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Reposted by Lisandro Milocco

bioRxiv SysBio @biorxiv-sysbio.bsky.social · 8d

Interpretable gene network inference with nonlinear causality https://www.biorxiv.org/content/10.1101/2025.09.28.678927v1

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Reposted by Lisandro Milocco

Jonathan Basile @jonothingeb.bsky.social · 23d

I'm excited to share with you all a conference I'm planning Oct. 10-12: Dialectical Biology Today: Legacies of Richard Lewontin.

It will be hybrid in Toronto and on zoom, so please join us however you can! Register for zoom link here: ihpst.utoronto.ca/events/diale...

Conference title: Dialectical Biology Today: Legacies of Richard Lewontin, and image of Lewontin in Black and White with intense expression in front of a chalkboard holding up a fist,
When and Where
Friday, October 10, 2025 11:30 am to Sunday, October 12, 2025 2:00 pm
Music Room (218)
Goldring Student Centre
150 Charles St W, Toronto, ON M5S 1K5 | and online via Zoom

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Reposted by Lisandro Milocco

Chris J Dallmann @chrisjdallmann.bsky.social · 21d

Now out in @nature.com: Our study discovering a neural circuit in Drosophila that predictively inhibits proprioceptor axons during voluntary leg movements, such as walking and grooming. www.nature.com/articles/s41...

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Lisandro Milocco @milocco.bsky.social · 21d

⏳ Only 2 weeks left to apply to our PhD in evolutionary prediction!

Lisandro Milocco @milocco.bsky.social · Aug 25

🚨 We're hiring!
PhD position in Evolutionary Systems Biology at Stockholm University & SciLifeLab

🎓 Focus: evolution, development, computational & mathematical modeling, prediction
📍 Stockholm, Sweden
🕒 4 years, fully-funded
🔍 Details: su.varbi.com/en/what:job/...

Please share!

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Ryan Savill @cryaaa.bsky.social · 26d

(1/14) I’m happy and proud to introduce: SpinePy – a framework to detect the "spine" of gastruloids and measure biological and physical signals in a local dynamic 3D coordinate system. www.biorxiv.org/content/10.1...

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Reposted by Lisandro Milocco

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 26d

Parallel but distinct adaptive routes in the budding and fission yeasts after 10,000 generations of experimental evolution https://www.biorxiv.org/content/10.1101/2025.09.11.675703v1

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Reposted by Lisandro Milocco

Guim Aguadé-Gorgorió @guimaguade.bsky.social · 26d

A central finding is that, even if we could measure pairwise interactions up to a certain precision, strong indirect effects can make our efforts useless: at high collectivity, pairwise interactions no longer inform about community coexistence
www.biorxiv.org/content/10.1...

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Reposted by Lisandro Milocco

Ákos T Kovács @evolvedbiofilm.bsky.social · Sep 4

Mutations in the circadian cycle drive adaptive plasticity in cyanobacteria

in #PNAS from Raúl Fernández-López
with @pabnik.bsky.social @amazeld.bsky.social

www.pnas.org/doi/10.1073/...

PNAS

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

www.pnas.org

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Reposted by Lisandro Milocco

bioRxiv SysBio @biorxiv-sysbio.bsky.social · Aug 31

DeepAtlas: a tool for effective manifold learning https://www.biorxiv.org/content/10.1101/2025.08.26.672474v1

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Reposted by Lisandro Milocco

Ricard Solé @ricardsole.bsky.social · Aug 27

Can a virus help uncover Turing patterns in nature? In this @commsbio.nature.com paper, researchers show how the tulip breaking virus triggers the expression of a pigment that can display a broad range of (observable) stripe patterns @philipcball.bsky.social
biorxiv.org/content/10.1...

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Reposted by Lisandro Milocco

Fabien Lafuma @paleofab.bsky.social · Aug 1

🚨New PhD research published in PNAS!🚨

Combining fossils and lab experiments, we found that simple changes in tooth #development explain 6 million years of molar #evolution in #voles 🐭🦷

Shoutout to my coauthors @cnrs.fr @helsinki.fi @gtk-fi.bsky.social!
www.pnas.org/doi/10.1073/... #FossilFriday

Six million years of vole dental evolution shaped by tooth development | PNAS

Morphological change occurs over macroevolutionary timescales under the action of natural selection and genetic drift combined with developmental p...

www.pnas.org

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Lisandro Milocco @milocco.bsky.social · Aug 26

Gracias Fabio!!

Lisandro Milocco @milocco.bsky.social · Aug 25

🚨 We're hiring!
PhD position in Evolutionary Systems Biology at Stockholm University & SciLifeLab

🎓 Focus: evolution, development, computational & mathematical modeling, prediction
📍 Stockholm, Sweden
🕒 4 years, fully-funded
🔍 Details: su.varbi.com/en/what:job/...

