Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10hEvolutionary branching under slowly evolving constraints www.biorxiv.org/content/10.64898/20… 044
Reposted by Lisandro MiloccoAndrej Spiridonov @andrejpaleo.bsky.social · 29/09/2026Dynamical [chemical] systems view on the emergence of heredity in evolution: "This paper proposes that early chemical systems could preserve and pass on differences through stable chemical states rather than through stored sequences like DNA or RNA" www.pnas.org/doi/10.1073/... 🧪 #Complexity #EvoBio 0167
Reposted by Lisandro MiloccoSMB - Society for Mathematical Biology @smbmathbiology.bsky.social · 28/09/2026Here's a new #BullMathBio paper by Evan Gorstein, Mengze Tang, Hailey Bruzzone, and Claudia Solís-Lemus on how Ancestral Sequences Cannot be Accurately Reconstructed via Interpolation in a Variational Autoencoder’s Latent Space. 🧪 link.springer.com/article/10.1...link.springer.comAncestral Sequences Cannot be Accurately Reconstructed via Interpolation in a Variational Autoencoder’s Latent Space - Bulletin of Mathematical BiologyStandard methods for ancestral sequence reconstruction (ASR) rely on substitution models for the residues in a biological sequence and assume independent evolution across these sites, ignoring the epi... 021
Reposted by Lisandro MiloccoPierre de Villemereuil @pdevillemereuil.bsky.social · 28/09/2026With fieldwork, I didn't get to advertise our (not so now) new paper on the quantitative genetics of growth in the 🦎 in @journal-evo.bsky.social: dx.doi.org/10.1093/evol... It's an exciting paper paper in which we disentangle what it means to treat the whole growth curve as a function-valued trait!dx.doi.orgQuantitative genetics of lifetime growth curves in a lizardAbstract. Body size is an iconic trait in quantitative genetics. For species with indeterminate growth however, growth curve, a function-valued trait, is t 23520
Reposted by Lisandro Miloccoepithelial mechanics fan club @epimechfc.bsky.social · 27/09/2026Can mathematics explain how biological patterns are formed? Alan Turing thought so. Join me, @benswedlund.bsky.social , as we explore his reaction-diffusion theory and how it transformed our understanding of pattern formation and self-organisation. 0149
Reposted by Lisandro MiloccoRichard Lenski @relenski.bsky.social · 22/09/2026"Philosophy of Biology: The power of theory in the life sciences" elifesciences.org/articles/112... @zdblount.bsky.social shared this thought-provoking paper with the lab group.elifesciences.orgPhilosophy of Biology: The power of theory in the life sciencesTheory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets. 110346
Reposted by Lisandro MiloccoJames 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... 07529
Reposted by Lisandro MiloccoÁkos T Kovács @evolvedbiofilm.bsky.social · 19/09/2026From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance @cp-trendsmicrobiol.bsky.social by @frankaarestrup.bsky.social Saria Otani, Anne Meyer, and Thomas Bjarnsholt www.cell.com/trends/micro...cell.comFrom resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistanceAntimicrobial resistance is often inferred from resistance genes and susceptibility phenotypes measured under standardized conditions. We argue that for many resistance genes, resistance is better vie... 095
Reposted by Lisandro MiloccoAlejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 11/08/2026As simulations grow in complexity, a set of non-trivial issues emerge: diminished identifiability as free parameters become too numerous relative to exp. constraints & difficulties grasping causality. In our new 📄, we point to potential avenues to move #CellBio forward 👇 arxiv.org/abs/2608.06998arxiv.orgSimulating is not always understanding: When model complexity obscures biologyIn cell biology, computational models of biological systems range from minimal representations with a handful of parameters to whole-cell simulations tracking thousands of molecular species across a c... 310735
