Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026This story took time to come to fruition, as we've encountered challenges along the way, from commercial and logistical to scientific (we were in uncharted territory with CLN3!). The power and determination of our collaborative team is what ultimately brought it over the line. 040
Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026www.nature.com/articles/s41...nature.comHigh-resolution promoter interaction analysis implicates genes involved in activation of type 3 innate lymphoid cells in immune disease risk - Nature GeneticsHigh-resolution mapping of promoter-anchored chromosomal contacts in type 3 innate lymphoid cells (ILC3s), coupled with GWAS effector gene prioritization and functional studies, identifies ILC3-linked... 150
Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026The paper was borne out of a close collaboration between our former team members Valeriya Malysheva, Helen Ray-Jones and Pavel Artemov with Chris Wallace in Cambridge, Nora Lakes, Tareian Cazares, Emily Miraldi, Stephen Waggoner, Rachel Brown and Eugene Oltz in the US, and many others. 120
Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026Our paper also presents methods that make this analysis possible: multiCOGS, a multivariate extension of our COGS gene prioritisation pipeline, and ABCC, Capture Hi-C-adapted ABC. While we used our low-input Capture Hi-C earlier, this work really showcases its power with rare cell types. 140
Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026Surprisingly, one of the genes we prioritised for Crohn's disease was CLN3, a mysterious lysosomal gene that causes the neurodegenerative Batten disease. We show that CLN3 overexpression, but not knockout, in an ILC3-like cell line affects cytokine secretion and inflammatory gene expression. 130
Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026We then used these 3D maps to reveal ILC3 regulatory architecture and link immune GWAS variants to target genes implicating this cell type. We show that many prioritised genes have a role in ILC3 inflammatory function. 120
Mikhail Spivakov @mspivakov.bsky.social · 04/08/2026Very happy to see this story finally out (link in comments)! We used low-input Capture Hi-C to profile promoter-anchored chromosomal interactions in Type 3 innate lymphoid cells (ILC3s) - rare tissue-resident lymphocytes that lack antigen receptors and regulate barrier immunity. 1198
Mikhail Spivakov @mspivakov.bsky.social · 27/07/2026This is a great perspective! However, while the authors call for "AI-first" perturbational experimental designs, an equally important conclusion from their overview, to me, is that we need a stronger mechanistic understanding of gene regulation and new ways to incorporate it into AI/ML frameworks. 030
Reposted by Mikhail SpivakovMRC Laboratory of Medical Sciences @mrc-lms.bsky.social · 08/06/2026A new study tracks how cells prepare gene regulatory decisions that will define their fate during the earliest stages of human development and highlights how the genome’s 3D structure helps shape cell identity and could offer clues to how developmental disorders arise 🧬lms.mrc.ac.uk3D genome architecture pre-wires early developmental decisionsNew research tracks how cells prepare gene regulatory decisions that will define their fate during the earliest stages of human development. The study reconstructs a timeline of chromosome folding tha... 021
Mikhail Spivakov @mspivakov.bsky.social · 08/06/2026Led by Marina Nocente and initiated by Monica Della Rosa in the lab, this has been a great collaboration with Maria Rostovskaya and Peter Rugg-Gunn's team at Babraham. 000
Mikhail Spivakov @mspivakov.bsky.social · 08/06/2026In human pluripotent stem cells, many enhancers, which will become active later in development, are already marked with poised (bivalent) chromatin features and form chromosomal contacts with gene promoters. This story adds to our understanding of when, how and why this happens. 100
Mikhail Spivakov @mspivakov.bsky.social · 08/06/2026Our story about the poising and connectivity of human developmental enhancers is out! www.cell.com/cell-reports... 1197
