Our invited paper “Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools” is finally out at Nature Protocols (after 3 months in typesetting)!
Led by Paula (one of the lead authors of the original Chicago), Helen and Lera (postdocs in the lab), with invaluable contributions from other present and former lab members and collaborators.
For context, see also this Q&A on our institute’s website.
Vanessa and Joe are leaving the lab to continue their studies. We are sorry that they are leaving and wish them all the best for their next steps. In the meantime, Namrata (another student in Joe’s masters course) is stepping in to continue the work started by Joe.
Joe Ellaway has joined the lab for his (fully remote) MSc project in bioinformatics. He will be working on the computational prediction of enhancer-promoter contacts capitalising on existing models and Capture Hi-C data. Welcome Joe – sorry we don’t have a chance to meet you offline!
The results of a large collaborative effort to understand the epigenetic effects of Covid infection on lung cells and propose a repurposed treatment have been published in Cell. A press release presenting the key findings of the study is available here.
Congratulations Helen, Valeriya from the lab and Michiel from Enhanc3D Genomics!
In collaboration with Enhanc3D Genomics Ltd, we have linked non-coding GWAS SNPs associated with COVID-19 susceptibility and severity with their putative target gene based on 3D chromosomal conformation in blood cells.
For this analysis, we have used the COGS approach and Promoter Capture Hi-C data from our earlier study (Javierre et al., Cell 2016). The GWAS data are coming from the COVID-19 Host Genetics Initiative that we have joined for this task.
Our data are currently available at https://osf.io/k2mxe/ and will evolve with the next releases of the GWAS meta-analysis dataset. Our results will also be posted on the www.covid19hg.org website in due course.
Pavel is starting his PhD with us, and Vanessa will be with us for her 3rd year BSc placement. Welcome Vanessa and Pavel!
A few people in our lab – including Helen, Valeriya and Emma, helped by Michiel who is now employed by our spinout company – have joined forces to help out in Covid-related research.
An article about Helen’s contribution has been posted on MRC LMS website.
Michiel’s paper on the effects of architectural protein depletion on promoter interactions is out in Cell Reports. It has been a stimulating collaboration with great people from IMP Vienna and Babraham Institute. Thanks also to Cell Reports for accommodating our inability to do wet lab experiments during revision!
A news article about this paper intended for a broad audience has been posted on MRC LMS website.
Jo Mitchelmore’s paper presenting her PhD work with us is finally out in Nucleic Acids Research:
Congratulations Jo and thanks Chris Wallace and Stasia Grinberg for invaluable help!
Monica’s and Mikhail’s News&Views article on two silencer papers is out in Nature Genetics. It was a very timely commission as a few relevant papers have been out recently elsewhere too!