Reposted by Lisandro MiloccoBiological Theory @biologicaltheory.bsky.social · 09/09/2026➡️ New article out! ⬅️ How Much Diversity Is Lost in Classification? Morphospaces as a Metric of Taxonomic Impact by Alberto González-Casarrubios Free reading link: rdcu.be/LMuvEcoSM6oa 0233
Reposted by Lisandro MiloccoPhilippe Batut @philippebatut.bsky.social · 10/09/2026🧬🔬 Why are enhancers transcribed and how does that impact gene regulation? I’m really excited to share our new paper in @science.org showing that noncoding RNAs control the timing of gene activation in embryos. With Mike Levine #ScienceResearch @columbiamed.bsky.social A few highlights below... 🧵👇science.orgNoncoding transcription controls the developmental dynamics of long-range gene regulationThe genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ... 5233115
Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10/09/2026Conserved covariance structure underlies 60 million years of morphological diversification in primates www.biorxiv.org/content/10.64898/20… 113
Reposted by Lisandro MiloccoBen Lehner @benlehner.bsky.social · 03/08/20261st genome sequenced (Sanger 1977), 1st genome synthesised (Venter 2003), 1st genome + proteome fully mutated (Huijin Xiangua 2026!) @crg.eu @sangerinstitute.bsky.social Complete Mutagenesis of the Genome and Proteome of ΦX174 www.biorxiv.org/content/10.6...biorxiv.orgComplete Mutagenesis of the Genome and Proteome of ΦX174The bacteriophage ΦX174 was the first genome to be sequenced and the first to be chemically synthesised. Here we present a complete map of the consequences of changing every nucleotide in the ΦX174 ge... 19742
Reposted by Lisandro MiloccoTrends in Genetics @cp-trendsgenetics.bsky.social · 08/09/2026"The Study of Evolvability in Gene Regulatory Networks" by Alger Jorritsma, Aaron Kiggen, Steven Van Belleghem, & Pieter van den Berg FREE till Oct 27th at authors.elsevier.com/a/1nkTMcQbJI... 065
Reposted by Lisandro MiloccoJessica Abbott @jessicakabbott.bsky.social · 05/09/2026Are you a mathematical modeller in ecology and evolution looking for a job? My department has an opening! Please spread the word! lu.varbi.com/en/what:job/...lu.varbi.comSenior Lecturer in Computational BiologyLund University welcomes applicants with different backgrounds and experiences. Gender equality, equal opportunities and diversity are fundamental principles in all parts of the University’s activit 03143
Reposted by Lisandro MiloccoNorbert Marwan @pucicu.de · 27/08/2026New Physics Reports paper out: "Reconstruction of interpretable causal network dynamics from time series data" including #recurrence_plot methods. 😃 free read: authors.elsevier.com/c/1ngh71KAVt... www.sciencedirect.com/science/arti...sciencedirect.comReconstruction of interpretable causal network dynamics from time series dataReconstructing causal dynamic networks from multivariate time series is a foundational problem in complex systems science. Yet, the key scientific iss… 044
Reposted by Lisandro MiloccoAlvaro Sanchez @asanchezlab.bsky.social · 21/08/2026New preprint from the lab: The Latent Simplicity of Microbial Ecological Interactions www.biorxiv.org/content/10.6... We're excited about this one. We find that high-order microbial interactions often obey simple linear laws making microbial communities far more predictable than one might expect 4277
Lisandro Milocco @milocco.bsky.social · 17/08/2026What can development contribute to predicting evolution? I argue it sets what evolution can access, and this depends on timescale since different parts of development evolve at different rates. Hence coarse-graining: keep only what matters 📣 New in @evojlinnsoc.bsky.social doi.org/10.1093/evol... 34110
Reposted by Lisandro Milocco📑 EvoDevo Papers @evodevo-papers.bsky.social · 12/08/2026Evolvability After Riedl onlinelibrary.wiley.com/doi/10.1002… #EvoDevo 042
