Professor Mark Blaxter (FRSE, FSBiol)

Director, Edinburgh Genomics


1978-1981    BSc (Honours Zoology), University of Edinburgh

1982-1987    PhD, London School of Hygiene and Tropical Medicine

1987-1990    MRC Postdoctoral Researcher, Imperial College, London

1990-1995    Wellcome Trust Research Fellow, Imperial College, London

1995-1996    Wellcome Trust Research Fellow, University of Edinburgh

1996-2001    Lecturer, University of Edinburgh

2001-2004    Reader, University of Edinburgh

2004-present    Professor of Evolutionary Genomics, University of Edinburgh

Responsibilities & affiliations

Member, Scientific Advisory Board, European Nucleotide Archive, and European Delegate to the International Sequence Database Archive Scientific Advisory Board

Member, Scientific Advisory Board of the EBI Metagenomics program.

Director, Edinburgh Node of the NERC Biomolecular Analysis Facility

Undergraduate teaching

Genomes and Genomics (third year)

Field Zoology (third year)

Zoology (honours)

Evolutionary Biology (honours)  

Postgraduate teaching

Bioinformatics (MSc)

Open to PhD supervision enquiries?


Current PhD students supervised

Lewis Stevens  The genomics of the genus Caenorhabditis

Past PhD students supervised

Student's Name    Funder    Title    Start Date    End Date    # papers    # 1st author

Dr Daphne Gerrits    EU    Tyrosinases and cuticle synthesis in Caenorhabditis elegans    1994    1997    0    0

Dr Mark Dorris    NERC    Mode and tempo in the evolution of nematodes    1996    2001    6    3

Dr David Guiliano    various    Analysis of the genome of the filarial nematode Brugia malayi    1997    2002    21    4

Dr Aziz Aboobaker    WT    HOX genes from nematodes and RNAi in Brugia malayi    1999    2004    9    6

Dr Robin Floyd    NERC    Molecular assessment of soil nematode diversity    1999    2002    3    1

Dr Katelyn Fenn    WT    A molecular study of the interactions between the parasitic nematode Brugia malayi and its endosymbiont Wolbachia    2001    2005    6    5

Dr Alasdair Anthony    NERC    A genomic study of the nuclear matrix attachment region recognition signature    2002    2007    2    1

Dr James Wasmuth    BBSRC CASE (Astra Zeneca)    Computational analysis of proteomes from parasitic nematodes    2002    2006    7    3

Dr Martin Jones    BBSRC    Multigene datasets for deep phylogeny    2004    2007    5    3

Dr Jenna Mann    DEFRA    DNA barcodes and meiofaunal identification    2006    2010    2    0

Dr Benjamin Elsworth    BBSRC    Unearthing the genome of the earthworm Lumbricus rubellus    2009    2012    3    1

Dr Sujai Kumar    SBS ORS    Next generation nematode genomes    2009    2012    13    6

Dr Rebekah Watt    NERC    The Transcriptomic Basis of Post-Mating Responses in Females of the Parasitic Wasp Nasonia vitripennis    2009    2012    2    0

Dr Graham Thomas    WT    The role of metabolism in alternative macrophage activation in vivo    2009    2013    2    1

Dr Jack Hearn    NERC    Transcriptomics of gall inducing cynipid wasps    2009    2013    3    2

Dr Georgios Koutsovoulos    BBSRC/SBS    Phylogenomics of Nematoda    2010    2013    13    3

Dr Dominik Laetsch    SBS/JHI    The secretome of plant parasitic nematodes    2013    2017    6    4

Research summary

I am interested in the structure and evolution of animal genomes, with a particular focus on the genomes of non-model organisms. In my group, we use high-throughput sequencing technologies to generate genome sequence data for many species (including nematodes, tardigrades, arthropods, fungi and bacteria), and analyse these with a variety of bioinformatics tools (including many we have written in house). In particular we are interested in the evolution of operons and trans-splicing in nematodes, the responses of soil invertebrates such as earthworms to heavy metals and pollutants, the origins of gene novelty, the deep phylogeny of animals and the evolution of development in the moulting animals such as tardigrades. We are also developing DNA barcoding techniques to identify meiofauna and other hard-to-identify taxa. We have collaborations with a wide range of colleagues round the world working on beautiful small invertebrates and their evolution.

Mark Blaxter founded and is Director of Genome Science of Edinburgh Genomics ( the University's advanced genomics facility.

Current research interests

Genome assembly. Genome evolution. The origins of parasitism in Nematoda. The symbiosis between Wolbachia bacteria and nematode hosts. The genomics of the genus Caenorhabditis.

Current project grants

BBSRC BBR "BlobToolKit" https//
This project is building a toolkit for the analysis of genome assemblies, with a particular focus on identification of potential contamination. It is a collaboration with the European Nucleotide Archive (co-I Guy Cochrane). Dr Richard Challis, the postdoc on the grant, is developing this exciting software toolkit.
BBSRC BBR "GenomeHubs"
This software development project is expanding our GenomeHubs genome databasing project, in particular integrating our BlobToolKit and KinFin software. We are collaborating widely to build and maintain genome databases for research communities, based on GenomeHubs. Dr Richard Challis is the lead software developer on GenomeHubs.
The NERC Biomolecular Analysis Facility is a NERC Services and Facilities project that supports the breadth of ecological, environmental and evolutionary science. In collaboration with colleagues in Sheffield and Liverpool we provide cutting edge genomics, functional genomics and bioinformatics support to researchers across the UK. NBAF Edinburgh is based within Edinburgh Genomics.

Past project grants

Source Reference Title amount £ UoE PI start end
BBSRC BBR BB/K020161/1 Lepbase: Building a genome analytic resource for the lepidopteran community 671,655 Blaxter Aug-13 Jul-17
BBSRC NORNEX: Ash Dieback 162,746 Blaxter Apr-13 Mar-16
BBSRC BB/J018791/1 Genetic basis of reproductive and plumage polymorphism in the ruff 176,281 Blaxter Nov-12 Oct-15
NERC NE/J011355/1 The evolutionary genomics of sexual recombination 422,671 Blaxter Sep-12 Aug-15
BBSRC / SCPRID BB/J011703/1 Resistance and virulence in the cereal-Striga interaction 28,200 Blaxter Jul-12 Jun-15
BBSRC BB/I023585/1 NextGenPartiGene: next generation transcriptome assembly, annotation and exploitation toolkit 151158 Blaxter Sep-11 Mar-13
BBSRC BB/G00661X/1 Genomic analysis of complex speciation in Heliconius 124,952 Blaxter Jan-11 Dec-14
DDJT/ NERC Fellowship support for Dr. Beate Nurnberger 80,547 Blaxter Sep-11 Aug-14
NERC NE/H019804/1 Development of optimal wet-lab and bioinformatics protocols for RAD 338845 Blaxter Nov-10 Jun-12
BBSRC BB/H023844/1 Developing RAD markers as a resource for plant breeding 88514 Blaxter Oct-10 May-12
EU SICA 242131 Enhanced protective Immunity Against Filariasis 115000 Taylor Sep-10 Aug-13
BBSRC BB/H014357/1 Investigating the role of a kinesin gene in butterfly mimicry 213994 Blaxter Sep-10 Oct-14
BBSRC BB/F021135/1 Unwinding snail chirality by a massive subtractive linkage analysis (MSLA) 164843 Blaxter Sep-08 Mar-12
Wellcome Trust 087418/Z/08/Z Macrophage transcriptome and systems responses to nematode infection 169000 Blaxter Sep-08 Aug-12

View all 291 publications on Research Explorer