Alan Tracey | Senior Computer Biologist

Tracey, Alan

My main focus is the improvement of helminth genome assemblies, drawing together various sequence, mapping and synteny data. Much of my work involves careful inspection of assembly data in Gap5, and working with scientists and bioinformaticians to develop algorithms to solve complex assembly issues. This approach produces world-class reference quality assemblies.

I am currently working on improving the genome assemblies of Haemonchus contortus and Schistosoma mansoni. Here the challenge has been to merge new PacBio data with existing mature assemblies and optical mapping data to produce greatly improved hybrid assemblies. In addition to genome assembly improvement I am also actively engaged in improving the structural and functional annotation of gene models currently focusing on S. mansoni.

Publications

  • Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.

    Foth BJ, Tsai IJ, Reid AJ, Bancroft AJ, Nichol S et al.

    Nature genetics 2014;46;7;693-700

  • The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction.

    Jackson AP, Otto TD, Darby A, Ramaprasad A, Xia D et al.

    Nucleic acids research 2014;42;11;7113-31

  • The zebrafish reference genome sequence and its relationship to the human genome.

    Howe K, Clark MD, Torroja CF, Torrance J, Berthelot C et al.

    Nature 2013;496;7446;498-503

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

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

    Nature 2013;496;7443;57-63

  • A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.

    Méndez-Lago M, Bergman CM, de Pablos B, Tracey A, Whitehead SL and Villasante A

    Molecular biology and evolution 2011;28;7;1967-71

  • Novel sequencing strategy for repetitive DNA in a Drosophila BAC clone reveals that the centromeric region of the Y chromosome evolved from a telomere.

    Méndez-Lago M, Wild J, Whitehead SL, Tracey A, de Pablos B et al.

    Nucleic acids research 2009;37;7;2264-73

  • The DNA sequence and biological annotation of human chromosome 1.

    Gregory SG, Barlow KF, McLay KE, Kaul R, Swarbreck D et al.

    Nature 2006;441;7091;315-21

  • The DNA sequence of the human X chromosome.

    Ross MT, Grafham DV, Coffey AJ, Scherer S, McLay K et al.

    Nature 2005;434;7031;325-37

  • The DNA sequence and comparative analysis of human chromosome 10.

    Deloukas P, Earthrowl ME, Grafham DV, Rubenfield M, French L et al.

    Nature 2004;429;6990;375-81

  • DNA sequence and analysis of human chromosome 9.

    Humphray SJ, Oliver K, Hunt AR, Plumb RW, Loveland JE et al.

    Nature 2004;429;6990;369-74

  • The DNA sequence and analysis of human chromosome 13.

    Dunham A, Matthews LH, Burton J, Ashurst JL, Howe KL et al.

    Nature 2004;428;6982;522-8

  • The DNA sequence and analysis of human chromosome 6.

    Mungall AJ, Palmer SA, Sims SK, Edwards CA, Ashurst JL et al.

    Nature 2003;425;6960;805-11

  • The DNA sequence and comparative analysis of human chromosome 20.

    Deloukas P, Matthews LH, Ashurst J, Burton J, Gilbert JG et al.

    Nature 2001;414;6866;865-71

Tracey, Alan