Reposted by Lisandro MiloccoFabian Fröhlich @frohlichlab.com · 05/08/2026Mechanistic ODE models encode pathway topology but are blind to anything outside the pathway. Representation learning compresses data into low-dimensional embeddings but says nothing about mechanism. Deep Mechanistic Models (DMMs) are our attempt at both in one model www.biorxiv.org/content/10.6...biorxiv.orgDeep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneityCells sense and respond to their environment through signalling pathways, and the dynamics of these pathways shape cell fate even within genetically identical populations. Two largely separate computa... 1101
Reposted by Lisandro MiloccoEmília Santos @emiliapsantos.bsky.social · 14/07/2026🎨 job alert 🐠 Come join us! We have two positions open! These are part of our @erc.europa.eu funded project on the mechanisms underpinning convergence of colour patterns in cichlid fishes! Closing date: 16th August. Postdoc: www.cam.ac.uk/jobs/researc... Technician: www.cam.ac.uk/jobs/researc...static.klipy.comCallipterus Cichlid Collecting ShellALT: Callipterus Cichlid Collecting Shell 09486
Reposted by Lisandro MiloccobioRxiv SysBio @biorxiv-sysbio.bsky.social · 31/07/2026Deep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneity www.biorxiv.org/content/10.64898/20… 001
Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 24/07/2026Beyond the Panglossian paradigm: adaptation, constraint, and anuran functional trait evolution. www.biorxiv.org/content/10.64898/20… 021
Reposted by Lisandro MiloccoPaul Francois @pfrancois.bsky.social · 14/07/2026New paper 🧵 What if the "landscape" that guides cell differentiation isn't fixed, but is sculpted, in real time, by the very cells moving through it? We call this a 'sandscape' : grains of sand that carve dunes as they move, while the dunes' shape simultaneously steers where the grains go next. 37938
Reposted by Lisandro MiloccoCarl T. Bergstrom @carlbergstrom.com · 04/07/20261. A bit of evolutionary biology. I'm really intrigued by a new perspective piece from Steve Frank that explores connections between how natural selection creates systems that generalize and recent work in machine learning about the surprising capabilities of massively overparameterized systems.academic.oup.comGeneralization as the great leap in evolvability: insights from machine learningAbstract. Natural selection encodes learned information in the genome. Learned solutions may be tuned specifically to past challenges, failing in altered e 9402119
Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 03/07/2026Models trained with noisy genomes extend bacterial phenotype prediction into deep time www.biorxiv.org/content/10.64898/20… 021
Reposted by Lisandro MiloccoKatie Abson @katieabson.bsky.social · 30/06/2026Our paper is out! 📣 we find that molecular measures of genetic variation do not predict heritable genetic variation across species - important implications for the application of genomic data for conservation! www.pnas.org/doi/10.1073/...pnas.orgNucleotide diversity is a poor predictor of short-term adaptive potential | PNASThe capacity to adapt is essential for a population to avoid extinction in a changing world and is recognized as a global conservation priority. Ad... 110167
Reposted by Lisandro MiloccoCraig Primmer @fishcongen.bsky.social · 29/06/2026Thanks to a couple of recent Ws on the funding front, we have 3 open postdoc positions in Helsinki, Finland in the field of salmonid fish ecological and evolutionary genomics. DL 7.8. More details in advert: jobs.helsinki.fi/job/Helsinki... 03343
Reposted by Lisandro Miloccoepithelial mechanics fan club @epimechfc.bsky.social · 14/06/2026Every 3D tissue is a map waiting to be drawn. Flatten a curved tissue, follow how it deforms, find its hidden axis, or measure its shape to explain how it moves: it's all cartography! 17018
Reposted by Lisandro MiloccoBianca Dumitrascu @bimidu.bsky.social · 12/06/2026How are two embryos alike? As we collect spatio-temporal microscopy data, we want to quantify variability in the timing of key developmental events. Alignment of multiple recordings is a core engineering challenge here and we suggest a solution; read about it: www.biorxiv.org/content/10.6...biorxiv.orgA quantitative coordinate system for developmental dynamicsQuantitative comparison of morphogenesis across individuals remains a fundamental challenge, as developing embryos vary in shape, orientation and developmental tempo. Moreover, real-time three-dimensi... 14313
