An atlas of mouse development

We contributed preliminary analyses to the publication (Diez-Roux et al, 2011) of the freely accessible Eurexpress digital transcriptome atlas (http://www.eurexpress.org), of the E14.5 mouse embryo. Over 15,000 genes were annotated for hundreds of anatomical structures and regions, down to (almost) cellular level, allowing the identification of tissue-specific and tissue-overlapping gene networks. We illustrated the value of the Eurexpress atlas by finding novel coexpressed clusters of genes active in particular structures such as the developing eye.

Network inference from high throughput expression data

Suzuki et al (2009) examine the genome-wide dynamics of promoter usage in a human leukemia cell line, using high throughput sequencing of RNA over a time course of growth arrest and differentiation. Many key transcription regulators and their target genes were identified and validated by systematic siRNA knockdown. The results emphasise the enormous and daunting complexity of networks maintaining cellular states.

Opinionated

Myself and Martin Taylor (2009) are invited to write an opinion piece for Science on recent discoveries in chromatin structure and genomic sequence evolution.

Loops matter

Michlewski et al (2008) show that many miRNA loop regions have been well conserved during vertebrate evolution, and have unanticipated roles in miRNA processing and regulation.

Promoter evolution across mammals

Taylor et al (2006) perform the largest study to date of evolutionary rates in mammalian promoters, allowing detailed comparisons between different promoter classes for the first time. This is also the first demonstration of the unusually accelerated sequence evolution within primate promoters.