Emilia Dimitrova

Happy to share our new preprint! 📊

We benchmarked methods for locus-level transposable element quantification in short-read scRNA-seq, using both real datasets and simulations with read-level ground truth.

Huge thanks to @catavallejos.bsky.social and @antonio-scialdone.bsky.social!

#TEsky

Thank you! 😊

Help needed: I know this has been discussed before - what are people doing now that phase lock tubes have disappeared from the market? Is everyone making their own and that's why companies are not selling them anymore? If so, what is the best vaccum grease you would recommend? 🤷‍♀️

Very nice review by @mileshuseyin.bsky.social and colleagues!

Excited to share @suminkim.bsky.social and @mileshuseyin.bsky.social 's new Current Opinion review on how Polycomb complexes mediate 3D genome interactions including mechanistic models and potential roles in gene regulation:
www.sciencedirect.com/science/arti...

1/3 New bioRxiv preprint from the lab: “Minute-scale coupling of chromatin marks and transcriptional bursts”. Led by Xiohui Gao & Chaebeen Ko. bioRxiv : www.biorxiv.org/cgi/content/...

In less than an hour. Will be great!

Come to hear Alan's great new story on SET1/MLL proteins and transcription next Wednesday. @fnucleosome.bsky.social

Come to hear Alan's great new story on SET1/MLL proteins and transcription next Wednesday. @fnucleosome.bsky.social

This was a really fantastic read. Felt like the eras tour albums with one hit unfolding after another!

🧬🎉Join us on Dec 17th for our last session of 2025! 🎉🧬Two fantastic talks on transcriptional regulation:
🔬JB Lalanne on developmental enhancers (and starting a lab in 2025?)
🔬 @rberrens.bsky.social on transposable elements in development
📋Register here: us06web.zoom.us/webinar/regi...

Read Alan's thread below to find out more about the latest work from the Klose lab @au-ho-yu.bsky.social @robklose.bsky.social @aleksszczurek.bsky.social

Also @au-ho-yu.bsky.social probably holds the world record for the most degron-tagged proteins in the same line. Guess how many!

Excited to see the latest from the Klose lab out this morning! Our brilliant PhD student Alan, now Dr Au, has dissected how SET1/MLL complexes shape H3K4me3 and shows they regulate transcription independently of their cat activity. He teamed up with Aleks to explore how. A few surprises!

Reversibility, regulation, and the community of development: the legacy of Sir John B. Gurdon - Nature Communications Nature Communications - Reversibility, regulation, and the community of development: the legacy of Sir John B. Gurdon

We have just published a tribute to John Gurdon, reflecting on his scientific legacy and the profound influence he had on generations of developmental biologists.

The piece is available open access in Nature Communications:
www.nature.com/articles/s41...

Heterochromatin boundaries maintain centromere position, size and number - Nature Structural & Molecular Biology Carty et al. identify the H3K9 methyltransferases that restrict the size and position of the centromere protein A chromatin domain, maintaining functional centromeres.

Very proud to have our latest work now online in
@natsmb.nature.com. A wonderful team effort across the centromere community, across @jansenlab.bsky.social @naltemose.bsky.social @dfachinetti.bsky.social and Giunta labs. Happy reading! 1/4

www.nature.com/articles/s41...

1/8🧵 Excited to share two studies in which I was involved within the Bird Lab📄📄 We have explored how the transcription factor SALL4 assembles and shapes chromatin in embryonic stem cells.
@kashyapchhatbar.bsky.social @saragiuliani.bsky.social @drphcb-uoe.bsky.social @edinburghbiology.bsky.social

New method by Davies lab pushing the boundaries of the C-technologies, going down to a single base-pair resolution. Glad we could contribute to the story. Well done, Hangpeng and team!

Awesome stuff James and team! Thanks for giving @edimitrova.bsky.social and I the opportunity to contribute.

Chromatin profiling identifies putative dual roles for H3K27me3 in regulating cell type-specific genes and transposable elements in choanoflagellates Nature Communications - Here, the authors investigate chromatin-based gene regulation in the closest relative of animal, choanoflagellates. They uncover a putative dual role for the histone...

Very happy to see our paper published online natcomms.nature.com. Thank you to @wellcometrust.bsky.social for funding this work during my time with @robklose.bsky.social and David Booth! Thanks also to collaborators @garcialabms.bsky.social @alexdemendoza.bsky.social and the other authors!

Modelling transcription with explainable AI uncovers context-specific epigenetic gene regulation at promoters and gene bodies Author summary Genes are turned on or off through complex processes involving many proteins that interact with DNA wrapped histones and modify their structure. These changes, known as epigenetic modif...

🚀 Excited to share my latest paper on using SHAP, to predict direct target genes of chromatin-associated factors! Check it out for insights into gene regulation and the power of explainable AI in genomics! #XAI #SHAP #Genomics

doi.org/10.1371/jour...

Let's break down what we found! 👇

Check out our new story on how broad enhancer inputs are restricted into tissue-specific gene expression 🧬
Hint: Promoter-proximal regions are the key!

Enhancer-promoter compatibility is mediated by the promoter-proximal region Gene promoters induce transcription in response to distal enhancers. How enhancers specifically activate their target promoter while bypassing other promoters remains unclear. Here, we find that the p...

What is a promoter? And how does it work?

We very happy to share our latest work trying to understand enhancer-promoter compatibility.
I am very excited about the results of @blanka-majchrzycka.bsky.social, which changed the way I think about promoters

www.biorxiv.org/content/10.1...

Béla Novák (1956–2025) – a legacy of scientific discovery and personal charm In February 2025, we were shocked and deeply saddened to hear about the death of Béla Novák, Professor in Integrative Systems Biology at the University of Oxford, UK, and a beloved grandfather, father...

Many of you know, we lost Béla Novák this year. John Tyson, Francis Barr & I tried to capture his wonderful character & great mind so that those that didn't know him can see what a fantastic person he was.

Thanks to @jcellsci.bsky.social for publishing.

journals.biologists.com/jcs/article/...

Wonderful opportunity to work with Martin Howard and my group trying to understand how chromatin influences gene transcription and expression. Integration of theory, modelling, and experimentation. Come and join the team!
Please repost!

jobs.jic.ac.uk/Details.asp?...

If you are a computational biologist come, apply and join Howard & Klose lab in a joint Norwich-Oxford collaboration on chromatin dynamics!

Very exciting opportunity for those with a quantitative background and interested in epigenetics / gene regulation. Highly collaborative environment!

If you are a computational biologist interested in how chromatin states are established and maintained to regulate transcription, this is the dream job for you! This will be in close collaboration with the Klose lab in Oxford and we have a lot of cool projects you can get involved in. Apply!

On my way back from the Transcription and Chromatin UK meeting in Manchester. It was a great meeting with lots of cool science discussed! At dinner we were trying to guess where it will be next year - Edinburgh or Birmingham? 😀 @biochemsoc.bsky.social #BiochemEvent

DDIAS is a single-stranded DNA-binding effector of the TOPBP1-CIP2A complex in mitosis DNA double-strand breaks and unresolved DNA replication intermediates are particularly dangerous during mitosis. Paradoxically, cells inactivate canonical DNA repair mechanisms during chromosome segre...

Delighted to share our lab's first preprint identifying DDIAS as a mitotic DNA repair protein. Great collaboration with the @andrewblackford.bsky.social, @tcr-miller.bsky.social and @profstewartlab.bsky.social labs, and many more. Read the paper here: www.biorxiv.org/content/10.1...