Martin Trick

BA (Cantab) 1979: Natural Sciences (Genetics)
MA, PhD (Cantab) 1983
Postdoc, Department of Genetics, University of Cambridge 1983-1986
Postdoc, Plant Breeding Institute 1986-1989
Project Leader, Brassica & Oilseeds Department, John Innes Centre 1989-2001
Strategic Research Scientist & Associate Head of Dept, Computational and Systems Biology, John Innes Centre 2001-present

Contact
Phone: +44 (0)1603 450557
E-mail: martin.trick@jic.ac.uk  

For a long time my interest was in the development of Computational Biology resources for research in comparative genomics at JIC, starting out with the Arabidopsis-Brassica model/crop system. Nowadays I'm engaged in developing methods for applying Illumina transcriptome sequencing for things like SNP discovery in polyploid crops such as oilseed rape and wheat. These methods were initially quite simple. MAQ was used to do the initial alignments of mRNA-seq reads against pseudoreference sequences comprising assembled and clustered ESTs. A complication is that MAQ doesn't really know about doubled haploid (or extensively selfed) polyploid genomes. In these situations, ambiguity codes called don't indicate allelic heterozygous positions, but rather the contribution of co-expressed homoeologous genes that differ in sequence. We have coined the term hemi-SNPs to describe these. Perl scripts were developed to recall SNPs using the indexed, plain text "pileup" files that MAQ can generate as a summary of its alignment maps. These basic methods are now being used for a variety of purposes, including genetic mapping, association genetics, digital transcriptomics and diversity/pedigree analysis. When I get the time I would like to port the meta-analysis scripts to the newer bwa alignment software and also perhaps investigate Bayesian methods to impute genotypes, rather than the simplistic rules that I've used so far. In addition, I also get to analyse a fair bit of genomic Illumina resequencing data in Arabidopsis, Brassica and wheat for mutation mapping and candidate gene identification.

GBrowse view of an example Brassica rapa BAC annotation. All 1,015 annotated BACs are available from here. A do-it-yourself (Lite) annotation pipeline is here!

BLAST searches of things Brassicaceous
          

A simple text search of BrassicaDB