Pathogen Informatics | Infection Genomics

Pathogen Informatics | Infection Genomics

Pathogen Informatics

pathogen-infomatics-14.jpgSanger Institute, Genome Research Limited

Our Research and Approach

The Pathogen Informatics team develop and maintain software applications and systems to support the research activities of the pathogen group. We develop and maintain scalable and robust automated tools for sequence and annotation tracking and analysis and provide ad-hoc informatics support and training to the researchers in the pathogen group.


Keane, Jacqui
Dr Jacqueline A Keane
Group Leader

Jacqui Keane has a PhD in Software Engineering and joined the Pathogen group at the Wellcome Trust Sanger Institute as a postdoctoral fellow in 2008. In 2010, she took on the role of managing the Pathogen Informatics team whose main responsibilities are to develop sequence analysis pipelines and provide informatics support to the Infection Genomics programme.

Key Projects, Collaborations, Tools & Data

The pathogen informatics team develop and maintain a number of software applications:

Research Programmes

Partners and Funders

The team works with and provides informatics support to the following faculty teams:
Internal Partners


  • A Phylogenetic and Phenotypic Analysis of Salmonella enterica Serovar Weltevreden, an Emerging Agent of Diarrheal Disease in Tropical Regions.

    Makendi C, Page AJ, Wren BW, Le Thi Phuong T, Clare S et al.

    PLoS neglected tropical diseases 2016;10;2;e0004446

  • Kinetoplastid Phylogenomics Reveals the Evolutionary Innovations Associated with the Origins of Parasitism.

    Jackson AP, Otto TD, Aslett M, Armstrong SD, Bringaud F et al.

    Current biology : CB 2016;26;2;161-72

  • Circlator: automated circularization of genome assemblies using long sequencing reads.

    Hunt M, Silva ND, Otto TD, Parkhill J, Keane JA and Harris SR

    Genome biology 2015;16;294

  • Roary: rapid large-scale prokaryote pan genome analysis.

    Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al.

    Bioinformatics (Oxford, England) 2015;31;22;3691-3

  • IVA: accurate de novo assembly of RNA virus genomes.

    Hunt M, Gall A, Ong SH, Brener J, Ferns B et al.

    Bioinformatics (Oxford, England) 2015;31;14;2374-6

  • Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events.

    Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ et al.

    Nature genetics 2015;47;6;632-9

  • Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

    Croucher NJ, Page AJ, Connor TR, Delaney AJ, Keane JA et al.

    Nucleic acids research 2015;43;3;e15

  • Drug resistance in Salmonella enterica ser. Typhimurium bloodstream infection, Malawi.

    Feasey NA, Cain AK, Msefula CL, Pickard D, Alaerts M et al.

    Emerging infectious diseases 2014;20;11;1957-9

  • A comprehensive evaluation of rodent malaria parasite genomes and gene expression.

    Otto TD, Böhme U, Jackson AP, Hunt M, Franke-Fayard B et al.

    BMC biology 2014;12;86

  • Epithelial IL-22RA1-mediated fucosylation promotes intestinal colonization resistance to an opportunistic pathogen.

    Pham TA, Clare S, Goulding D, Arasteh JM, Stares MD et al.

    Cell host & microbe 2014;16;4;504-16

  • Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.

    Tsai IJ, Hunt M, Holroyd N, Huckvale T, Berriman M and Kikuchi T

    DNA research : an international journal for rapid publication of reports on genes and genomes 2014;21;3;243-54

  • Genome sequence of the tsetse fly (Glossina morsitans): vector of African trypanosomiasis.

    International Glossina Genome Initiative

    Science (New York, N.Y.) 2014;344;6182;380-6

  • A comprehensive evaluation of assembly scaffolding tools.

    Hunt M, Newbold C, Berriman M and Otto TD

    Genome biology 2014;15;3;R42

  • The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode.

    Cotton JA, Lilley CJ, Jones LM, Kikuchi T, Reid AJ et al.

    Genome biology 2014;15;3;R43

  • Dense genomic sampling identifies highways of pneumococcal recombination.

    Chewapreecha C, Harris SR, Croucher NJ, Turner C, Marttinen P et al.

    Nature genetics 2014;46;3;305-9

  • The genome and transcriptome of Haemonchus contortus, a key model parasite for drug and vaccine discovery.

    Laing R, Kikuchi T, Martinelli A, Tsai IJ, Beech RN et al.

    Genome biology 2013;14;8;R88

  • REAPR: a universal tool for genome assembly evaluation.

    Hunt M, Kikuchi T, Sanders M, Newbold C, Berriman M and Otto TD

    Genome biology 2013;14;5;R47

  • Characterization and comparative analysis of the complete Haemonchus contortus β-tubulin gene family and implications for benzimidazole resistance in strongylid nematodes.

    Saunders GI, Wasmuth JD, Beech R, Laing R, Hunt M et al.

    International journal for parasitology 2013;43;6;465-75

  • The genomes of four tapeworm species reveal adaptations to parasitism.

