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Alex Donovan

@apadonovan.bsky.social
2.4K followers 2.2K following 75 posts

Biologist at the MRC LMB, Cambridge, interested in human evolution and how stem cells behave and misbehave 🧠🧬🏳️‍🌈 Previously Gurdon Institute & NYU

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Alex Donovan @apadonovan.bsky.social · 4h
I was on a podcast! Chatting about the promise and limitations of brain organoids, and the unexpected origins of one of the most commonly used cerebral organoid protocols! 🧠🧫
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Teif lab @teiflab.bsky.social · 23/09/2026
Zeng et al, 2026. Transcription factors read a second regulatory code in chromatin www.biorxiv.org/content/10.6... "our findings establish that TFs interpret two complementary layers of genomic information: the primary DNA sequence and a second code written into the nucleosome architecture"
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James Briscoe @jamesbriscoe.bsky.social · 22/09/2026
Our latest paper on building models of cell fate decisions -with David Rand, Marine Fontaine & @joadelas.bsky.social- combines developmental biology, dynamical systems theory and bioinformatics. I wrote a short piece to summarise it & explain ideas behind the approach briscoelab.org/blog-quantif...
briscoelab.org
Quantifying Waddington's Landscape | Briscoe Lab
I have written before about how two conceptual frameworks have shaped our thinking about cell fate, Waddington's epigenetic landscape and Davidson's gene...
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Buzz Baum @buzzbaum.bsky.social · 22/09/2026
We are looking for a research assistant! Come join the team: www.jobs.ac.uk/job/DSZ826/r...
jobs.ac.uk
Research Support Officer | Cell Biology | Dr Buzz Baum | LMB 2904 at MRC Laboratory of Molecular Biology
Start your UK & international job search for academic jobs, research jobs, science jobs and managerial jobs in leading universities and top...
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Justus Kebschull @justuskebschull.bsky.social · 21/09/2026
NEW PREPRINT! An evo-devo look at how new cerebellar nuclei are made. Spoiler: it’s all driven by region-specific excitatory progenitors in the early rhombic lip; inhibitory neurons fill in later. If you care about brain evolution or cerebellar development, check it out: tinyurl.com/CNdevelopment
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Alex Donovan @apadonovan.bsky.social · 11/09/2026
Our paper tying up some loose ends in our understanding of temporal patterning is out now! 🧠🪰 We show a single transcription factor (Tailless/TLX) terminates the temporal cascade across multiple neural stem cell lineages in the fly brain! journals.biologists.com/dev/article/...
journals.biologists.com
Tailless terminates the neural stem cell temporal cascade in both the optic lobe and central brain
Summary: Are temporal cascades conserved in different neural lineages? Combining genetic manipulation and chromatin-binding assays in Drosophila, this study identifies Tailless/TLX as a conserved fact...
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James Briscoe @jamesbriscoe.bsky.social · 01/09/2026
Our latest: Dynamic Landscape Analysis of cell fate decisions provides predictive models of neural development from single-cell data From Marine Fontaine and @joadelas.bsky.social with David Rand in @plosbiology.org A thread 🧵 doi.org/10.1371/jour...
doi.org
Dynamic Landscape Analysis of cell fate decisions provides predictive models of neural development from single-cell data
Applying dynamical systems theory to single-cell data can provide a detailed picture of the cellular states observed during cell fate decisions. This study presents a dynamic landscape analysis (DLA) ...
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IMP @impvienna.bsky.social · 25/08/2026
The IMP lab of Alexander Stark used AI to design enhancers—DNA switches controlling gene activity—for specific mouse tissues: the first from-scratch design in a mammal. News: imp.ac.at/news/article/ai-learns-to-write-code-that-activates-genes-in-mammals Paper: nature.com/articles/s41588-026-02729-1
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 18/08/2026
Exciting plans for a new national hub at @scicambridge.bsky.social to advance novel alternative methodologies for disease models. @lancasterlab.bsky.social will co-lead neuroscience models, including brain organoids. Read more: www.bbc.co.uk/news/article... #LMBintheNews @cellbiol-mrclmb.bsky.social
bbc.co.uk
Plans for £20m hub in Cambridge to develop new medicines using AI
The hub is funded by the Medical Research Council and based at Cambridge Biomedical Campus.
