did:plc:4nbxg32atozhtv4imwa6cz7l
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lIn a really fun collaboration with Max Wilson’s lab at UCSB, we’ve developed a simple model that can capture the non-monotonic expression of Wnt target genes with respect to frequency in periodic (optogenetic) Wnt pulses: elifesciences.org/articles/107.... Great work Sam, Olivier, Naomi and Ryan :)
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNew preprint! We show how mesoscopic nonequilibrium fluctuations in active gels emerge from the breaking of detailed balance at the molecular scale. Warning: Long technical paper ahead! Enjoy! @mpipks.bsky.social @ub.edu @ubics.bsky.social @icreacommunity.bsky.social arxiv.org/abs/2601.20483
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lOur latest: A gene selection method for single-cell RNA-seq that identifies developmental & spatial patterns missed by other analysis pipelines ESFS: A Noise-Resilient Framework for Feature Selection and Marker Gene Discovery in Single-Cell Transcriptomics | bioRxiv www.biorxiv.org/content/10.6...
- Our review on Marr's levels in embryonic development is now out in @prxlife.bsky.social ! journals.aps.org/prxlife/abst...
- How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework? We propose to think along Marr's 3 levels: computational problem, algorithm, implementation Check out our review: arxiv.org/abs/2510.24536
- Visiting @hhmijanelia.bsky.social just before the winter storm hits! So much awesome science here!
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lProf. Fiona Doetsch has been awarded the 2026 Louis-Jeantet Prize for Medicine! Her discoveries reveal how neural stem cells support lifelong brain plasticity and repair. 🧠 Read more: www.biozentrum.unibas.ch/news/detail/...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lMy time at @institutcurie.bsky.social is done! Over the past months, I completed my PhD, published my first first-author paper in DevCell (www.cell.com/developmenta..., and submitted my first last-author manuscript to bioRxiv (www.biorxiv.org/content/10.1...).
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lFeb 1 deadline approaching for our @kitp-ucsb.bsky.social QBio summer course on Physical Principles of Morphogenesis in Plants and Animals. @streichan.bsky.social @maurazimmermann.bsky.social @maizel-lab.org @yusuke-mori.bsky.social @akankshi.bsky.social @nicolettapetridou.bsky.social
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lInterested in the biophysics of organoids? We just published a review in Dev Cell—take a look! dlvr.it/TPyTb8 #Organoids #Biophysics
- Self-organized or instructed? My @natrevgenet.nature.com Journal Club traces how classic papers revealed two modes of developmental patterning & why the debate between Turing and Wolpert is as timely as ever for organoid engineering today www.nature.com/articles/s41...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lAnd here is the PDF of the 4th course @college-de-france.fr. You will find the justification and presentation of geometric representation of cell decisions, a parsimonious mathematical model for signalling and cell state transitions tinyurl.com/yc7u296j
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lHere is the link to download the PDF of my course#5 on Biological computation. I present & discuss Self-tuning, Adaptation and Learning in biological (non-neuronal) systems, in particular during embryonic development. This course contains various personal ideas/proposals. tinyurl.com/hcpwsbtm
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lPlease find below the link to watch the VIDEO of my course#5 @college-de-france.fr on Biological computation. I present and discuss Self-tuning, Adaptation and Learning in biological (non/neuronal) systems, in particular during embryonic development. Enjoy! tinyurl.com/4pv95an9
- Super nice to see this awesome set of lectures online! A really timely perspective on biology through the lens of information, which inspires much of our own research as well.
- And here is the link to access the whole pdf. Enjoy! I strongly believe that focusing on information & computation during Development provides an important framework, that encapsulates the genetic, chemistry & mechanics, but focusses on organisation, dynamics & logic. PDF: tinyurl.com/4hn34t8w
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lMunro, E., Nance, J., & Priess, J. R. (2004). Cortical flows powered by asymmetrical contraction transport PAR proteins to establish and maintain anterior-posterior polarity in the early C. elegans embryo. Developmental cell, #EpithelialMechanics www.sciencedirect.com/science/arti...
- How can cells use information from neighboring cells to improve the spatial precision of morphogen patterns? 🤔 We show that cells can gain positional information by "talking" to their neighbors - how much depends critically on spatial correlations of the patterns. buff.ly/w56OUJT
- In our recent paper on self-organized patterning, we demonstrated how the total information of a pattern is composed of positional (PI) and correlational information (CI). While PI measures local accuracy, CI is determined by the spatial correlations of a pattern. www.pnas.org/doi/10.1073/...
