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Rob Beagrie

@rbeagrie.bsky.social
817 followers 251 following 10 posts

Group leader and Wellcome Sir Henry Dale Fellow based at the Centre for Human Genetics at Oxford University. Interested in genomics, single-cell technologies, 3D DNA folding and chromatin disruption in human disease. He/him.

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Reposted by Rob Beagrie
Wendy Bickmore @wbickmor.bsky.social · 08/05/2026
Although cohesin-sensitive, long-range enhancer activation is equivalent in nature to proximal activation. Cooperativity can arise from different levels of activation inputs operating on a non-linear response function. @eliasfriman.bsky.social @uoe-igc.bsky.social www.biorxiv.org/content/10.6...
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Duncan Sproul @sproullab.bsky.social · 10/04/2026
Very pleased to say that the paper version of our study examining the role of de novo DNMTs in cancer-associated hypomethylation is now out in @plos.org Genetics 🎉: doi.org/10.1371/jour... You can read more on the previous thread but here is a summary of the main updates! #epigenetics 🧵 1/9
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Max Perutz Labs Vienna @maxperutzlabs.ac.at · 08/03/2026
One frame. Many voices. ✨ This International Women’s Day, our Women in Science series features group leader Christa Bücker 🙌 Today, @chribue.bsky.social shares an important perspective on finding role models and becoming one for the next generation 👩‍🔬 @univie.ac.at @meduniwien.ac.at
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Jeremy Van Cleve @vancleve.theoretical.bio · 03/03/2026
This is a common reply to concerns about GenAI research as if it were just another computational tool that saves us times from tedious tasks and whose accuracy can be rigorously quantified. It is not. GenAI research poses at least 2 serious problems... /n
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Rob Beagrie @rbeagrie.bsky.social · 19/02/2026
New preprint from @anadopico.bsky.social (who I have had the great pleasure of supervising with Tom Milne) and our fantastic collaborators in the @davieslab.bsky.social www.biorxiv.org/content/10.6... #genomics #GeneRegulation #chromatin
A pictographic model of chromatin folding in the nucleus. DNA wrapped around nucleosomes aggregates into nanoscale domains, whilst newly nucleosome depleted DNA that forms after acute degradation of FACT projects from these domains and engages in long-range interactions that can span TAD boundaries
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Ben Sabari @bsabari.bsky.social · 06/02/2026
I am excited to share a new review @cp-molcell.bsky.social written in collaboration with @tanjamittag.bsky.social , Mikayla Eppert, and Ambuja Navalkar where we review the current evidence for and against the role of density transitions in regulating transcription www.cell.com/molecular-ce...
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Miguel Branco @brancolab.bsky.social · 02/02/2026
New preprint from the lab! We dig into the regulatory roles of TEs in the mouse placenta, with some surprising findings. Led by the awesome @smamante.bsky.social. Particular kudos to him for navigating the many twists and turns of the project.
biorxiv.org
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Christa Buecker @chribue.bsky.social · 27/11/2025
This is probably my favorite paper of 2025. Beautiful work by @elphegenoralab.bsky.social and @karissalhansen.bsky.social that should be on the top of the reading list for everyone with even a slight interest in gene expression!
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Jessica Reid 🌈 @j-reid.bsky.social · 26/11/2025
“It is not acceptable to recruit a variety of students into the laboratory, subject them to a variety of stress tests and abuses, and then keep the students who thrive under abuse and get rid of the students who aren't able to thrive in the lab. That's straight-up exploitation.” 👏👏👏
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Aga Gambus @agagambus.bsky.social · 22/11/2025
Last few days to apply for this PhD project in our lab. Mix of biochemistry and structural biology, DNA replication and ubiquitin signalling. Get in touch if interested. Full application through official university portal. Deadline on 27th of November!
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James Davies @jojdavies.bsky.social · 05/11/2025
Our latest paper has just been published in Cell! doi.org/10.1016/j.ce... We developed a new method called MCC ultra, which allows 3D chromatin structure to be visualised with a 1 base pair pixel size.