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Cedric Boeckx @cedricboeckx.bsky.social · 13/08/2026
2 great papers on species-specific developmental tempo now @cp-devcell.bsky.social Congrats @trayon.bsky.social @jamesbriscoe.bsky.social @ebisuyamiki.bsky.social & their teams 🧪 1. On protein degradation in neural progenitors 2. On differences in protein stability www.cell.com/developmenta...
cell.com
Proteasome-dependent protein degradation shapes developmental tempo in mouse and human neural progenitors
Why do mammalian species develop at different speeds? Nakanoh, Stamataki, et al. show that mouse neural progenitors have faster protein synthesis and proteasome-mediated degradation than human. Manipu...
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Alex Donovan @apadonovan.bsky.social · 12/08/2026
Exciting times to be working with in vitro models in Cambridge! 🧫 - www.cam.ac.uk/research/new...
cam.ac.uk
Cambridge to lead new £20m MRC Hub to transform development of new medicines using stem cells and AI
The Medical Research Council (MRC) has announced a £20 million investment in a new Pre-clinical Translational Models Hub, led by Cambridge, which will transform the development and testing of new medi...
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Jesse Veenvliet @jesseveenvliet.bsky.social · 10/08/2026
Very interesting work that reminded me of the Bonini Paradox from computer science that I often reference in the context of stem-cell-based embryo models and organoids:
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Alex Donovan @apadonovan.bsky.social · 08/08/2026
We have our favourite - "Oh my God, how I do hate species & varieties" up in the lab to remind us that everyone can feel frustrated at this job sometimes 😂
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Alex Donovan @apadonovan.bsky.social · 08/08/2026
Encourage anyone having trouble with PSC differentiation protocols to try this, it really works!
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MRC Laboratory of Molecular Biology @mrclmb.ac.uk · 07/08/2026
Magdalena Sutcliffe, @lancasterlab.bsky.social & @stefanschoenfelder.bsky.social demonstrate how epigenetic ‘memory’ shapes stem cell potential, but a chemical reset can restore differentiation ability. Read more: shorturl.at/PZ4tV #LMBResearch @cellbiol-mrclmb.bsky.social @babrahaminst.bsky.social🧪
Human pluripotent stem cells favour either anterior or posterior formation, but this can be mediated by chromatin restoration (CHR) treatment.Fluorescent micrograph of an organoid with intricate folds and patterns in blue and purple
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Liam Dougherty @liamdougherty.bsky.social · 07/08/2026
New pre-print led by the amazing @patricepottier.bsky.social - very little evidence for evolution of life history traits in response to warming, even in insects. Rapid adaptation is unlikely to mitigate the continuing impacts of climate change 🔥🔥🔥
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Alex Donovan @apadonovan.bsky.social · 03/08/2026
Interesting finding that rats have a disproportionate expansion of deep cortical layers when compared to other mammalian species - an output of extended duration in deep-layer neurogenesis, mediated by prolonged canonical WNT activity - link.springer.com/article/10.1...
link.springer.com
Interspecific diversity in the neuronal composition of the mammalian cortex arises from heterochrony in neurogenesis - The EMBO Journal
Mammals share a laminar cerebral cortex, with excitatory neuron subtypes organized in distinct layers. Although this framework is conserved, subtype balance varies markedly between species due to larg...
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Arnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026
Happy to share the final version of our study on the evolution of chromatin states across eukaryotes, out today in @natgenet.nature.com Led by @crisnava.bsky.social and @seanamontgomery.bsky.social www.nature.com/articles/s41... Some highlights below
nature.com
Diversity and evolution of chromatin regulatory states across eukaryotes - Nature Genetics
This study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar...
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Developmental Biology @devbiol.bsky.social · 22/07/2026
#DBfeature A tribute to Gail R Martin, mouse geneticist and mentor extraordinaire (April 12, 1944 - Feb 9, 2026) By Alexandra Joyner doi.org/10.1016/j.ydbio.2026.05.007
Gail Martin looking at the camera, sitting on a bench in front of a lily pad pond in her garden in Berkeley. Photo from Brigid Hogan.
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Alex Donovan @apadonovan.bsky.social · 23/07/2026
Maybe they can just join up the extensive network of potholes we already have 👀
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Teresa Rayon @trayon.bsky.social · 19/07/2026
🐙 Octopuses appear to have evolved a ribosomal innovation that increases protein translation fidelity. *suggests that evolution can tune core components of the proteostasis machinery, extending adaptation beyond gene regulation www.biorxiv.org/content/10.6...
biorxiv.org
Evolution of a core ribosomal innovation in octopus
Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations in other steps of the central dogma. Octopuses exhibit complex nervous systems and soph...
