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Two new preprints

Today sees the publication of not just one, but two preprints from our lab and our close collaborators.

The first preprint is work led by Jo Mitchelmore (our group’s first ever PhD student, now at Novartis), in which she has used changes in transcription factor binding affinity at promoter-connected regulatory regions as predictor variables to detect eQTLs. Using this method, she’s uncovered hundreds of novel associations – and a bunch of epromoters, regions that function both as distal enhancers and promoters of other genes. Great collaboration with Chris Wallace and her postdoc Stasiya Grinberg.

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Chicdiff is released!

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!

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Lina’s paper is out!

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:
Link to press release:

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Our group is moving to Imperial College London!

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 website will be updated and its name will change accordingly ( The previous URL,, will remain operational.

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!


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Our public science project makes it to London’s Science Museum Lates

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!


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