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Lisandro Milocco

@milocco.bsky.social
314 followers 260 following 21 posts

Asst. Prof. and DDLS fellow Dept. Zoology, Stockholm University and SciLifeLab 🇦🇷 -> 🇫🇮 -> 🇸🇪 Evo-devo and dynamical systems lisandromilocco.github.io

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Reposted by Lisandro Milocco
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10h
Evolutionary branching under slowly evolving constraints www.biorxiv.org/content/10.64898/20…
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Andrej Spiridonov @andrejpaleo.bsky.social · 29/09/2026
Dynamical [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
Behavior of compartments in environments selecting for different autocatalyst composition.
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Reposted by Lisandro Milocco
SMB - Society for Mathematical Biology @smbmathbiology.bsky.social · 28/09/2026
Here'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.com
Ancestral Sequences Cannot be Accurately Reconstructed via Interpolation in a Variational Autoencoder’s Latent Space - Bulletin of Mathematical Biology
Standard 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...
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Reposted by Lisandro Milocco
Pierre de Villemereuil @pdevillemereuil.bsky.social · 28/09/2026
With 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.org
Quantitative genetics of lifetime growth curves in a lizard
Abstract. Body size is an iconic trait in quantitative genetics. For species with indeterminate growth however, growth curve, a function-valued trait, is t
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epithelial mechanics fan club @epimechfc.bsky.social · 27/09/2026
Can 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.
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Reposted by Lisandro Milocco
Richard 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.org
Philosophy of Biology: The power of theory in the life sciences
Theory can help address cell and molecular biology’s major challenges, particularly those arising from large omics datasets.
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Reposted by Lisandro Milocco
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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Reposted by Lisandro Milocco
Ákos T Kovács @evolvedbiofilm.bsky.social · 19/09/2026
From 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.com
From resistance genes to resistance states and enzymatic context-dependence in antimicrobial resistance
Antimicrobial 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...
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Reposted by Lisandro Milocco
Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 11/08/2026
As 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/2608.06998
arxiv.org
Simulating is not always understanding: When model complexity obscures biology
In 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...
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Biological 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
Fig. 1
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Philippe 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.org
Noncoding transcription controls the developmental dynamics of long-range gene regulation
The 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 ...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 10/09/2026
Conserved covariance structure underlies 60 million years of morphological diversification in primates www.biorxiv.org/content/10.64898/20…
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Ben Lehner @benlehner.bsky.social · 03/08/2026
1st 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.org
Complete Mutagenesis of the Genome and Proteome of ΦX174
The 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...
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Trends 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...
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Jessica Abbott @jessicakabbott.bsky.social · 05/09/2026
Are 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.com
Senior Lecturer in Computational Biology
Lund 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
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Norbert Marwan @pucicu.de · 27/08/2026
New 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.com
Reconstruction of interpretable causal network dynamics from time series data
Reconstructing causal dynamic networks from multivariate time series is a foundational problem in complex systems science. Yet, the key scientific iss…
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Alvaro Sanchez @asanchezlab.bsky.social · 21/08/2026
New 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
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Lisandro Milocco @milocco.bsky.social · 17/08/2026
What 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...
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📑 EvoDevo Papers @evodevo-papers.bsky.social · 12/08/2026
Evolvability After Riedl onlinelibrary.wiley.com/doi/10.1002… #EvoDevo
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Fabian Fröhlich @frohlichlab.com · 05/08/2026
Mechanistic 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.org
Deep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneity
Cells 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...
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Reposted by Lisandro Milocco
Emília 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.com
Callipterus Cichlid Collecting Shell
ALT: Callipterus Cichlid Collecting Shell
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bioRxiv SysBio @biorxiv-sysbio.bsky.social · 31/07/2026
Deep Mechanistic Models reveal pathway-extrinsic drivers of mammary MAPK signalling heterogeneity www.biorxiv.org/content/10.64898/20…
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 24/07/2026
Beyond the Panglossian paradigm: adaptation, constraint, and anuran functional trait evolution. www.biorxiv.org/content/10.64898/20…
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Paul Francois @pfrancois.bsky.social · 14/07/2026
New 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.
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Carl T. Bergstrom @carlbergstrom.com · 04/07/2026
1. 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.com
Generalization as the great leap in evolvability: insights from machine learning
Abstract. Natural selection encodes learned information in the genome. Learned solutions may be tuned specifically to past challenges, failing in altered e
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Reposted by Lisandro Milocco
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 03/07/2026
Models trained with noisy genomes extend bacterial phenotype prediction into deep time www.biorxiv.org/content/10.64898/20…
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Katie Abson @katieabson.bsky.social · 30/06/2026
Our 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.org
Nucleotide diversity is a poor predictor of short-term adaptive potential | PNAS
The capacity to adapt is essential for a population to avoid extinction in a changing world and is recognized as a global conservation priority. Ad...