Please share!

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Reposted by Lisandro Milocco

Gavin Woodruff @weirdworms.bsky.social · Aug 23

!

Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades

www.pnas.org/doi/10.1073/...

Evolution of developmental bias explains divergent patterns of phenotypic evolution in two nematode clades | PNAS

Rates of phenotypic evolution vary across traits, and these evolutionary patterns themselves evolve. Understanding how development contributes to s...

www.pnas.org

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Reposted by Lisandro Milocco

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Aug 21

Developmental bias explains the evolutionary trend towards simple leaf shapes https://www.biorxiv.org/content/10.1101/2025.08.17.670617v1

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Reposted by Lisandro Milocco

Jukka-Pekka Verta @jpverta.bsky.social · Aug 21

How do regulatory genes control alternative life histories? We have an open PhD position to answer this question using functional genomics in Atlantic salmon.

Apply by October 15th through www.jobbnorge.no/en/available...

Please share widely! 🧬🦑🖥️

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Reposted by Lisandro Milocco

Ricard Solé @ricardsole.bsky.social · Aug 17

What is emergence? This is one of the most central ingredients of complexity, and a challenging one to formalize. Here's a paper by @seanmcarroll.bsky.social & Achyth Parola that attempts to classify different forms of emergence. @manlius.bsky.social @sfiscience.bsky.social arxiv.org/pdf/2410.15468

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Reposted by Lisandro Milocco

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Aug 17

Adaptive radiation along ecological and morphological lines of least resistance in Cyprinodon pupfishes https://www.biorxiv.org/content/10.1101/2025.08.13.670168v1

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Reposted by Lisandro Milocco

Robin Pranter @robinpranter.bsky.social · Aug 15

Join us on the 26/9 in Lund for a symposium about #evolution #stemcells #development #EvoDevo and #plasticity

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Reposted by Lisandro Milocco

James Briscoe @jamesbriscoe.bsky.social · Aug 14

Latest on Waddington Landscapes: Computational methods to fit dynamical landscapes directly to single cell data

Applied to neural tube patterning shows morphogen-signalling landscapes can be linearly interpolated

Connects interpretable landscape models with data

www.biorxiv.org/content/10.1...

Reconstructing Waddington's Landscape from Data

The development of a zygote into a functional organism requires that this single progenitor cell gives rise to numerous distinct cell types. Attempts to exhaustively tabulate the interactions within d...

www.biorxiv.org

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Reposted by Lisandro Milocco

Jordan S. Martin @jsmartin.bsky.social · Aug 11

My first solo author paper is now available in early view at Methods in Ecology and Evolution! I develop a covariance reaction norm (CRN) model for estimating continuous, multivariate, and nonlinear environmental effects on G and P matrices.

besjournals.onlinelibrary.wiley.com/doi/10.1111/...

Covariance reaction norms: A flexible method for estimating complex environmental effects on trait (co)variances

Estimating quantitative genetic and phenotypic (co)variances is crucial for investigating evolutionary ecological phenomena such as developmental integration, life history trade-offs and niche spe...

besjournals.onlinelibrary.wiley.com

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José Cerca @naturalselection.bsky.social · Aug 10

*PhD position* 🦉

Would you like to do a PhD with Indo-Pacific birds and evolutionary genomics? Join us in Stockholm:

05 September 2025, 23:59

PhD student in Evolution of Indo-Pacific birds
recruit.visma.com/spa/public/a...

PhD student in Evolution of Indo-Pacific birds

The Department of Bioinformatics and Genetics is offering a four-year PhD position focused on analyzing population-level genomic data from museum bird samples. The project will employ cutting-edge gen...

recruit.visma.com

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Manuel Kleiner @manuelkleiner.bsky.social · Aug 7

I am really excited to see this article on basic experimental design principles published. Definitely will be mandatory reading for incoming graduate students in my lab. Maggie Wagner who led this article did an amazing job with the illustrations of basic principles www.nature.com/articles/s41...

How thoughtful experimental design can empower biologists in the omics era - Nature Communications

Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

www.nature.com

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Reposted by Lisandro Milocco

bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · Aug 8

Constrained variation in the internal architecture of avian wing bones https://www.biorxiv.org/content/10.1101/2025.08.07.669070v1

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Reposted by Lisandro Milocco

Constantin Ahlmann-Eltze @const-ae.bsky.social · Aug 4

Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉

www.nature.com/articles/s41...

We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!

🧵

Beeswarm plot of the prediction error across different methods of double perturbations showing that all methods (scGPT, scFoundation, UCE, scBERT, Geneformer, GEARS, and CPA) perform worse than the additive baseline.

Line plot of the true positive rate against the false discovery proportion showing that none of the methods is better at finding non additive interactions than simply predicting no change.

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