- Here, we ask how CI can be useful to single cell decision making, by predicting the additional PI gained when cells interact with their neighbors. Depending on the spatial correlations of the input pattern, completely different strategies to communication are required to gain information
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View full threadThis was a fun theory collaboration led by amazing postdoc Alex Zhang, in collab with Gasper Tkacik (ISTA)
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lGood to see the peer reviewed version of this published A chemo-optogenetic system for spatiotemporal control of gene expression We use it to: - Reconstruct SHH mediated neural tube patterning in vitro - Measure extracellular half-life of Shh www.cell.com/developmenta...
- Group xmas event - Curling! Pictured with our curling trainer Jean-Claude.
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lPlease find below the link to watch the VIDEO of my 3rd course @college-de-france.fr on Biological computation. I present and discuss Network motifs that reveal the hidden logic of complex genetic and biochemical networks. Enjoy! tinyurl.com/yyky4w2m
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7l🧪⚛️ Surface tension—driven by non-equilibrium currents not forces—in pattern formation leads to the same type of interface laws as in liquid foams: Plateau laws, von Neumann evolution; and a new emergent phenomenon: domain splitting akin to cell division. nature.com/articles/s4156…
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNew preprint! Do you like ocean waves? We found similar waves on bacterial colonies! We found that this collective behavior, known as rippling, is nothing but surface waves on an active nematic. @princeton.edu @mpipks.bsky.social @ub.edu @icreacommunity.bsky.social www.biorxiv.org/content/10.1...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lThis coming wednesday Dec. 3rd @college-de-france.fr, the annual #FrançoisJacob symposium. This year is about ‘Biology in the Flow of Time’⏱️. Superbe line up of speakers on various aspects. Come and enjoy (should you have time), free access, no registration🤘
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7l🚨 New preprint! We built a single-cell atlas of 14 multilayered epithelia and revealed a conserved transcriptomic program guiding tissue architecture and fate composition. Our work brings decades of tissue-specific studies together into a unified evo-devo framework. www.biorxiv.org/content/10.1...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lGreat science & fruiful discussions last Friday the 14th Nov. around "the physics of Stem cells" , the 2025 Stem Cell Initiative & QBio joint symposium. An honour to have Meryem Baghdadi & David Brückner as keynote speakers, who gave inspiring talks. 🙏🙏 to all our speakers & poster presenters.
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lAdvanced grad students + postdocs: apply for the 2026 #kitpqbio summer course, "Physical Principles of Morphogenesis in Plants and Animals," at buff.ly/OXXMKEv. Apply by Feb. 1. Course directors Adrienne Roeder (Cornell) and Sebastian Streichan (UCSB)
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lGood to see the peer reviewed version of this in print The cis-regulatory logic integrating spatial and temporal patterning in the vertebrate neural tube A global temporal chromatin program operates across the vertebrate nervous system to control neural cell diversity www.cell.com/developmenta...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lWonderful to see the beautiful preprint from Sabate et al now published - TADs are also dynamic structures in human cells, with remarkably similar parameters between mESCs and HCT116 cells www.nature.com/articles/s41...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lActive droplets are fundamental in cell biology and origin of life. With Jonathan Bauermann, @boekhovenlab.bsky.social, Frank Jülicher, and @m-pol.bsky.social, we show that a critical transition influences their size, morphology, ripening and division propensity journals.aps.org/prx/abstract...
- Super excited to finally visit our collaborators @heemskerklab.bsky.social at the University of Michigan! Seminar tomorrow at 1 PM singlecellspatialanalysis.umich.edu/scsap-monthl...
- Had a great time at the "Physics of Stem Cells" Meeting at Institut Pasteur last week! Many inspiring talks with different perspectives on how stem cells make decisions
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lHi, I’m David Brückner @davidbrueckner.bsky.social. I’ll take you through how cells in a tissue can use information distributed by biochemical gradients to make decisions, and how we can measure such positional information. buff.ly/RFxVeHh
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lEver wondered what drives enhancer-promoter specificity? Why would an enhancer activate one gene rather than another neighboring one? Check our latest preprint, led by @mmasoura.bsky.social, to find out! www.biorxiv.org/content/10.1...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lWolpert, L. (1969). Positional information and the spatial pattern of cellular differentiation. Journal of theoretical biology, 25(1), 1-47. #EpithelialMechanics
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7l🌍Open call: Junior Group Leader positions! Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery. Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lJan Rozman, Sumesh P. Thampi, Julia M. Yeomans: Why Extensile and Contractile Tissues Could be Hard to Tell Apart arxiv.org/abs/2511.07012 arxiv.org/pdf/2511.07012 arxiv.org/html/2511.07012
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lSwitzerland is joining Horizon Europe! We are uniting two research powerhouses. For cutting-edge innovation that will boost our energy security, digital transformation, health and so much more. Today is a good day for science, and for our EU-Switzerland partnership.