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Vicki Metzis @vmetzis.bsky.social · 17/07/2026
How does an embryo generate the right cells in the right place? Delighted to share our latest findings on how neural crest cells acquire vagal or trunk identities Spoiler alert: The timing & combination of CDXs preconfigures cell identity & distinct HOX states www.biorxiv.org/content/10.6...
biorxiv.org
Temporally distinct CDX programmes preconfigure vagal and trunk neural crest
Neural crest cells (NCCs) are progenitor cells vital in establishing the head, heart, gut and peripheral nervous system of vertebrate embryos. Disruptions to NCC development underlie neurocristopathie...
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Jan Philipp Kreysing @jpkreysing.bsky.social · 13/07/2026
Delighted that our story on chromatin architecture inside human cells is now published — the last chapter of my PhD. It was a pleasure working with @sergiocruzleon.bsky.social, @johannesbetz.bsky.social, and everyone involved. #teamtomo www.nature.com/articles/s41...
nature.com
Molecular architecture of heterochromatin at the nuclear periphery of primary human cells - Nature Communications
The 3D organisation of chromatin inside a human cell is still not fully resolved. Here the authors reveal that in situ cryo-ET resolves individual nucleosomes and predicts DNA linkers, thus showing th...
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John Doench @johndoench.bsky.social · 06/07/2026
New preprint from the group, comparing CRISPRko and CRISPRi via a Perturb-seq readout: www.biorxiv.org/content/10.6...
biorxiv.org
Direct comparison of CRISPR knockout and interference with Perturb-seq
CRISPR knockout (CRISPRko) and CRISPR interference (CRISPRi) are two workhorse technologies for loss-of-function studies, yet direct comparisons between the two are scant relative to their widespread ...
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Chung Hyun Cho @chc-evobio.bsky.social · 04/07/2026
Excited to share our new preprint led by Fred and me in collaboration with the archaeal community! We found that the molecular foundation of histone-based chromatin has pre-eukaryotic roots in Asgard archaea. (1/4) #ArchaeaSky www.biorxiv.org/content/10.6...
biorxiv.org
Emergence of histone-based chromatin complexity in Asgard archaea
The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the e...
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Simon Fisher @profsimonfisher.bsky.social · 05/07/2026
25 years ago, we implicated rare variants of the FOXP2 gene in a severe speech disorder. I’ve spent much time stressing that FOXP2, while interesting, is not the mythical “gene for language”. Weirdly, on occasion I also need to explain why it’s not “proof of aliens”. Full disclosure in this 🧵. 1/n 🧪
Promotional poster for the 2026 science fiction film Disclosure Day.
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Jason Tan @yjtan.bsky.social · 30/06/2026
Does every enhancer work with every promoter? With @jengreitz.bsky.social and Will Greenleaf, we revisit this long-debated question and resolve an outstanding contradiction in the field. A tour 🧵👇 www.biorxiv.org/content/10.6...
biorxiv.org
Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers
Enhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac...
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Prisca Liberali @priscaliberali.bsky.social · 30/06/2026
It is out 😍 check it out!! Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning. @cschwayer.bsky.social @silviabarbiero.bsky.social @davidbrueckner.bsky.social @ehannezo.bsky.social www.cell.com/cell/fulltex...
cell.com
Multiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterning
During regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen...
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dimitristypas.bsky.social @dimitristypas.bsky.social · 30/06/2026
I am on paternity leave but I need to talk about this work by the @andersshansen.bsky.social lab that was published @natsmb.nature.com. The authors provide absolute quantification of chromatin loops across the genome. www.nature.com/articles/s41... Putting actual numbers in E-P, P-P and all loops!
nature.com
Genome-wide absolute quantification of chromatin looping - Nature Structural & Molecular Biology
By calibrating Micro-C against live-imaging data in mouse embryonic stem cells, Jusuf et al. quantified 65,929 chromatin loops genome-wide, finding that most loops form pairwise interactions with an a...
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ImmuNoah's Ark (Noe Rodriguez) @immunoah.bsky.social · 29/06/2026
Led by @jamesdmanton.bsky.social & Jacob Lamb @mrclmb.ac.uk, take a look at this cool new approach to image cleared whole-mount tissues with LSFM! Great to have participated in it, even if it was Ksena Longrin, a great postdoc in my lab, who did our contribution. www.biorxiv.org/content/10.6...
biorxiv.org
Index-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolution
We present cleared-tissue direct-view oblique plane microscopy (CtDvOPM), which enables optically sectioned subcellular resolution imaging of centimetre-scale tissues at high throughput over the full ...