    Tsai IJ, Zarowiecki M, Holroyd N, Garciarrubio A, Sanchez-Flores A et al.

    Nature 2013;496;7443;57-63

  • BamView: visualizing and interpretation of next-generation sequencing read alignments.

    Carver T, Harris SR, Otto TD, Berriman M, Parkhill J and McQuillan JA

    Briefings in bioinformatics 2013;14;2;203-12

  • Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.

    Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M et al.

    GigaScience 2013;2;1;10

  • Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.

    Jackson AP, Berry A, Aslett M, Allison HC, Burton P et al.

    Proceedings of the National Academy of Sciences of the United States of America 2012;109;9;3416-21

  • Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data.

    Carver T, Harris SR, Berriman M, Parkhill J and McQuillan JA

    Bioinformatics (Oxford, England) 2012;28;4;464-9

  • A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.

    Protasio AV, Tsai IJ, Babbage A, Nichol S, Hunt M et al.

    PLoS neglected tropical diseases 2012;6;1;e1455

  • GeneDB--an annotation database for pathogens.

    Logan-Klumpler FJ, De Silva N, Boehme U, Rogers MB, Velarde G et al.

    Nucleic acids research 2012;40;Database issue;D98-108

  • Optimal enzymes for amplifying sequencing libraries.

    Quail MA, Otto TD, Gu Y, Harris SR, Skelly TF et al.

    Nature methods 2011;9;1;10-1

  • Genomic insights into the origin of parasitism in the emerging plant pathogen Bursaphelenchus xylophilus.

    Kikuchi T, Cotton JA, Dalzell JJ, Hasegawa K, Kanzaki N et al.

    PLoS pathogens 2011;7;9;e1002219

  • The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.

    Jackson AP, Sanders M, Berry A, McQuillan J, Aslett MA et al.

    PLoS neglected tropical diseases 2010;4;4;e658

  • Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans.

    Jackson AP, Gamble JA, Yeomans T, Moran GP, Saunders D et al.

    Genome research 2009;19;12;2231-44

  • Analysis of expressed sequence tags from the four main developmental stages of Trypanosoma congolense.

    Helm JR, Hertz-Fowler C, Aslett M, Berriman M, Sanders M et al.

    Molecular and biochemical parasitology 2009;168;1;34-42

  • The genome of the blood fluke Schistosoma mansoni.

    Berriman M, Haas BJ, LoVerde PT, Wilson RA, Dillon GP et al.

    Nature 2009;460;7253;352-8

  • Genomic-scale prioritization of drug targets: the TDR Targets database.

    Agüero F, Al-Lazikani B, Aslett M, Berriman M, Buckner FS et al.

    Nature reviews. Drug discovery 2008;7;11;900-7

  • The genome of the simian and human malaria parasite Plasmodium knowlesi.

    Pain A, Böhme U, Berry AE, Mungall K, Finn RD et al.

    Nature 2008;455;7214;799-803

  • Comparative genomic analysis of three Leishmania species that cause diverse human disease.

    Peacock CS, Seeger K, Harris D, Murphy L, Ruiz JC et al.

    Nature genetics 2007;39;7;839-47

  • Gene Ontology annotation status of the fission yeast genome: preliminary coverage approaches 100%.

    Aslett M and Wood V

    Yeast (Chichester, England) 2006;23;13;913-9

  • The genome of the African trypanosome Trypanosoma brucei.

    Berriman M, Ghedin E, Hertz-Fowler C, Blandin G, Renauld H et al.

    Science (New York, N.Y.) 2005;309;5733;416-22

  • Genome of the host-cell transforming parasite Theileria annulata compared with T. parva.

    Pain A, Renauld H, Berriman M, Murphy L, Yeats CA et al.

    Science (New York, N.Y.) 2005;309;5731;131-3

  • Integration of tools and resources for display and analysis of genomic data for protozoan parasites.

    Aslett M, Mooney P, Adlem E, Berriman M, Berry A et al.

    International journal for parasitology 2005;35;5;481-93

  • GeneDB: a resource for prokaryotic and eukaryotic organisms.

    Hertz-Fowler C, Peacock CS, Wood V, Aslett M, Kerhornou A et al.

    Nucleic acids research 2004;32;Database issue;D339-43

  • Parasites are GO.

    Berriman M, Aslett M, Hall N and Ivens A

    Trends in parasitology 2001;17;10;463-4

  • Parasite genome initiatives.

    Degrave WM, Melville S, Ivens A and Aslett M

    International journal for parasitology 2001;31;5-6;532-6

  • Kinetoplast DNA minicircle database.

    Brewster S, Aslett M and Barker DC

    Parasitology today (Personal ed.) 1998;14;11;437-8

  • TcruziDB, an integrated database, and the WWW information server for the Trypanosoma cruzi genome project.

    Degrave W, de Miranda AB, Amorim A, Brandão A, Aslett M and Vandeyar M

    Memórias do Instituto Oswaldo Cruz 1997;92;6;805-9