Paula’s paper on the dynamics of promoter interactions and chromatin states at promoter-interacting regions as human ES cells differentiate to neural progenitors is out in eLife! This has been a close and exciting collaboration with Peter Rugg-Gunn’s and Peter Fraser’s labs, and Stefan Schoenfelder from the Fraser lab is the co-lead author. Congratulations everyone!
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February saw two new group members join us.
Valeriya Malysheva, funded by a commercialisation grant from Babraham’s Knowlegde Exchange Committee, joins us after a PhD at IGBMC in Strasbourg and will work on optimising the experimental and bioinformatics sides of promoter capture Hi-C.
Pawel Bednarz will stay with us for 6 months on a visiting studentship from Poland and will work on the relationship between genetic variation and promoter interactions.
Welcome Valeriya and Pawel!
The team of Babraham PhD students Lina Dobnikar, Michiel Thiecke, Natasha Morgan and Rachael Huntley (the first two of them from our group!) has won the prestigious Biotechnology YES competition, pitching their startup proposal on a new chemical for fighting bee parasites to a panel of judges at the Royal Society in London. The proposal is currently fictional, but it is based on real science and Michiel’s practical knowledge of beekeeping, so who knows – perhaps the prize will inspire the winners to put their proposal into practice? Either way, huge congratulations!
Our recent paper on linking GWAS SNPs to target genes using Promoter Capture Hi-C has made the (local) news. Watch Chris Wallace and Mikhail explain 3D regulatory architecture to Cambridge TV’s Karen Thomas here.
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
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.
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 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!
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.
The Chicago and PCHiCdata R packages are now part of the new Bioconductor release (3.3).
Their stable versions are now available here:
The chicagoTools scripts are not part of Bioconductor and will continue to be available from our Bitbucket repository:
As Bioconductor releases only happen twice a year, the Bitbucket repository will also continue to host the most recent versions of the R packages.