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lBrückner, D. B., & Tkačik, G. (2024). Information content and optimization of self-organized developmental systems. Proceedings of the National Academy of Sciences, #EpithelialMechanics www.pnas.org/doi/10.1073/...
- How can we organize current theoretical approaches for developmental biology - from information to dynamical systems & GRNs - into a common framework? We propose to think along Marr's 3 levels: computational problem, algorithm, implementation Check out our review: arxiv.org/abs/2510.24536
- We propose that many current approaches are not competing ideas, but look at the same fundamental problem - egg to embryo - from different perspectives: 1️⃣ Normative theories & optimality formalize the computationa problem 2️⃣ Dynamical systems provide algorithms 3️⃣ GRNs & others model implementation
- We propose a way to organize our current thinking about the algorithmic level along a set of architectures formalizing the computational capacity and amount of lateral coupling between cells
- We provide a perspective on how this framework could help to formalize the spectrum of patterning processes from instructed to self-organized development at multiple levels.
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lWe finally made it over here ! And excited to share our new paper on mechanical forces regulating stem cell plasticity in colorectal cancer, involving force transduction via mechanosensitive calcium channels! www.cell.com/cell-reports...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lEpithelial convergent extension as a tuning process biorxiv.org/content/10.1101/202…
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7l[This post could not be retrieved]
- Excited to visit CRG & EMBL Barcelona tomorrow!
- Nice highlight by Joseph d’Alessandro & Mélina Heuzé on our recent paper about mechanical memory in migrating cells with @sgabriele.bsky.social and @kyohalie.bsky.social www.nature.com/articles/d41...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lREMINDER! One week left to apply for what (in my humble and somewhat biased opinion) is one of the best academic jobs on the planet! Come join our vibrant and collaborative community here at the @biozentrum.unibas.ch @unibas.ch 🧪
- EXCITING NEWS!! We're searching for a new professor colleague at the Biozentrum🇨🇭. Ideal candidates are exploring novel biological questions with structure, biophysics, or high-resolution imaging. 🧪 🧶🧬 🔬 The call closes Nov 3. Please get in touch if you would like more information. Come join us! 👩🔬🤓
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lYour go-to tutorial for simulating mesoscale membranes is here. Look no further for: -Understanding the state of the field -A guide for creating new models for your science -Hands-on tutorials to simulate your very own membranes See tinyurl.com/punk3tcu and the below 🧵 start your journey 💻
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7l📣Announcing the 4th edition of the EMBL‑IBEC Conference on “Engineering Multicellular Systems”, taking place 11–13 March 2026 in Barcelona. Exploring organoids, mechanobiology, embryo models, organ-on-chip systems, multiomics and more. Abstracts open now! events.ibecbarcelona.eu/embl-ibec-co...
- 🤔 Can tissue patterning & tumor heterogeneity emerge in a self-organized way? We show that self-organized mechanical stress & density gradients pattern tumors in vitro & in vivo, and this behavior is quantitatively predicted by a mechano-chemical active fluid model! Check out Carlos' thread ⬇️
- 1/ 🎉Excited to share our new preprint @vignjeviclab.bsky.social @davidbrueckner.bsky.social : "Self-organization of tumor heterogeneity and plasticity" biorxiv.org/content/10.1... Tumor heterogeneity and plasticity drive metastasis and relapse. How is tumor patterning coordinated? A thread👇
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lThe @crick.ac.uk is recruiting Early Career Group Leaders - Lab set-up, research costs, salaries for up to 5 researchers - Support for up to 12 years - Access to our core facilities - Competitive salary - Fantastic colleagues - All areas of biology Deadline 27 Nov www.crick.ac.uk/careers-stud...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lAppreciate Quanta for shining a light on our joint work with Simon Gsell, Sham Tlili (@shamtlili.bsky.social), and Matthias Merkel (@merkellab.bsky.social).
