Other current projects

Bdelloid rotifer genomics

Bdelloid rotifers are microscopic animals that reproduce asexually and are able to survive dessication. As such, their genomes contain unique adaptations, some of which are the focus of this project.
A project in collaboration with Alan Tunnacliffe.
Genomics of coral reefs

We are sequencing the dinoflagellate (Symbiodinium) and the host Stylophora genomes, in order to study symbiotic interactions of coral reefs, as well as host-parasite dynamics.
Synthetic biology

We are developing a data warehouse for the exploitation of standard genetic parts from a range of organisms. We also co-organise the Cambridge iGEM competition team and a Cambridge synthetic biology forum.
Toxoplasma: parasitic subversion of host function

Infection by Toxoplasma are a cause of morbidity and mortality worldwide. This project, in collaboration with Jim Ajioka in Pathology and Arnab Pain at KAUST, focuses on the genomics and proteomics of Toxoplasma infection, and the changes it brings about in the host, with a focus on potential therapy targets.

Past projects

Data integration

We have created and continue to develop the data warehouse system InterMine, as well as a number of databases that use the system, including FlyMine for the Drosophila community, modMine for modENCODE project data, and metabolicMine for human, rat and mouse metabolic disease data. We are currently in the process of developing HumanMine for a wide range of human genetic data.

In collaboration with a number of major model organism databases, we lead the InterMOD consortium – an initiative to implement InterMine databases for budding yeast, nematode worm, rat, mouse, zebrafish and fruit fly, as well as creating cross-organism analysis tools to enable users to benefit from their diverse datasets.

More information on the InterMine system is available at http://www.intermine.org. For links to the known public InterMine databases, see our Resources page.

Selected publications

InterMine: a flexible data warehouse system for the integration and analysis of heterogeneous biological data	2012	Bioinformatics	Smith RN, Aleksic J, Butano D, Carr A, ..., Micklem G
modMine: flexible access to modENCODE data	2012	Nucleic Acids Research	Contrino S, Smith RN, Butano D, Carr A, ..., Micklem G
FlyMine: an integrated database for Drosophila and Anopheles genomics	2007	Genome Biology	Lyne R, Smith R, Rutherford K, Wakeling M, ..., Micklem G

Micklem Lab

University of Cambridge

Projects

Data integration

Selected publications