Imperial College London


Faculty of MedicineDepartment of Metabolism, Digestion and Reproduction

Honorary Research Officer



+44 (0)20 7594 Website




126Sir Alexander Fleming BuildingSouth Kensington Campus





James Abbott is a member of the Bioinformatics Data Science Group, located with the Department of Surgery and Cancer. He obtained an honours degree in Biology with Biotechnology, before undertaking a PhD in plant molecular biology at the University of Dundee. James then worked as a Bioinformatics Specialist at Zeneca Agrochemicals/Syngenta for three years before joining the Bioinformatics Support Service when it was setup in 2002, and has remained with the service following it's transfer to the Department of Surgery and Cancer and subseqeunt renaming as the Bioinformatics Data Science Group.

James works primarily on topics involving genomes and sequencing, with specific interests inthe areas of next-generation sequencing technologies and de-novo assembly. He has contributed to numerous sequence-based projects including the Blumeria graminis sequencing project, the South Asian Genome, and the Tomato Genome Project, and has also developed in-house pipelines for bacterial genome assembly and analysis (BugBuilder), and whole-metagenome assembly (IMP).

James also maintains the services computational infrastructure, managing a range of Unix, Linux and WIndows systems and various storage resources totalling around 400Tb. James holds Red Hat Certified Technician and Red Hat Certified Engineer certifications

Selected Publications

Journal Articles

Florea M, Hagemann H, Santosa G, et al., 2016, Engineering control of bacterial cellulose production using a genetic toolkit and a new cellulose-producing strain, Proceedings of the National Academy of Sciences of the United States of America, Vol:113, ISSN:0027-8424, Pages:E3431-E3440

Chambers JC, Abbott J, Zhang W, et al., 2014, The South Asian Genome, PLOS One, Vol:9, ISSN:1932-6203

, 2012, The tomato genome sequence provides insights into fleshy fruit evolution, Nature, Vol:485, ISSN:1476-4687, Pages:635-641

Spanu PD, Abbott JC, Amselem J, et al., 2010, Genome expansion and gene loss in powdery mildew fungi reveal functional tradeoffs in extreme parasitism, Science, Vol:330, Pages:1543-1546

Abbott JC, Aanensen DM, Rutherford K, et al., 2005, WebACT - an online companion for the artemis comparison tool, Bioinformatics, Vol:21, ISSN:1367-4803, Pages:3665-3666

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