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.
Whipworm genome and dual-species transcriptome analyses provide molecular insights into an intimate host-parasite interaction.
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.
Nucleic acids research 2014;42;11;7113-31
The zebrafish reference genome sequence and its relationship to the human genome.
The genomes of four tapeworm species reveal adaptations to parasitism.
A large palindrome with interchromosomal gene duplications in the pericentromeric region of the D. melanogaster Y chromosome.
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.
Nucleic acids research 2009;37;7;2264-73
The DNA sequence and biological annotation of human chromosome 1.
The DNA sequence of the human X chromosome.
The DNA sequence and comparative analysis of human chromosome 10.
DNA sequence and analysis of human chromosome 9.
The DNA sequence and analysis of human chromosome 13.
The DNA sequence and analysis of human chromosome 6.
The DNA sequence and comparative analysis of human chromosome 20.