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Alex Donovan @apadonovan.bsky.social · 29/06/2026
Never too many 💪
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Cedric Boeckx @cedricboeckx.bsky.social · 28/06/2026
Terrific resource, now on @biorxivpreprint.bsky.social: The Vertebrate Genomes Project Phase I: A global reference genome resource 🧪🧬 www.biorxiv.org/content/10.6...
biorxiv.org
The Vertebrate Genomes Project Phase I: A global reference genome resource
The Vertebrate Genomes Project (VGP) aims to produce complete and near-error-free reference genomes for all ∼70,000 extant vertebrate species. Organized in four phases, it progressively targets all ve...
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Mateja Hajdinjak @matejahajdi.bsky.social · 24/06/2026
Our late Neandertal paper is officially out! 💀❤️🧬 www.nature.com/articles/s41... It was years in the making, a tremendous feat spearheaded by our PhD student Alba Bossoms Mesa and co-led by @janetk.bsky.social and @benmpeter.bsky.social
nature.com
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Science Magazine @science.org · 22/06/2026
In what may be one of Earth’s craziest forms of mimicry, researchers in 2023 reported a species of rove beetle that grows a termite puppet on its back to fool real termites into feeding it. Learn more during #InsectWeek: scim.ag/4mM2aS9
Austrospirachtha carrijoi, a species of rove beetle
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Alex Donovan @apadonovan.bsky.social · 22/06/2026
Such a nice use of a synthetic promoter + cis-regulatory element system to actually ask the fundamental questions about gene regulation in 3D! Also love how the caveats of each method are accounted for by combining them. Thoroughly enjoyed reading this.
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Anders Sejr Hansen @andersshansen.bsky.social · 22/06/2026
(1/n) Very excited to share tri-lab collab (Mirny & Zechner) led by Harvey, Henrik & Jack: Q: How do enhancers & promoters interact in space (contact vs. action-at-a-distance) and time (stable vs. transient)? A: Transient E-P contact (~25-42 nm lasting ~10-20 sec): www.biorxiv.org/content/10.6...
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 12/06/2026
If you want to get a glimpse of how long range sequencing has revolutionized our view of the human genome, unveiling the true complexity of copy number variation between individuals and using spinal muscular atrophy as an example of the clinical impact, this is for you! 🧪
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Oxford Biology @biology.ox.ac.uk · 11/06/2026
Whole genome duplications over 450 million years ago enabled the emergence of different kinds of brain cells 🧠 These cellular innovations are shared across vertebrates - from primitive fish to mammals - and form the basis of the sophisticated brains seen today 👇
bit.ly
Ancient genome duplications laid the foundations of complex brains
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James Briscoe @jamesbriscoe.bsky.social · 08/06/2026
Our latest: Minimal essential requirements for neural tube self-organisation How does a single cell give rise to a tissue with the right cell types in the right proportions? We deconstruct and rebuild a self-organising tissue from first principles A thread🧵 www.biorxiv.org/content/10.6...
biorxiv.org
Minimal essential requirements for neural tube self-organisation
The reliable generation of diverse cell types in precise proportions is essential for the formation of functional tissues during embryonic development. Three-dimensional organoid models derived from p...
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MaxCyte @maxcyte.com · 02/06/2026
What can 70,000+ human and chimpanzee regulatory elements tell us about skeletal evolution? A new study in @genomebiolevol.bsky.social uncovered genomic differences linked to skeletal development using a massively parallel reporter assay. We're glad our ATx® could support! 🔗 bit.ly/3PV2naf
academic.oup.com
In Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to Chimpanzee
Abstract. Every element of the human skeleton exhibits some differences in comparison to our closest living relatives, chimpanzees. Many of these skeletal
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Science Magazine @science.org · 28/05/2026
Researchers have identified superparamagnetic macrophages in the livers of rock pigeons to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation. scim.ag/4nTQ3nq
How animals sense Earth’s magnetic field is one of biology’s enduring mysteries. Researchers have now identified superparamagnetic macrophages in the livers of rock pigeons (Columba livia) to be crucial for magnetic sensing. The finding uncovers an unexpected role for immune cells in sensory perception and may fundamentally change our understanding of animal navigation.