Mikhail Spivakov @mspivakov.bsky.social · 29/04/2026I agree. I can see only a very limited number of scenarios in which it is useful and/or helps catch errors/data manipulation. Sharing detailed analysis pipelines and raw data is so much more important for reproducibility. 041
Mikhail Spivakov @mspivakov.bsky.social · 11/03/2026A very important editorial: Don’t deprioritize curiosity-driven research www.nature.com/articles/d41...nature.comDon’t deprioritize curiosity-driven researchAround the world, governments are demanding that research funding follow broader political priorities. They should be careful what they wish for. 0145
Mikhail Spivakov @mspivakov.bsky.social · 11/03/2026Have just seen a social media post from a Nobel Prize winner about how they are actually not afraid of their core grant renewal interview. I don't even know from what side to start unpacking this as an insight into the sociology of science... 010
Mikhail Spivakov @mspivakov.bsky.social · 02/03/2026Happy to have contributed to this exciting study! 040
Mikhail Spivakov @mspivakov.bsky.social · 25/11/2025I'm guest-editing a collection on "Enhancer-promoter interactions" at Genome Biology. Please send us your exciting stories! link.springer.com/collections/...link.springer.comEnhancer-promoter interactionsGenome Biology is calling for submissions to our Collection on enhancer-promoter interactions. Enhancer–promoter interactions are central to the regulation ... 04732
Mikhail Spivakov @mspivakov.bsky.social · 17/11/2025Voice isn't enough either. I'm going to watch the voting record closely... 010
Mikhail Spivakov @mspivakov.bsky.social · 17/11/2025Thank you, my local Labour MP @stellacreasy.bsky.social for a bit of common sense. www.theguardian.com/commentisfre...theguardian.comICE-style raids on Britain's streets: that's all Labour's brutal asylum reforms will achieve | Stella CreasyIf we want to ‘stop the boats’, we need to stop the BS when it comes to what creates refugees, and how to respond to them, says Labour MP Stella Creasy 120
Mikhail Spivakov @mspivakov.bsky.social · 14/11/2025I elaborated on my proposal for a "grants commons" in an opinion piece for Times Higher Education. www.timeshighereducation.com/opinion/comm...timeshighereducation.comA common grant application database would cut the waste of resubmissionFinancial restrictions oblige funders to reject vast numbers of sound proposals. Why not retain them for other funders to consider, asks Mikhail Spivakov 060
Mikhail Spivakov @mspivakov.bsky.social · 08/11/2025Totally agree and had been proposing this for a while. Time to join forces and make this happen? 151
Reposted by Mikhail SpivakovHetan Shah @hetanshah.bsky.social · 21/10/2025The costs of the UK’s Global Talent Visa looks a trifle high in comparison to competitor countries - largely through the Immigration Health Surcharge (which critics say is a form of double taxation as they contribute to the NHS through normal tax on their earnings) 18297190
Mikhail Spivakov @mspivakov.bsky.social · 19/10/2025Our departing flight was once moved to a different airport in France, because at the small airport it was supposed to take off from, firefighters went home. 000
Mikhail Spivakov @mspivakov.bsky.social · 16/10/2025From a sample of over 10 papers (on most of which I'm either not an author or not a senior author), over a year-long revisions in our field are becoming common. Before we accept this as the norm, I suggest we consider the consequences & inequalities this creates, even in the era of preprints. 062
Mikhail Spivakov @mspivakov.bsky.social · 10/10/2025The PhD opportunities in our group and in many others at @mrc-lms.bsky.social are now open! lms.mrc.ac.uk/work-and-stu...lms.mrc.ac.ukStudentships and PhD trainingWe have two core PhD programmes - traditional and transdisciplinary. Our PhD students are registered with Imperial and are embedded in our dedicated research facility. 052
Mikhail Spivakov @mspivakov.bsky.social · 09/10/2025If you are interested in studying enhancers, enhancer-promoter communication and/or enhancer-based gene regulatory networks using multidisciplinary approaches, feel free to send an informal inquiry or watch the space on findAphd.com and lms.mrc.ac.uk, where the ads will go live soon! 000
Mikhail Spivakov @mspivakov.bsky.social · 09/10/2025A quick heads-up that we will have two PhD positions available to start in October 2026. One as part of MRC LMS PhD programme, and one as a transdisciplinary studentship with @srinjan.bsky.social and Thomas Ouldridge at Imperial. 111