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Jase Gehring @skyjase.bsky.social · 21/09/2025
don't release preprints without a Methods section don't release preprints with a Supplementary Materials section don't release preprints without data don't release preprints without code use preprint servers to share your science, not advertisements
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Johannes Stein @jmstein.bsky.social · 13/08/2025
(1/n) DNA-PAINT imaging inside the nucleus at single antibody resolution using TIRF? Ultrathin sectioning makes it happen! Grateful to share my postdoctoral work introducing “tomographic & kinetically-enhanced DNA-PAINT” or in brief: tkPAINT. Out in @pnas.org! doi.org/10.1073/pnas... 👇🧵
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Bluma Lesch @ambystoma22.bsky.social · 20/08/2025
New paper on the role of H3K4me3 at enhancers! We (led by Haoming Yu) used dCas9 epigenome editing to add H3K4me3 to intergenic enhancers. This was (1) sufficient to turn up transcription at open, active regions and (2) has no effect on target gene transcription. genesdev.cshlp.org/content/earl...
genesdev.cshlp.org
H3K4me3 amplifies transcription at intergenic active regulatory elements
A biweekly scientific journal publishing high-quality research in molecular biology and genetics, cancer biology, biochemistry, and related fields
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Guillaume Andrey @guandrey.bsky.social · 09/07/2025
Our work bridging enhancer-promoter proximity to phenotypic outcomes in vivo is out! Shout out to @olimpiabompadre.bsky.social, to Marie Kmita's lab, and to all the co-authors. www.nature.com/articles/s41...
nature.com
Liebenberg syndrome severity arises from variations in Pitx1 locus topology and proportion of ectopically transcribing cells - Nature Communications
Here the authors show that reducing enhancer-promoter distance at the Pitx1 locus increases proportion of Pitx1 forelimb expressing cells, worsening skeletal defects in Liebenberg syndrome. They also ...
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Evgeny Kvon @evgenykvon.bsky.social · 02/07/2025
Our paper describing the Range Extender element which is required and sufficient for long-range enhancer activation at the Shh locus is now available at @nature.com. Congrats to @gracebower.bsky.social who led the study. Below is a brief summary of the main findings www.nature.com/articles/s41... 1/
nature.com
Range extender mediates long-distance enhancer activity - Nature
The REX element is associated with long-range enhancer–promoter interactions.
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Maxim Greenberg @maxvcg.bsky.social · 06/06/2025
This is the type of transgender mouse research that would get its money stripped away in the US... (jk jk) www.nature.com/articles/s41...
nature.com
Maternal iron deficiency causes male-to-female sex reversal in mouse embryos - Nature
Iron-deficient conditions in pregnant mice can cause XY mouse embryos to develop female rather than male genitalia, revealing that iron metabolism has a role in determining male sex in mice.
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Molecular Systems Biology @molsystbiol.org · 15/05/2025
Extensive differences observed in 3D genome structure between homologous heterozygous chromosomes revealed by Genome Architecture Mapping #GAM in the @apombo1.bsky.social lab ➡️ www.embopress.org/doi/full/10....
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franmartinezgr.bsky.social @franmartinezgr.bsky.social · 16/04/2025
Systematic identification of disease-causing promoter and untranslated region variants in 8040 undiagnosed individuals with rare disease #RareDisease #Genetics genomemedicine.biomedcentral.com/articles/10....
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Jordan Meier @doc-jlmeier.bsky.social · 30/03/2025
My favorite science is the kind that makes you says, "Man, I wish I thought of that!" This is such a paper. Mass action turns an eraser into a pen. HDACs are metabolite-dependent histone acyltransferases. @dremilygoldberg.bsky.social @gburslem.bsky.social www.nature.com/articles/s41...
nature.com
Reversible histone deacetylase activity catalyzes lysine acylation - Nature Chemical Biology
Tsusaka et al. discover that histone deacetylases, which are well known to remove protein modifications, such as lysine acetylation and β-hydroxybutyrylation, can also reverse their chemical activity ...
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Jeff Spence @jeffspence.github.io · 28/03/2025
A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes. While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6) www.biorxiv.org/content/10.1...
biorxiv.org
Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations
Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...
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Rob Beagrie @rbeagrie.bsky.social · 27/03/2025
Delighted to have been able to help out with this project - congratulations Ali and the rest of the @drakesmith-lab.bsky.social - such a fascinating #genetics and #GeneRegulation story 🧪
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Connor Rogerson @doctorconnor.bsky.social · 26/03/2025
This is going to be such a disaster. Cis-women will be outed as trans for genetics they had no idea about. What then?
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Yvette Cendes @whereisyvette.bsky.social · 16/03/2025
Pet peeve: I hate how often ppl claim “all the researchers will just move to Europe/Canada!” You vastly under-estimate how little money there is there vs the USA- and unless that changes ASAP this loss is just going to decimate global science, full stop. 🧪🔭
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Michael Erard @michaelerard.bsky.social · 15/03/2025
I wrote up some thoughts on the idea of recruiting embattled American scientists to Europe. My main point: it would work best to keep the talent pipeline going, but not to salvage individual careers, especially mature ones. The barriers are many. michaelerard.com/blog/a-few-t...
michaelerard.com
Michael Erard
would it work to recruit American scientists to Europe?
