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

Links

Research group links

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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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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'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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