Reposted by Lisandro MiloccoNobuto Takeuchi @nobuto.bsky.social · 05/06/2026Sharing our new paper, led by Dominic Devlin, now in Shuji Ishihara’s group at UTokyo. We show that 𝗺𝗼𝗿𝗽𝗵𝗼𝗴𝗲𝗻𝗲𝘁𝗶𝗰 𝗿𝗲𝗽𝗿𝗼𝗱𝘂𝗰𝗶𝗯𝗶𝗹𝗶𝘁𝘆 can evolve as a by-product of complex morphogenesis, even without direct selection for reproducibility. doi.org/10.1371/jour...doi.orgCell differentiation can underpin the reproducibility of morphogenesisAuthor summary An astounding property of multicellular animals is the reliable formation of morphological structures, such as organs and limbs. How does this reliable formation, termed reproducibility... 011
Lisandro Milocco @milocco.bsky.social · 04/06/2026Looking forward to it! Full program here! 👇 www.evodevoconference26.com/programevodevoconference26.com10th European Society for Evolutionary Developmental Biology Meeting 2026The European Society for Evolutionary Developmental Biology is delighted to welcome you to the 10th biennial meeting, to be held at the University of Glasgow from June 9th - 12th in 2026. 042
Reposted by Lisandro MiloccoNature Cell Biology @natcellbio.nature.com · 01/06/2026☕ @nicolettapetridou.bsky.social & co report a feedback loop between Nodal signaling and tissue phase transitions in zebrafish #embryos. Nodal alters adhesion, triggering tissue rigidification and reduced porosity, which limits its diffusion and speeds up Lefty expression. go.nature.com/4vgBYmogo.nature.comTissue rigidity phase transition shapes morphogen gradients - Nature Cell BiologyAutorino et al. report a feedback loop between Nodal signalling and tissue phase transitions in zebrafish embryos. Nodal alters adhesion, triggering tissue rigidification and reduced porosity, which l... 1297
Reposted by Lisandro MiloccoKevin Mitchell @wiringthebrain.bsky.social · 28/05/2026Indeterminism and the physics of open neural dynamics www.cell.com/trends-open/... - the brain is not a deterministic system 05924
Reposted by Lisandro MiloccoSimon Fisher @profsimonfisher.bsky.social · 27/05/2026A study in @nature.com shows that while complex traits are polygenic in population at large, they have distinct architecture at tails, where rare variants of large effect act as key drivers. Not a surprising finding but neat to see it demonstrated in large UK Biobank cohort across traits & methods.🧪nature.comDistinct genetic architecture in the tails of complex traits - NatureGenome-wide analyses in multiancestry and European cohorts show that in complex traits, rare alleles have disproportionately large effects at the tails of the phenotypic spectrum compared with common ... 25217
Reposted by Lisandro MiloccoAlejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 18/05/2026I am genuinely humbled by the kind words from the first readers of my book! The 📗 is fully #openaccess, made possible by the generosity of libraries worldwide and @mitpress.bsky.social's D2O program: direct.mit.edu/books/oa-mon... Please help spread the word! #booksky #philsci #philsky #histscidirect.mit.eduThe Organism-Environment Pairing: A Historical and Philosophical ReappraisalA historical and philosophical exploration of the organism-environment relationship and its role in shaping biological thought.In this first systematic boo 05015
Reposted by Lisandro MiloccoPessoaBrain @pessoabrain.bsky.social · 07/05/2026𝗠𝗮𝗷𝗼𝗿 𝗱𝗲𝗽𝗿𝗲𝘀𝘀𝗶𝗼𝗻 𝘁𝗵𝗿𝗼𝘂𝗴𝗵 𝘁𝗵𝗲 𝗹𝗲𝗻𝘀 𝗼𝗳 circuit 𝗱𝘆𝗻𝗮𝗺𝗶𝗰𝘀 Finally research is considering the functional/ anatomical complexity of the brain. It's not about regions, but how circuits function dynamically. www.cell.com/neuron/abstr... #neuroskyence 511330
Reposted by Lisandro MiloccoBerta Verd @bertaverd.bsky.social · 21/04/2026New Pre-Print Alert! Evolving initial conditions: an alternative developmental route to morphological diversity with Shannon Taylor and @jamesehammond.bsky.social www.biorxiv.org/content/10.6... 613051