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Nicky Whiffin @nickywhiffin.bsky.social · 02/03/2025
A few weeks ago, I had an incredibly emotional call with James Coney, a writer for the Sunday Times whose son Charlie was in the @genomicsengland.bsky.social 100k project and was recently diagnosed with ReNU syndrome. This beautiful article tells their story ❤️ www.thetimes.com/article/0bcc...
thetimes.com
My son Charlie — and the breakthrough that changed our lives
James Coney and his wife, Sarah, struggled not knowing why their 12-year-old was born with a severe learning disability. In their darkest moments, they blamed themselves. Then, out of the blue, came a...
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Pedro Rocha @pedroprocha.bsky.social · 26/02/2025
Here is the peer-reviewed version of our study showing how some TAD borders are essential for gene regulation and development. Loss of a single CTCF motif is sufficient to cause embryonic lethality. www.sciencedirect.com/science/arti...
sciencedirect.com
Deletion of a single CTCF motif at the boundary of a chromatin domain with three FGF genes disrupts gene expression and embryonic development
Chromatin domains delimited by CTCF can restrict the range of enhancer action. However, disruption of some domain boundaries results in mild gene dysr…
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STITCHES Medicine - the Best of Medical Research @medicine.stitches.today · 21/02/2025
Prenatal DNA screening successfully predicts preeclampsia risk early in pregnancy, identifying tissue dysfunction months before onset. by Adil M, Kolarova TR (...) Shree R et 15 al. in Nat Med #MedSky 📖 read the article:
nature.com
Preeclampsia risk prediction from prenatal cell-free DNA screening - Nature Medicine
Using 1,854 routinely collected clinical samples from early in pregnancy, with validation in an external cohort, low-coverage cfDNA sequence data identified distinctive features among those who developed preeclampsia.
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Sarah Marzi @sj-marzi.bsky.social · 12/02/2025
📢 Our lab is looking for a bioinformatics postdoc. We have lots of exciting projects to work on, including single cell (epi-)genomics, microglia xenotransplantations and nanopore long reads splicing analysis. Look out for the official advert next week and get in touch in the meantime 🧬🧠
The Marzi Lab in epigenetics band t-shirts
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Hannah Long @hannahlong.bsky.social · 09/02/2025
Reminder of an exciting conference 'Hidden Cell, Dark Genome', Edinburgh 3-4th April 2025! Sessions: • Regulatory functions of the dark genome • Uncharted proteins and RNA complexity • Cellular diversity • Atomic structures at the cellular scale Early bird and registration deadline: 28th February!
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Science Magazine @science.org · 11/02/2025
When asked to draw a scientist, school-age kids in the United States are increasingly sketching women, according to a study from 2018. Read more on #WomenInScienceDay: scim.ag/4hOUuvx
SCIENCESHOTS What does a scientist look like? Children are drawing women more than ever before
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WHO @who.int · 11/02/2025
Today is International Day of Women & Girls in Science. Marie Curie, the first woman to win a Nobel Prize. Her contributions have left an indelible mark on the world of science & health & continue to inspire generations of scientists & innovators. 🔬 #WomenInScience #WomenInSTEM
Nothing in life is to be feared, it is only to be understood. Marie Curie, Physicist and chemist.
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Rob Beagrie @rbeagrie.bsky.social · 10/02/2025
Anyone else worried about what might happen if funding gets pulled for the Gene Expression Omnibus? Is everything mirrored at EBI or only some of it? #genomics #bioinformatics
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Dan Jagger @auditorynerves.bsky.social · 07/02/2025
Prenatal stress effects on the placenta. Maternal stress is a critical factor in the long-term health of offspring. A recent study (below) profiled the effects of prenatal stress on DNA methylation + gene expression in rat placenta & fetal brain. 🧪🧠🐀 #neuroskyence www.nature.com/articles/s41...
nature.com
Prenatal stress effects on the placenta - Nature Neuroscience
Nature Neuroscience - Prenatal stress effects on the placenta
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Robin Andersson @randersson.bsky.social · 06/02/2025
Job alert! We are hiring a postdoc or PhD student focusing on * developing computational methods to resolve gene regulation in single cells * investigating the mechanisms and cell-type specific effects of genetic variants PhD student: bsky.app/profile/jobr... Postdoc: bsky.app/profile/jobr...
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Rob Beagrie @rbeagrie.bsky.social · 06/02/2025
Disruption of chromatin contacts by cohesin being at least as important as stabilisation has been one of my pet hypotheses for a while now - nice to see this properly reasoned out in print!
