol, 4 Abstract.  Author URL.
Tucker NP, D'Autréaux B, Studholme DJ, Spiro S, Dixon R (2004). DNA binding activity of the Escherichia coli nitric oxide sensor NorR suggests a conserved target sequence in diverse proteobacteria. J Bacteriol, 186(19), 6656-6660. Abstract.  Author URL.
Studholme DJ, Dixon R (2004). In silico analysis of the sigma54-dependent enhancer-binding proteins in Pirellula species strain 1. FEMS Microbiol Lett, 230(2), 215-225. Abstract.  Author URL.
Guo J, Chen S, Huang C, Chen L, Studholme DJ, Zhao S, Yu L (2004). MANSC: a seven-cysteine-containing domain present in animal membrane and extracellular proteins. Trends Biochem Sci, 29(4), 172-174.  Author URL.
Liu XH, He QY, Studholme DJ, Wu Q, Liang SP, Yu L (2004). NCD3G: a novel nine-cysteine domain in family 3 GPCRs (vol 19, pg 458, 2004). TRENDS IN BIOCHEMICAL SCIENCES, 29(11), 571-571.  Author URL.
Studholme DJ, Fuerst JA, Bateman A (2004). Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica. FEMS Microbiology Letters, 236(2), 333-340.
Studholme DJ, Fuerst JA, Bateman A (2004). Novel protein domains and motifs in the marine planctomycete Rhodopirellula baltica. FEMS Microbiol Lett, 236(2), 333-340. Abstract.  Author URL.
Scorpio DG, Caspersen K, Ogata H, Park J, Dumler JS (2004). Restricted changes in major surface protein-2 (<i>msp2</i>) transcription after prolonged in vitro passage of <i>Anaplasma phagocytophilum</i> -: art. no. 1. BMC MICROBIOLOGY, 4  Author URL.
Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer ELL, et al (2004). The Pfam protein families database. Nucleic Acids Res, 32(Database issue), D138-D141. Abstract.  Author URL.
Studholme DJ, Pau RN (2003). A DNA element recognised by the molybdenum-responsive transcription factor ModE is conserved in Proteobacteria, green sulphur bacteria and Archaea. BMC Microbiol, 3 Abstract.  Author URL.
Studholme DJ, Rawlings ND, Barrett AJ, Bateman A (2003). A comparison of Pfam and MEROPS: two databases, one comprehensive, and one specialised. BMC Bioinformatics, 4 Abstract.  Author URL.
Yost CK, Clark KT, Del Bel KL, Hynes MF (2003). Characterization of the nodulation plasmid encoded chemoreceptor gene <i>mcpG</i> from <i>Rhizobium leguminosarum</i> -: art. no. 1. BMC MICROBIOLOGY, 3  Author URL.
Studholme DJ, Dixon R (2003). Domain architectures of sigma54-dependent transcriptional activators. J Bacteriol, 185(6), 1757-1767.  Author URL.
Studholme DJ (2002). Enhancer-dependent transcription in Salmonella enterica Typhimurium: new members of the sigmaN regulon inferred from protein sequence homology and predicted promoter sites. J Mol Microbiol Biotechnol, 4(4), 367-374. Abstract.  Author URL.
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. J Mol Biol, 320(1), 23-37. Abstract.  Author URL.
Studholme DJ, Wigneshwereraraj SR, Gallegos MT, Buck M (2000). Functionality of purified sigma(N) (sigma(54)) and a NifA-like protein from the hyperthermophile Aquifex aeolicus. J Bacteriol, 182(6), 1616-1623. Abstract.  Author URL.
Studholme DJ, Buck M, Nixon T (2000). Identification of potential sigma(N)-dependent promoters in bacterial genomes. Microbiology (Reading), 146 Pt 12, 3021-3023.  Author URL.
Studholme DJ, Buck M (2000). Novel roles of sigmaN in small genomes. Microbiology (Reading), 146 ( Pt 1), 4-5.  Author URL.
Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer ELL (2000). The Pfam protein families database. NUCLEIC ACIDS RESEARCH, 28(1), 263-266.  Author URL.
Studholme DJ, Buck M (2000). The alternative sigma factor sigma(28) of the extreme thermophile Aquifex aeolicus restores motility to an Escherichia coli fliA mutant. FEMS Microbiol Lett, 191(1), 103-107. Abstract.  Author URL.
Studholme DJ, Buck M (2000). The alternative sigma factor σ<sup>28</sup>of the extreme thermophile<i>Aquifex aeolicus</i>restores motility to an<i>Escherichia coli fliA</i>mutant. FEMS Microbiology Letters, 191(1), 103-107.
Buck M, Gallegos MT, Studholme DJ, Guo Y, Gralla JD (2000). The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J Bacteriol, 182(15), 4129-4136.  Author URL.
Studholme DJ, Buck M (2000). The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. FEMS Microbiology Letters, 186(1), 1-9.
Studholme DJ, Buck M (2000). The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. FEMS Microbiol Lett, 186(1), 1-9. Abstract.  Author URL.
Studholme DJ, Jackson RA, Leak DJ (1999). Phylogenetic analysis of transformable strains of thermophilic Bacillus species. FEMS Microbiol Lett, 172(1), 85-90. Abstract.  Author URL.
Studholme DJ, Jackson RA, Leak DJ (1999). Phylogenetic analysis of transformable strains of thermophilic<i>Bacillus</i>species. FEMS Microbiology Letters, 172(1), 85-90.
Studholme DJ, Finn RD, Chaney MK, Buck M (1999). The C-terminal 12 amino acids of sigma(N) are required for structure and function. Arch Biochem Biophys, 371(2), 234-240. Abstract.  Author URL.