Reposted by Lisandro Miloccocanaztekin.bsky.social @canaztekin.bsky.social · 10/04/2026🚨 Why can’t mammals regenerate limbs like frog tadpoles or salamanders? In our new paper in @science.org , we show that species-specific oxygen sensing acts as a gatekeeper for initiating limb regeneration 🐭🐸 🔗 www.science.org/doi/10.1126/... #EvoDevoscience.orgSpecies-specific oxygen sensing governs the initiation of vertebrate limb regenerationWhy mammals cannot regenerate limbs like amphibians do presents a long-standing puzzle in biology. To uncover the underlying differences, we compared amputation responses of embryonic mouse (Mus musculus) and Xenopus laevis tadpole limbs. Lowering ... 21270115
Reposted by Lisandro MiloccoParichy Lab | Dave Parichy @dparichy.bsky.social · 03/04/2026Zebrafish finds Nemo. New paper with our great collaborators on gap junctional communication in widely divergent species. www.nature.com/articles/s41... 23915
Reposted by Lisandro MiloccoQuentin Horta @quentinevo.bsky.social · 02/04/2026Our work as Editor's choice in @evolletters.bsky.social !✨️ Developmental biases & micro- to macroevution in the lizard skull 🦎 academic.oup.com/evlett/advan... 0108
Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 30/03/2026Impacts of genome architecture on the repeatability of polygenic adaptation www.biorxiv.org/content/10.64898/20… 062
Reposted by Lisandro MiloccoPLOS Biology @plosbiology.org · 27/03/2026Predicting the effect of a #mutation on #fitness is hard. @oliviamghosh.bsky.social @petrovadmitri.bsky.social &co use fitness effects of adaptive yeast mutants to show that underlying genotype-phenotype-fitness maps are low-dimensional but context-dependent @plosbiology.org 🧪 plos.io/4dLy2Ez 03512
Reposted by Lisandro MiloccoLisandro Milocco @milocco.bsky.social · 02/03/2026🚨 We're hiring! Postdoctoral positions in modeling of development and evolution at @stockholm-uni.bsky.social & @scilifelab.se Focus: dynamical systems, time-series, phylogenetics, dimensionality reduction 📍 Stockholm 🕒 2+1 years 🔍 Details: su.varbi.com/en/what:job/... Please share! 12219
Reposted by Lisandro MiloccoAissam Ikmi @aikmi.bsky.social · 20/03/2026Our study on shape diversity in cnidarians is now published. The final version includes extensive new data that substantially extend the original bioRxiv preprint. Congrats to everyone who contributed to this work! www.cell.com/cell/fulltex... @embl.orgcell.comDeciphering mechanical determinants of morphological evolutionA comparative analysis of cnidarian larval morphogenesis combined with active surface theory identifies a set of mesoscale mechanical modules that predict species-specific shapes. Manipulating these m... 514164
Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 17/03/2026An Empirical Bayes approach for the study of phenotypic evolution from high-dimensional data www.biorxiv.org/content/10.64898/20… 033
Reposted by Lisandro MiloccoNicholas Tolley @ntolley.bsky.social · 18/03/2026Happy to share a new preprint from my PhD thesis! “A novel framework for expanding RNNs with biophysical detail to solve cognitive tasks” 🧠💻 📝 www.biorxiv.org/content/10.6... @jonescompneurolab.bsky.social 15618
Reposted by Lisandro MiloccoPablo J. Sáez @pjsaez.bsky.social · 16/03/2026This is why we love #CalciumSignaling Look how mechanical damage triggers long range Ca2+ waves in this plant !! By @annalisabellandi.bsky.social, who is now around here ;) Full www.science.org/doi/10.1126/... @science.org #microscopy #cell #mechanobiology 🧪🔬 319860
Reposted by Lisandro MiloccoTzer Han Tan @tzerhan29.bsky.social · 15/03/2026PhD student Ouyang Xuan is going to present our work using representation learning to map developmental flow in morphological landscape: Mon Mar 16 3:30pm 'Morphogenesis' @apsdsoft.bsky.social @aps-dbio.bsky.social Check it out! #APSGlobalSummit2026 0111
Reposted by Lisandro MiloccobioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 16/03/2026Evolutionary dynamics under phenotypic uncertainty www.biorxiv.org/content/10.64898/20… 001