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Jonathan Coxhead @4130chromo.bsky.social · 05/02/2025
Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues www.nature.com/articles/s41...
nature.com
Multiplexed spatial mapping of chromatin features, transcriptome and proteins in tissues - Nature Methods
Spatial-Mux-seq offers a multimodal spatial platform capable of profiling multiple molecular modalities, including the transcriptome, chromatin accessibility, histone modifications and targeted protei...
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Deniz Gökbuget @denizgoekbuget.bsky.social · 04/02/2025
🚨 New Paper Alert! 🚨 Our latest study on KMT2C/KMT2D (mutated in 20% of cancers) reveals a new function for H3K4me1 in regulating DNA replication timing (RT) and origin activity during cell state transitions. Check it out: www.cell.com/cell-reports.... More info ⬇️
cell.com
KMT2C/KMT2D-dependent H3K4me1 mediates changes in DNA replication timing and origin activity during a cell fate transition
Gökbuget et al. use machine learning to quantify chromatin state changes that predict DNA replication timing changes during cell differentiation. By following up on top predictors through functional v...
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Generic white guy SysAdmin @westbynoreaster.bsky.social · 05/02/2025
If you aren't a faculty member but work at a Uni, please join the local staff union. It's a big tent. ✊🏻 We need the entire sector to be organized, even if not under the same banner.
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Christa Buecker @chribue.bsky.social · 17/01/2025
It was already very special to coordinate the manuscript with my (former) mentor Joanna. But the preview by @mariekeoudelaar.bsky.social puts the cherry on top! Thank you!
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Teif lab @teiflab.bsky.social · 14/01/2025
Here is a growing list of conferences and schools in gene regulation for 2025 generegulation.org/conferences-.... You can order/filter this list by the date, deadline, location. Please reply here to suggest new events* *should be specific to gene regulation
generegulation.org
Conferences & Schools – 2025 – Gene Regulation – Teif Lab
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Jorge Ferrer @jorge-ferrer.bsky.social · 31/12/2024
📣 Hiring, please forward widely!! Two postdoc openings to work on genomics of diabetes 1. Computational regulatory genomics/statistical genetics. 2. Experimental cell-based modeling DM if interested @crg.eu shorturl.at/O3wMi shorturl.at/ieyZy
shorturl.at
Postdoctoral scientist, gene regulatory mechanisms and diabetes | CRG Online Recruitment Portal
The Centre for Genomic Regulation (CRG) is an international biomedical research institute of excellence, based in Barcelona, Spain, with more than 400 scientists from 44 countries. The CRG is composed by an interdisciplinary, motivated and creative scientific team which is supported both by a flexible and efficient administration and by high-end and innovative technologies.
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Sebastian Bae @sebastianbae.bsky.social · 22/12/2024
We are pursuing the wrong applications for AI.
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Anthony Mathelier @amathelier.bsky.social · 18/11/2024
🧵 Bioinformatics faces a critical challenge: despite its importance, software quality often falls short due to the lack of proper development practices. In our latest paper, we advocate for improving software quality in bioinformatics through teamwork. academic.oup.com/bioinformati...
Illustration comparing the improvement process in software writing to rock climbing.
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James Briscoe @jamesbriscoe.bsky.social · 19/12/2024
Our latest: how to generate the notochord "Timely TGFβ signalling inhibition induces notochord" A thread: www.nature.com/articles/s41...
nature.com
Timely TGFβ signalling inhibition induces notochord - Nature
Through analysis of developing chick embryos and in vitro differentiation of embryonic stem cells, a study develops a method to generate a model of the human trunk with a notochord.
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Cees Dekker @ceesdekker.bsky.social · 13/12/2024
I guess I told you about the fact that SMC proteins like cohesin and condensin are a novel class of molecular motors that make loops into DNA (something we visualized first in 2018). These DNA loops are the fundamental motif that organize our chromosomes. 0/
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Jeffrey Barrett @jeffbarrett.eu · 12/12/2024
This is one of the most interesting plots I’ve seen in ages. Just look at the professional dendrogram that results from clustering in this way!
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Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8
bmcgenomics.biomedcentral.com
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
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Christa Buecker @chribue.bsky.social · 02/12/2024
By definition, enhancers can activate from a distance. But with increased distance between enhancer and promoter, the activation drops. To study this systematically, we build a synthetic locus: www.cell.com/molecular-ce... 1/12
doi.org
Redirecting
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Science News @scinews.bsky.social · 01/12/2024
This study presents replication-aware single-molecule accessibility mapping (RASAM), a method to nondestructively measure replication status and protein-DNA interactions on chromatin genome-wide. #Cell #scisky Open Access www.cell.com/cell/fulltex...
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