- Biophysicists are realizing that there is an undervalued element at play in early development: Aside from genes, mechanical forces also steer the growth of embryos. @annademming.bsky.social reports: www.quantamagazine.org/genes-have-h...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNew preprint from the lab! We discovered a transient fluidization in the basal region of human forebrains by tracking microdroplets in cerebral organoids.This “basal fluidization”, absent in gorilla and mouse, may contribute to greater surface expansion in human forebrains 1/ doi.org/10.1101/2025...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lPleasure to announce the program of my new series of lectures at the College de France in Nov-Dec. Continuing on the theme of Biological information. I will focus on the computational aspects, building on David Marr's tri-level of analysis in biological systems. YouTube link sent when it starts.
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lOur paper is on the cover of @cp-devcell.bsky.social . Image: embryonic murine salivary-gland explants stained for fate determinants; p63 (cyan) and HES1 (yellow). Thanks to everyone involved. doi.org/10.1016/j.de...
- Had a lot of fun at our first group retreat in Graubünden🇨🇭🏔️🌄
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNew Review! #devbiol #bioelectricity #CellBiology #tissueregeneration In our new @annualreviews.bsky.social piece, we explore how bioelectricity is generated, sensed & translated into responses that sculpt tissues, guide growth & enable tissue regeneration. www.annualreviews.org/content/jour...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNew job, new preprint! We found that embryo implantation can be understood as active wetting! Embryos from older mothers have trouble implanting because they are too contractile and viscous. Check out the wonderful thread (and movies!) by @katecavanaugh.bsky.social. www.biorxiv.org/content/10.1...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lAre you interested in a PhD in the area of "Mechanisms of translational control during embryogenesis?" Apply now for a PhD @mpi-cbg.de! Overview of all participating RGLs: imprs.mpi-cbg.de/5761/researc...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lIf anyone ever wants to brush up on a lot of cell migration concepts don't forget we have several wonderful scientists who have given talks previously in cell migration seminars. I find it so comforting to go look at old videos, maybe someone else who will do as well!! youtube.com/@cellmigrati...
- Come join us in Basel! @biozentrum.unibas.ch is an amazing place to start your group.
- Assistant/Associate Professor in Structural Biology, Biophysics or Biological Imaging www.biozentrum.unibas.ch/open-positio... #biozentrum #University #Basel #Professor #Structural #Biology #Biophysics #Biological #Imaging
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNew preprint 🎉 What began as Frieder Johannsen’s bachelor thesis in the @zwickergroup.bsky.social (which I had the pleasure to supervise) evolved into our latest paper: “Chemically Active Liquid Bridges Generate Repulsive Forces” — unlike passive ones, which attract. 📄 arxiv.org/abs/2509.18777
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lSo proud of the exciting story from my PhD student Jakub Sumbal on contractile fibroblasts shaping branching morphogenesis! Fantastic collaboration with the lab of Zuzana Koledova in Prague! @sumbalovakoledova.bsky.social It just came out online, check it out here: rdcu.be/eIIKD
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lEEE meeting is BACK! Early Embryogenesis & Epigenetics conference in Berlin 02/2026. Checkout great program and over 12 slots for (not so) short talks for submitted abstracts!. Early registration now open - w.molgen.mpg.de/embryo2026
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lNow out in final published form - with a new title "Mechanical control of cell fate decisions in the skin epidermis" and simulations/quantifications! See below for thread of how unbalanced tensions can bias fate choices in minimal 3D models of tissues! www.nature.com/articles/s41...
- Happy to share the latest work from Preeti Sahu, with Adriana Sanchez-Danes on the biomechanics of cell fate choices during tumor initiation! We implement/test a 3D vertex model with proliferation and fate choices for multilayered tissues! See 🧵 below (1/n) bit.ly/3ZXxJzk
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lHappy to share that my PhD has finally taken the shape of a paper! ✨ Huge thanks to all authors, especially @davidbrueckner.bsky.social & @ehannezo.bsky.social for leading the modeling and @raimonsunyer.bsky.social & @xaviertrepat.bsky.social for their invaluable supervision. 🧵👇
- How do cells navigate up gradients of adhesive proteins? 🤔 Termed "Haptotaxis", this effect is ubiquitous in cell migration, but it's mechanism was poorly understood We show that passive friction directs cells & explains complex trajectories on gradients 👉 www.nature.com/articles/s41...
- Reposted by did:plc:4nbxg32atozhtv4imwa6cz7lTime for a thread!🧵 How different is the molecular organization of thylakoids in “higher” plants🌱? To find out, we teamed up with @profmattjohnson.bsky.social to dive into spinach chloroplasts with #CryoET ❄️🔬. Curious? ..Read on! #TeamTomo #PlantScience 🧪 🧶🧬 🌾 elifesciences.org/articles/105... 1/🧵
