Lecturer in Bioinformatics, Queen Mary University London
bioinformatics, idiot-proof software, reproducible research, social insects, ants, evolutionary genomics, emerging model organisms,
I am interested in taking advatange of modern technologies - such as the recent 10,000-fold drop in DNA sequencing costs - and applying them to the study of ant societies. Doing this includes the development of generic bioinformatics tools.
My group has two main research streams. The first focuses on developing computational tools for dealing with modern biological data - which is exploding thanks to a 10,000-fold drop in DNA sequencing costs since 2007! We try to use development and deployment tools and approaches as well as user experience principles commonly used in tech startups. Taking advantage of lessons they have learnt allows us to create useful biological software with great user experiences and robust easily maintained code. Examples of this include SequenceServer which aims to make it easy for biologists to use the bioinformatics tool BLAST, the antgenomes.org repository for genetic data about ants, the NESCent Google Summer of Code project GeneValidator that helps biologists identify problematic gene predictions, and a BBSRC-funded platform to crowd-source the correction of problematic gene predictions.
Our second research approach uses the new tools to study ant societies. Indeed, extensive theoretical work has explained how and why complex societies evolve. However, only little is known about the genes and molecular mechanisms responsible for social phenotypes. Taking advantage of the sudden drop in DNA sequencing costs & innovative bioinformatics approaches, we have been identifying genes and mechanisms involved in the evolution of insect societies using genomics. In particular we recently sequenced the fire ant genome (PNAS 2011) and discovered that a fundamental social trait in this species (how many queens are accepted in the colony) is determined by variants of a social chromosome