Sequence algorithms and intra-species variation

Birney group figureThe association of Drosophila SNPs across a 20 kb genomic region with RNA expression levels of the FBgn0031191 gene contained in the region. The level of association is shown as –log10 of the P value on the Y-axis with genomic position on the X axis in the top panel. The genomic structure of the FBgn0031191 gene is shown in the bottom panel, with the direction of transcription from left to right. The most strongly associated SNPs in this case are clustered at the start of the gene, consistent with an effect through modification of promoter efficiency.

DNA sequence remains at the heart of molecular biology and bioinformatics. Dr Birney is joint Associate Director of EMBL-EBI and shares strategic oversight of bioinformatics services. He also has a modest research group, focused on sequence algorithms and using intra-species variation to explore elements of basic biology.

Dr Birney’s group has a long-standing interest in developing sequencing algorithms. Over the past four years a considerable focus has been on compression, with theoretical and now practical implementations of compression techniques. Dr Birney's "blue skies" research includes collaborating with Dr Nick Goldman on a method to store digital data in DNA molecules. The Birney group continues to be involved in this area as new opportunities arise - including the application of new sequencing technologies.

We are also interested in the interplay of natural DNA sequence variation with cellular assays and basic biology. Over the past five years there has been a tremendous increase in the use of genome-wide association to study human diseases. However, this approach is very general and need not be restricted to the human disease arena. Association analysis can be applied to nearly any measureable phenotype in a cellular or organismal system where an accessible, outbred population is available. We are pursuing association analysis for a number of both molecular (e.g. RNA expression levels and chromatin levels) and basic biology traits in a number of species where favourable populations are available including human, and Drosophila. In the future we hope to expand this to a variety of other basic biological phenotypes in other species, including establishing the first vertebrate near-isogenic wild panel in Japanese Rice Paddy fish (Medaka, Oryzias latipes).

Future plans

The Birney Research group will continue to work on sequence algorithms and intra species variation. In humans there will be work on molecular phenotypes in an iPSC panel generated as part of the HipSci consortium. In Drosophila we will look at multi-time point developmental biology measures; and we will assess the near isogenic panel in Japanese Rice Paddy fish.

Birney group news

Selected publications

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74, doi:10.1038/nature11247 (2012). 

Goldman, N., et al. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature, doi:10.1038/nature11875 (2013).

Spivakov, M., et al. Analysis of variation at transcription factor binding sites in Drosophila and humans. Genome biology 13, R49, doi:10.1186/gb-2012-13-9-r49 (2012).