We have released Chicdiff, an R package for differential analysis of Capture Hi-C data. Joint work by the power team: Jonathan (now at AstraZeneca), William (now back at Cambridge) and Valeriya. The package is available on github, and the preprint describing it is on bioRxiv. If you work with Capture Hi-C data, please try it out and let us know what you think!
Archive for Uncategorized
Our study of vascular smooth muscle cell heterogeneity using single-cell transcriptomics and lineage tracing is finally out! Co-led by our group’s Lina Dobnikar and Annabel Taylor fro Helle Jørgensen’s lab at Cambridge University.
Vascular smooth muscle cells (VSMCs) from are interesting for at least two reasons: (1) they originate from at least two different embryonic layers, depending on location and (2) in response to inflammation or injury, they lose their muscle cell phenotype and turn into migrating, proliferating fibroblast-like ‘synthetic’ cells.
We found that VSMCs homogeneously bear the footprints of their embryonic origins, but are heterogeneous with respect to other expressed genes. In particular, we found a rare VSMC subpopulation in healthy vessels that express a transcriptional signature (including progenitor marker Sca1) that is prevalent in vascular disease and potentially defines cells in the process of switching to the synthetic state.
Notably, Helle previously showed that only a small proportion of VSMCs expand in response to injury, so being able to catch cells ‘in the act’ of switching may help to understand ‘what makes them tick’.
Link to paper: https://www.nature.com/articles/s41467-018-06891-x.
Link to press release: https://www.babraham.ac.uk/news/2018/11/observation-of-blood-vessel-cells-changes-could-lead-to-early-detection-of-blocked-arteries.
An exciting postdoctoral position is available in our group at MRC LMS / ICS.
Please see the job posting at Jobs.ac.uk for more details.
Look forward to receiving your application!
From 1st of July, we are moving to MRC LMS in West London (part of Imperial College Institute of Molecular Sciences) to become Functional Gene Control group. We will continue to operate from both locations for the time being, although the expectation is that our presence at Babraham Institute will be gradually withering out.
The move opens an exciting new chapter in our group’s life and we are looking forward to fostering new links within MRC LMS, Imperial College and the broader London scientific ecosphere. Nonetheless, we will continue to draw on our close collaborations with many Babraham and Cambridge researchers, which will still be within reach and equally valuable!
Jo, our lab’s first PhD student, has successfully passed her PhD viva at Cambridge University – a great achievement for her and quite a milestone for our lab!
A collaborative public science project between Babraham Institute scientists, electronic musician Max Cooper and video artist Andy Lomas that was initiated by Mikhail has made it to Science Museum Lates yesterday!
The centrepiece of our exhibit, “Chromos”, was a virtual reality walkthrough the 3D structure of chromosomes based on 3D models of interphase chromatin generated from single-cell Hi-C data. The project also featured a music video based on the same data and a presentation about the science behind this work.
Molecular dynamics simulations by Csilla Varnái (Peter Fraser’s group) using single-cell Hi-C data from Takashi Nagano were used for both the video and the VR. The science presentation was put together by Stefan Schoenfelder, Csilla and Mikhail. Special thanks go to Babraham Institute’s public engagement team (and particularly Tacita Croucher) who managed and funded this project, and Babraham scientists Valeriya Malysheva, Zahra Fahmi, Daisy Luff and Rafeah Alam who volunteered at the event!
Jonathan has moved on to become a Senior Research Statistician at AstraZeneca. We wish him best of luck with his new job and wave him goodbye with a CHiCAGO-inspired jigsaw puzzle as a leaving present…
Hashem has left us to start his own group at Oxford University’s Radcliffe Department of Medicine. We are sad to see Hashem go, but are very proud of his success and wish him all the best in his independent career!
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!
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!