Photo: Andreas Teichmann/laif/Redux
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Thiago Carvalho @cyrilpedia.bsky.social · 23/05/2026
'We primarily do comparative analysis using human stem cells/organoids and genetically modified mouse models, with some minor use of frog models. We use this approach because, for developmental anomalies, it is impossible to assess true function without in vivo models' @karenjliu.bsky.social
journals.biologists.com
Why in vivo models of disease remain indispensable
Summary: The call to arms for alternatives to model organisms of disease will fail without ongoing integration with – and validation against – complex animal models and support from the animal modelli...
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PLOS Biology @plosbiology.org · 22/05/2026
Bilaterian BMP signaling gradients suggest an ancestral anti-neural role. Study of #cnidarians shows that #BMP signalling promotes neurogenesis; its "anti-neural" function is a side effect of its role in the DV axis @paulknabl.bsky.social @genikhovich.bsky.social @plosbiology.org 🧪 plos.io/4dJHoiR
In the box jellyfish Tripedalia cystophora, BMP signaling is active in ganglionic neurons of the umbrella, the ring nerve and in the rhopalium. Top left: Oral view of the umbrella, black arrowheads highlight the location of the rhopalia (rh). Top right: lateral and frontal detail of the rhopalium anatomy. Bottom, from left to right: pSMAD1/5 activity in the rhopalia, lateral view of the rhopalium, view from the top highlights pSMAD1/5 activity around the stalk, detailed view of the pit eye and the area around it (pSMAD1/5 is observed in a sector of the pit eye retina, the upper lens eye and some cells between the pit eye and the stalk).
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Alex Donovan @apadonovan.bsky.social · 22/05/2026
If you are interested in the mechanisms linking variants in histone modifying enzymes to Autism Spectrum Disorder phenotypes, have a read! New from @bassonlab.bsky.social 🧠 congrats to @lperezsisques.bsky.social and everyone else! www.science.org/doi/10.1126/...
science.org
Autism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiency
Inhibitors targeting NMDA receptors may represent viable therapies for KDM5B neurodevelopmental disorders.
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Rabih Alameddine @rabihalameddine.bsky.social · 21/05/2026
This is red shanked douc langur.
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Simon Hammann @simonhammann.bsky.social · 20/04/2026
Don't be shy to take on a little two-week side project. These five months will be the most precious three years of your academic journey.
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Alex Donovan @apadonovan.bsky.social · 29/04/2026
Check out this incredibly cool paper from my friends Jocelyn Tang and Laura Gherghina in the Brand lab - they found that neural stem cells have the capacity to become "neuron-like", synapsing with neurons to mediate quiescence and reactivation! 🪰🧠 link.springer.com/article/10.1...
link.springer.com
Quiescent neural stem cells transiently become neuron-like to coordinate long-range reactivation - The EMBO Journal
Reactivation of quiescent neural stem cells (NSCs) in the central nervous system (CNS) is a tightly controlled process that generates new neurons and glia to maintain homeostasis or enable repair post...
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Jan Żylicz @jzylicz.bsky.social · 25/04/2026
New paper out in @cp-cellstemcell.bsky.social. We uncover unexpected complexity in how metabolism changes when the embryo implants or when stem cells exit naive pluripotency, revealing a central role for dynamic TCA cycle rewiring in cell fate decisions. www.cell.com/cell-stem-ce...
cell.com
TCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotency
Using carbon tracing and functional experiments, Kafkia, Pladevall-Morera, et al. show that TCA cycle rewiring underlies mouse embryo implantation and the exit from naive pluripotency. In this context...
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Alex Donovan @apadonovan.bsky.social · 24/04/2026
Wake up, new giant apex predator cephalopod just dropped 🦑 - www.science.org/doi/10.1126/...
science.org
Earliest octopuses were giant top predators in Cretaceous oceans
Top predators drive changes in ecosystem structure. For the last ~370 million years, large-sized vertebrates have dominated the apex of the marine food chain, while invertebrates have served as smalle...
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Epigenetics Podcast @epigeneticspod.bsky.social · 24/04/2026
In this episode of the Epigenetics Podcast, we talked with Iva Tchasovnikarova from the @gurdoninstitute.bsky.social about her work on heterochromatin formation and epigenetic control. #podcast #epigenetics #chromatin Listen here: activemotif.com/podcasts-iva...
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