Chapters

Venkatesan L, Muzemil S, Fiche F, Grant M, Studholme DJ (2022). Genome Resources for Ensete ventricosum (Enset) and Related Species. In  (Ed) Underutilised Crop Genomes, Springer Nature, 355-371.
Paszkiewicz K, Studholme DJ (2012). High-throughput sequencing data analysis software: Current state and future developments. In  (Ed) Bioinformatics for High Throughput Sequencing, 231-248. Abstract.
Paszkiewicz K, Studholme DJ (2011). High-Throughput Sequencing Data Analysis Software: Current State and Future Developments. In  (Ed) Bioinformatics for High Throughput Sequencing, Springer New York, 231-248.
MacLean D, Studholme DJ (2009). Bioinformatics Aspects of High-Throughput Sequencing Technology. In Jackson RW (Ed) Plant Pathogenic Bacteria: Genomics and Molecular Biology, Caister Academic Press.
. Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bradley P, Bordoli L, Studholme DJ, Wu CH, et al (2004). InterPro -prediction of protein families, domains and functional sites. In Williams CR (Ed) Focus on Genome Research, New York: Nova Science Publishers Inc. 169-204.

Conferences

Stulberg MJ, Kasiborski B, Studholme D, Munkvold GP, Block CC, Arias S, Rascoe J, Nakhla MK (2017). Genomics-informed molecular detection of <i>Xanthomonas vasicola</i> causing bacterial leaf streak of corn in the United States.  Author URL.
Samac D, Studholme DJ, Ao S (2014). Characterization of the bacterial stem blight pathogen of alfalfa, <i>Pseudomonas syringae</i> pv. <i>syringae</i> ALF3.  Author URL.

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External Engagement and Impact