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Craig Primmer @fishcongen.bsky.social · 29/06/2026
Thanks 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...
Basic details of the amazing post doc positions on offer with amazing image of a large Teno River salmon in background
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epithelial mechanics fan club @epimechfc.bsky.social · 14/06/2026
Every 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!
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Bianca Dumitrascu @bimidu.bsky.social · 12/06/2026
How 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.org
A quantitative coordinate system for developmental dynamics
Quantitative comparison of morphogenesis across individuals remains a fundamental challenge, as developing embryos vary in shape, orientation and developmental tempo. Moreover, real-time three-dimensi...
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Reposted by Lisandro Milocco
Nobuto Takeuchi @nobuto.bsky.social · 05/06/2026
Sharing 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.org
Cell differentiation can underpin the reproducibility of morphogenesis
Author 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...
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Lisandro Milocco @milocco.bsky.social · 04/06/2026
Looking forward to it! Full program here! 👇 www.evodevoconference26.com/program
evodevoconference26.com
10th European Society for Evolutionary Developmental Biology Meeting 2026
The 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.
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Nature 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/4vgBYmo
go.nature.com
Tissue rigidity phase transition shapes morphogen gradients - Nature Cell Biology
Autorino 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...
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Kevin Mitchell @wiringthebrain.bsky.social · 28/05/2026
Indeterminism and the physics of open neural dynamics www.cell.com/trends-open/... - the brain is not a deterministic system
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Simon Fisher @profsimonfisher.bsky.social · 27/05/2026
A 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.com
Distinct genetic architecture in the tails of complex traits - Nature
Genome-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 ...
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Alejandro Fábregas-Tejeda @alejandrofabregastejeda.com · 18/05/2026
I 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 #histsci
direct.mit.edu
The Organism-Environment Pairing: A Historical and Philosophical Reappraisal
A historical and philosophical exploration of the organism-environment relationship and its role in shaping biological thought.In this first systematic boo
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PessoaBrain @pessoabrain.bsky.social · 07/05/2026
𝗠𝗮𝗷𝗼𝗿 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
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Berta Verd @bertaverd.bsky.social · 21/04/2026
New 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...
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canaztekin.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/... #EvoDevo
science.org
Species-specific oxygen sensing governs the initiation of vertebrate limb regeneration
Why 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 ...
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Parichy Lab | Dave Parichy @dparichy.bsky.social · 03/04/2026
Zebrafish finds Nemo. New paper with our great collaborators on gap junctional communication in widely divergent species. www.nature.com/articles/s41...
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Quentin Horta @quentinevo.bsky.social · 02/04/2026
Our work as Editor's choice in @evolletters.bsky.social !✨️ Developmental biases & micro- to macroevution in the lizard skull 🦎 academic.oup.com/evlett/advan...
Lizard head on the journal
cover
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 30/03/2026
Impacts of genome architecture on the repeatability of polygenic adaptation www.biorxiv.org/content/10.64898/20…
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PLOS Biology @plosbiology.org · 27/03/2026
Predicting 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
Two models for the nature of pleiotropy in adaptation. Left: Schematic of the environmental structure in this study. Environments can be mapped onto a multidimensional environment space characterized by chemical and physical compositions. The large green circle represents an environment where adaptive mutants evolved, and the large pink circle is a distant environment. Around each base, a set of identical environmental perturbations (arrows) is applied, generating clusters of similar environments around distinct base environments. Top right: Schematic of fitnotype map for adaptive mutants near their home base environment. By measuring fitness in each of the green environments, one can infer how many fitnotypes matter for this set of mutants in their home environment. Here, only four of the possible 8 fitnotypes matter. Bottom right: When the mutants are moved to the distant base environment, and their fitness is measured in all pink environments (base and perturbations), there are two possibilities. Either more fitnotypes become important and the space appears higher-dimensional (left, pleiotropic expansion), or the set of fitnotypes that matters remains low-dimensional, but shifts (right, pleiotropic shift).
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Lisandro 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!
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Aissam Ikmi @aikmi.bsky.social · 20/03/2026
Our 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.org
cell.com
Deciphering mechanical determinants of morphological evolution
A 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...
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 17/03/2026
An Empirical Bayes approach for the study of phenotypic evolution from high-dimensional data www.biorxiv.org/content/10.64898/20…
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Nicholas Tolley @ntolley.bsky.social · 18/03/2026
Happy 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
Multipanel figure illustrating the key components of the paper: 1) biophysical reservoir computing where a network of biophysically detailed excitatory and inhibitory neurons are randomly connected, receive a brief input, and produce a sustained spiking pattern in response, 2) an illustration of the task the biophysical reservoir computer is trained on: a simplified working memory task where the network must produce distinct fixed point attractors in response to different inputs.
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Pablo J. Sáez @pjsaez.bsky.social · 16/03/2026
This 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 🧪🔬
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Tzer Han Tan @tzerhan29.bsky.social · 15/03/2026
PhD 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
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bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 16/03/2026
Evolutionary dynamics under phenotypic uncertainty www.biorxiv.org/content/10.64898/20…
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