Paper on linking GWAS SNPs with target genes with Promoter Capture Hi-C is out!

This paper, published in today’s issue of Cell, presents a high-resolution analysis of interactions involving nearly all annotated promoters in 17 human primary blood cell types. Integrating promoter interaction maps with chromatin and population genetics data, we link enhancers and promoters, and disease-associated variants with their putative target genes. The paper is the result of a large multi-centre collaboration of Peter Fraser’s and our labs at Babraham Institute with fantastic colleagues and friends from other Cambridge centres. It’s been a hugely productive and exciting collaboration, which will hopefully continue beyond this project.

Paper (open access): http://www.cell.com/cell/fulltext/S0092-8674(16)31322-8.
A minireview presenting this paper in the same issue of Cell: http://www.cell.com/cell/fulltext/S0092-8674(16)31519-7 (Open Access).
Press release: http://www.babraham.ac.uk/news/2016/11/researchers-identify-missing-links-that-connect-human-dna-variation-with-disease

Paula is moving to the LMB

We are saying goodbye to the first brave person who joined Mikhail’s group when it was starting from scratch. Paula is moving several miles up the road to MRC LMB – to work on establishing a core bioinformatics service there. We are very sorry Paula is leaving us, but congratulate her on securing a job at such a fantastic place.

Group retreat – science at the Eagle and Laser Tag

This year’s group retreat started with science brainstorming at the famous Eagle pub (which, bizarrely, opens for business at 8am). We then went over to Letchworth for an hour of laser tag! Turns out shooting at your colleagues is a lot of fun – especially when they don’t feel anything (unlike in paintball or in the more extreme version of laser tag involving electric shocks)…

The paper presenting CHiCAGO is published

The CHiCAGO paper led by Jonathan and Paula is finally out: http://www.genomebiology.com/2016/17/1/127. We released the manuscript as a preprint first, and it was already widely read and cited in this capacity. However, it’s still great to see our story formally published!

Hashem’s paper is out!

Hashem’s collaborative work with Anne Corcoran’s group on the cis-regulatory logic of V(D)J recombination has just been published!

Congratulations to Hashem and everyone at the Corcoran lab, particularly Daniel Bolland who led this work jointly with Hashem!

This has been a productive and enjoyable collaboration, which now continues to address exciting follow-up questions.

CHiCAGO is part of Bioconductor 3.3 release

The Chicago and PCHiCdata R packages are now part of the new Bioconductor release (3.3).

Their stable versions are now available here:

http://bioconductor.org/packages/release/bioc/html/Chicago.html
http://bioconductor.org/packages/release/data/experiment/html/PCHiCdata.html

The chicagoTools scripts are not part of Bioconductor and will continue to be available from our Bitbucket repository:

https://bitbucket.org/chicagoTeam/chicago

As Bioconductor releases only happen twice a year, the Bitbucket repository will also continue to host the most recent versions of the R packages.

Lina starts her rotation in the lab

We welcome Lina Dobnikar from the Cambridge BBSRC DTP PhD programme for her rotation project in the lab. Lina will be using single-cell RNA-seq data analyses to characterise the vascular smooth muscle cell niche.

CHiCAGO paper preprint is out on bioRxiv

The promised “next few weeks” since CHiCAGO release have passed, and the paper preprint describing this software is finally out on bioRxiv.

Feedback welcome!

Michiel joins the group

Michiel Thiecke is joining the group as an MRC-funded PhD student. Michiel has a Masters degree in bioinformatics and an impressive number of research internships all over the world under his belt. Welcome!

Science and bubble football

Our group retreat this year featured science discussions… and bubble football!

Both were a great success, despite the few bruises (from football!) and the pouring rain (which is why it was impossible to take pictures at the pitch). The match has ended in a draw – as a true testament of our team spirit!