Administrative responsibilities


Committee/panel activities


Editorial responsibilities


External Examiner Positions

  • 2010. External examiner for a PhD thesis for the University of Cambridge (Cahill).
  • 2012. External examiner for a PhD thesis for the University of Birmingham (Loman).
  • 2012. External examiner for a PhD thesis for the University of Warwick .
  • 2012. External examiner for a PhD thesis for the University of East Anglia (Mohorianu).
  • 2013-2014. External examiner for MSc in Computational Biology at the University of East Anglia.
  • 2014. External examiner for a PhD thesis for the University of York.
  • 2015. External examiner for a PhD thesis for Anna University, Chennai.
  • 2016. External examiner for a PhD thesis for the University of Warwick.
  • 2016. External examiner for a PhD thesis for the University of Mauritius (Baichoo).
  • 2017. External examiner for a PhD thesis for the Universidad Politécnica de Madrid (Marconi).
  • 2020. External examiner of a PhD thesis for the University of Dundee (McLeod).
  • 2020. External examiner of a PhD thesis for the National University of Ireland, Galway.
  • 2020.  External examiner of a PhD thesis for University of Pretoria (Zim).
  • 2020.  External examiner of a PhD thesis for Maynooth University (McGowan).
  • 2021. External examiner of a PhD thesis at University College Dublin (Ajaz).
  • 2021. External examiner of a PhD thesis for the Swedish University of Agricultural Sciences  (Persson).
  • 2022. External examiner of PhD thesis for the University of East Anglia (Alzahrani).

Invited lectures


Media Coverage

SARS-CoV-2 genomics

Metabolite markers of resistance to ash dieback

Genomics of tree diseases

  • Television interview on BBC 1 South West on 12th April 2013.
  • Radio interview on BBC Cornwall on 12th April 2013.

E. coli outbreak

Bleeding canker disease of horse chestnuts


Major awards, Prizes and Honorary degrees, including election to national and international learned societies


Workshops/Conferences organised

  • 7th September 2016. Co-chaired session "Dynamic evolution and adaption of fungi" at Focused Meeting is being jointly hosted by the Microbiology Society and the British Mycological Society entitled "The dynamic fungus".
  • 2018. Member of Scientific Committee: 6th Xanthomonas Genomics Conference 2018.

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Teaching

  • BIO2092 Genomics and Introductory Bioinformatics. I am the module coordinator and deliver much of the teaching on this new module.
  • BIOM567 Application of Genomics to Infectious Disease. I am the module coordinator and deliver much of the teaching on this new module.
  • Responsible for delivering and assessing the bioinformatics course within the SWBIO doctoral training program (sometimes known as BIOM502).
  • Run a "specialist topic" in genomics and infectious disease as part of BIOM528.
  • Deliver a two-hour workshop on BIOM563 Crop Security.
  • Act as an Academic Tutor for a number of undergraduate students in Biological Sciences.
  • Supervise several undergraduate and MSc research projects each year.
  • As a Deputy Director of Post-Gradudate Research, I am involved in recruitment and assessment of PhD and MbyRes students.
  • Previously the Programme Director for the MSc courses in Bioinformatics and Medical Informatics. I previously contributed to several other modules including BIO3092 and BIO3080.

Modules

2023/24


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Supervision / Group

Postgraduate researchers

  • James Harrison Jamie uses computational comparative genomics methods to study recent evolution in bacterial pathogens. His PhD studentship is funded by the BBSRC.
  • Georgina Karamura Gina's project is titled Developing a lateral flow device specific to Xanthomonas campestris species and other related species (Banana Xanthomonas Wilt).
  • Dr Christine Sambles Christine is a bioinformatician working on the genomes and transcriptomes of the ash dieback pathogen.

Alumni

  • Thomas Laver Tom worked on the application of second-generation sequencing technologies to applications in biological and environmental metrology. His PhD studentship is funded by a BBSRC CASE award in partnership with LGC. After his PhD, he moved to the University of
  • Paul O&#39;Neil Paul worked on comparative genomics of Phytophthora ramorum, the fungus-like pathogen responsible for disease outbreaks on larch and other important trees in the UK. HE subsequently moved into the Exeter Sequencing DNA Service.
  • John Bosco Tayebwa John Bosco was sponsored by NARO of Uganda during 2010-11 to work on bioinformatic analysis of complete genome sequences of bacteria causing disease on the East African banana crop. He then pursued an MSc in Bioinformatics at the University of Skovde.
  • Arthur Wasukira Arthur was sponsored by NARO in 2010-11 to work on molecular basis of pathogenesis in the phytopathogenic bacteria infecting banana. He is now continuing his research at Makerere University in Uganda.

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Office Hours:

University of Exeter students, please email me to make an appointment at a mutually convenient time. During term time, I will normally respond by the end of the next full working day and offer a meeting during the following seven days.

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