Reposted by Alex DonovanSimon Fisher @profsimonfisher.bsky.social · 04/10/2025Twenty-four years ago today, our paper “A forkhead-domain gene is mutated in a severe speech and language disorder” was published: www.nature.com/articles/350.... A personal thread about the ups & downs of the journey we took to get to that point....1/n 🗣️🧬🧪 49236
Alex Donovan @apadonovan.bsky.social · 01/10/2026I 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! 🧠🧫 051
Reposted by Alex DonovanTeif lab @teiflab.bsky.social · 23/09/2026Zeng 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" 1278
Reposted by Alex DonovanJames Briscoe @jamesbriscoe.bsky.social · 22/09/2026Our 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.orgQuantifying Waddington's Landscape | Briscoe LabI have written before about how two conceptual frameworks have shaped our thinking about cell fate, Waddington's epigenetic landscape and Davidson's gene... 07629
Reposted by Alex DonovanBuzz Baum @buzzbaum.bsky.social · 22/09/2026We are looking for a research assistant! Come join the team: www.jobs.ac.uk/job/DSZ826/r...jobs.ac.ukResearch Support Officer | Cell Biology | Dr Buzz Baum | LMB 2904 at MRC Laboratory of Molecular BiologyStart your UK & international job search for academic jobs, research jobs, science jobs and managerial jobs in leading universities and top... 02946
Reposted by Alex DonovanJustus Kebschull @justuskebschull.bsky.social · 21/09/2026NEW 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 26127
Alex Donovan @apadonovan.bsky.social · 11/09/2026Our 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.comTailless terminates the neural stem cell temporal cascade in both the optic lobe and central brainSummary: 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... 0102
Reposted by Alex DonovanJames Briscoe @jamesbriscoe.bsky.social · 01/09/2026Our 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.orgDynamic Landscape Analysis of cell fate decisions provides predictive models of neural development from single-cell dataApplying 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) ... 13912
Reposted by Alex DonovanIMP @impvienna.bsky.social · 25/08/2026The 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 04015
Reposted by Alex DonovanMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 18/08/2026Exciting 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.socialbbc.co.ukPlans for £20m hub in Cambridge to develop new medicines using AIThe hub is funded by the Medical Research Council and based at Cambridge Biomedical Campus. 074
Reposted by Alex DonovanCedric Boeckx @cedricboeckx.bsky.social · 13/08/20262 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.comProteasome-dependent protein degradation shapes developmental tempo in mouse and human neural progenitorsWhy 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... 0259
Alex Donovan @apadonovan.bsky.social · 12/08/2026Exciting times to be working with in vitro models in Cambridge! 🧫 - www.cam.ac.uk/research/new...cam.ac.ukCambridge to lead new £20m MRC Hub to transform development of new medicines using stem cells and AIThe 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... 040
Reposted by Alex DonovanJesse Veenvliet @jesseveenvliet.bsky.social · 10/08/2026Very 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: 1274
Alex Donovan @apadonovan.bsky.social · 08/08/2026We 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 😂 030
Alex Donovan @apadonovan.bsky.social · 08/08/2026Encourage anyone having trouble with PSC differentiation protocols to try this, it really works! 000
Reposted by Alex DonovanMRC Laboratory of Molecular Biology @mrclmb.ac.uk · 07/08/2026Magdalena 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🧪 0188
Reposted by Alex DonovanLiam Dougherty @liamdougherty.bsky.social · 07/08/2026New 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 🔥🔥🔥 03819
Alex Donovan @apadonovan.bsky.social · 03/08/2026Interesting 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.comInterspecific diversity in the neuronal composition of the mammalian cortex arises from heterochrony in neurogenesis - The EMBO JournalMammals 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... 072
Reposted by Alex DonovanArnau Sebé-Pedrós @arnausebe.bsky.social · 03/08/2026Happy 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 belownature.comDiversity and evolution of chromatin regulatory states across eukaryotes - Nature GeneticsThis study introduces iChIP2, a low-input chromatin immunoprecipitation followed by sequencing method that profiles histone post-translational modifications (hPTMs) simultaneously across diverse eukar... 1018481
Reposted by Alex DonovanDevelopmental 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 23519
Alex Donovan @apadonovan.bsky.social · 23/07/2026Maybe they can just join up the extensive network of potholes we already have 👀 000
Reposted by Alex DonovanTeresa 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.orgEvolution of a core ribosomal innovation in octopusMuch 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... 1459
Reposted by Alex DonovanVicki Metzis @vmetzis.bsky.social · 17/07/2026How 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.orgTemporally distinct CDX programmes preconfigure vagal and trunk neural crestNeural 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... 16724
Reposted by Alex DonovanJan Philipp Kreysing @jpkreysing.bsky.social · 13/07/2026Delighted 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.comMolecular architecture of heterochromatin at the nuclear periphery of primary human cells - Nature CommunicationsThe 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... 37423
Reposted by Alex DonovanJohn Doench @johndoench.bsky.social · 06/07/2026New preprint from the group, comparing CRISPRko and CRISPRi via a Perturb-seq readout: www.biorxiv.org/content/10.6...biorxiv.orgDirect comparison of CRISPR knockout and interference with Perturb-seqCRISPR 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 ... 14117