Mikhail Spivakov @mspivakov.bsky.social · 03/10/2025A great collaboration between Marina Nocente and Monica Della Rosa in our lab, and human naive pluripotency experts Maria Rostovskaya and Peter Rugg-Gunn in Cambridge. 010
Mikhail Spivakov @mspivakov.bsky.social · 03/10/2025Many enhancers that drive tissue-specific gene expression are already connected to gene promoters in human pluripotent cells. In a new preprint, we share some clues about when, how, and why this happens! www.biorxiv.org/content/10.1...biorxiv.orgPoising and connectivity of emergent human developmental enhancers in the transition from naive to primed pluripotencyIn primed human pluripotent stem cells (hPSCs) resembling post-implantation epiblast, numerous lineage-specific enhancers assume the poised chromatin state, co-marked by H3K4me1 and Polycomb-associate... 15620
Mikhail Spivakov @mspivakov.bsky.social · 28/08/2025Hi Alexis, not sure if I'm on your list - would love to be added if not. Thanks! 100
Mikhail Spivakov @mspivakov.bsky.social · 14/08/2025...and a welcoming Ryanair check-in gate with no queue! 010
Mikhail Spivakov @mspivakov.bsky.social · 19/07/2025Translational research is digging for gold. Basic research is learning where and what to dig. The more funding is diverted to translation, the more we deplete the research ecosystem, driving the supplies of "gold" - immediately translatable findings and innovations - to unsustainably low levels. 37027
Mikhail Spivakov @mspivakov.bsky.social · 15/07/2025My colleagues at @mrc-lms.bsky.social are hiring (five postdoc positions in total!). 051
Mikhail Spivakov @mspivakov.bsky.social · 10/07/2025Congratulations to Will Scott and the team from @mrc-lms.bsky.social on this exciting study! 030
Mikhail Spivakov @mspivakov.bsky.social · 05/07/2025"We’re reaping the fruits of what happened economically 50 years ago, when... decisions began to prioritize efficiency and making as much money as possible over what was ethically correct." english.elpais.com/culture/2025...english.elpais.comPhilip Kitcher, philosopher: ‘Life is a human project, not God’s’The British thinker is an advocate of collective progress and laments our contemporary individualism. In an interview with EL PAÍS, he says that there is value in idealism, even when it is absurd 010
Mikhail Spivakov @mspivakov.bsky.social · 24/06/2025I have no doubt about that - but this in itself is commendable :) 010
Mikhail Spivakov @mspivakov.bsky.social · 24/06/2025Wow. Saying this as someone trained in classical piano... 100
Mikhail Spivakov @mspivakov.bsky.social · 02/06/2025www.theguardian.com/commentisfre... This is all a painful deja vu from 2007. And it's important to remember that despite all the suffering and literal lives lost (www.independent.co.uk/news/uk/this...) Labour had lost hopelessly then to the party whose policies it tried to mimic.theguardian.comI got British citizenship via the five-year route. Labour’s new 10-year rule will cause untold pain | Nesrine MalikStarmer claims to want integration. Yet denying people safety, belonging and the right to vote for a decade amounts to the exact opposite, says Guardian columnist Nesrine Malik 000
Mikhail Spivakov @mspivakov.bsky.social · 02/06/2025AI models go dumb when fed their own output. But as we are increasingly reading AI-generated text and looking at AI-generated images, how about us? www.nature.com/articles/s41...nature.comAI models collapse when trained on recursively generated data - Nature Analysis shows that indiscriminately training generative artificial intelligence on real and generated content, usually done by scraping data from the Internet, can lead to a collapse in th... 010
Mikhail Spivakov @mspivakov.bsky.social · 18/05/2025Hi @Maria, sorry I missed your poster and didn't meet you at the meeting. Which is a shame because I could also then ask for feedback on our project :) 010
Mikhail Spivakov @mspivakov.bsky.social · 14/05/2025The two JRs can be found here and may be useful for people who consider campaigning against the proposed changes via either the lobbying or judicial route: www.casemine.com/judgement/uk... www.casemine.com/judgement/uk... 100