Reposted by Alex DonovanChung Hyun Cho @chc-evobio.bsky.social · 04/07/2026Excited 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.orgEmergence of histone-based chromatin complexity in Asgard archaeaThe 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... 814776
Reposted by Alex DonovanSimon Fisher @profsimonfisher.bsky.social · 05/07/202625 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 🧪 513750
Reposted by Alex DonovanJason Tan @yjtan.bsky.social · 30/06/2026Does 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.orgIntrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancersEnhancers activate specific target promoters, but whether intrinsic enhancer-promoter compatibility contributes to this specificity is debated. Recent studies using different reporter assays have reac... 37139
Reposted by Alex DonovanPrisca Liberali @priscaliberali.bsky.social · 30/06/2026It 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.comMultiscale integration of tissue and chromatin context converts cell heterogeneity into stable intestinal patterningDuring regeneration, tissues must translate transient cellular variability into stable spatial organization. Tissue architecture generates a density-dependent window of heterogeneity in the mechanosen... 310937
Reposted by Alex Donovandimitristypas.bsky.social @dimitristypas.bsky.social · 30/06/2026I 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.comGenome-wide absolute quantification of chromatin looping - Nature Structural & Molecular BiologyBy 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... 1246
Reposted by Alex DonovanImmuNoah's Ark (Noe Rodriguez) @immunoah.bsky.social · 29/06/2026Led 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.orgIndex-agnostic oblique plane light sheet microscopy of centimetre-scale cleared tissues at subcellular resolutionWe 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 ... 041
Reposted by Alex DonovanCedric Boeckx @cedricboeckx.bsky.social · 28/06/2026Terrific resource, now on @biorxivpreprint.bsky.social: The Vertebrate Genomes Project Phase I: A global reference genome resource 🧪🧬 www.biorxiv.org/content/10.6...biorxiv.orgThe Vertebrate Genomes Project Phase I: A global reference genome resourceThe 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... 13022
Reposted by Alex DonovanMateja Hajdinjak @matejahajdi.bsky.social · 24/06/2026Our 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.socialnature.com 311551
Reposted by Alex DonovanScience Magazine @science.org · 22/06/2026In 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 419964
Alex Donovan @apadonovan.bsky.social · 22/06/2026Such 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. 020
Reposted by Alex DonovanAnders 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... 215277
Reposted by Alex DonovanMark Peifer (He, him) @peiferlabunc.bsky.social · 12/06/2026If 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! 🧪 082
Reposted by Alex DonovanOxford Biology @biology.ox.ac.uk · 11/06/2026Whole 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.lyAncient genome duplications laid the foundations of complex brains 02310
Reposted by Alex DonovanJames Briscoe @jamesbriscoe.bsky.social · 08/06/2026Our 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.orgMinimal essential requirements for neural tube self-organisationThe 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... 312542
Reposted by Alex DonovanMaxCyte @maxcyte.com · 02/06/2026What 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/3PV2nafacademic.oup.comIn Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to ChimpanzeeAbstract. Every element of the human skeleton exhibits some differences in comparison to our closest living relatives, chimpanzees. Many of these skeletal 072
Reposted by Alex DonovanScience Magazine @science.org · 28/05/2026Researchers 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 12520196
Reposted by Alex DonovanThiago 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.socialjournals.biologists.comWhy in vivo models of disease remain indispensableSummary: 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... 03316
Reposted by Alex DonovanPLOS Biology @plosbiology.org · 22/05/2026Bilaterian 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 03215
Alex Donovan @apadonovan.bsky.social · 22/05/2026If 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.orgAutism-like phenotypes and increased NMDAR2D expression in mice with KDM5B histone lysine demethylase deficiencyInhibitors targeting NMDA receptors may represent viable therapies for KDM5B neurodevelopmental disorders. 091
Reposted by Alex DonovanRabih Alameddine @rabihalameddine.bsky.social · 21/05/2026This is red shanked douc langur. 57517
Reposted by Alex DonovanSimon Hammann @simonhammann.bsky.social · 20/04/2026Don'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. 191958537
Alex Donovan @apadonovan.bsky.social · 29/04/2026Check 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.comQuiescent neural stem cells transiently become neuron-like to coordinate long-range reactivation - The EMBO JournalReactivation 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... 1134
Reposted by Alex DonovanJan Żylicz @jzylicz.bsky.social · 25/04/2026New 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.comTCA cycle rewiring underpins histone acetylation sourcing and cell-fate transitions during exit from naive pluripotencyUsing 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... 18932
Alex Donovan @apadonovan.bsky.social · 24/04/2026Wake up, new giant apex predator cephalopod just dropped 🦑 - www.science.org/doi/10.1126/...science.orgEarliest octopuses were giant top predators in Cretaceous oceansTop 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... 031