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Antoine Taly

@ataly.bsky.social

Researcher at CNRS interested in the biophysics of proteins. Modelling membrane proteins and their interaction with ligands. Working in Paris.

197 Posts746 Follower591 Folgt
Elisa Frezza@elisafrezza.bsky.social · last wk.

Happy to share our Application Note on RNA and chemical probing. MARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing Data pubs.acs.org/jcisd8/artic...

MARS-RNA: An Automated Pipeline for Correlating RNA Molecular Dynamics Trajectories with Chemical Probing Data

Abstract. Ribonucleic acid (RNA) molecules fold into complex, highly dynamic three-dimensional conformational structures that govern their biological activ

pubs.acs.org

Janani Durairaj (Jay)@ninjani.bsky.social · 2w ago

The PhD and Postdoc application links are now live! Come join me at UNIL to work on deep learning for protein structure, interactions & design. pickybinders.org#open-positions

Career Opportunities: PhD student position in deep learning for enzyme structure & catalysis (22980)

career5.successfactors.eu

Janani Durairaj (Jay)@ninjani.bsky.social · last mo.

Some exciting news: I'm joining the University of Lausanne @unil.bsky.social @dbc-unil.bsky.social as an Assistant Professor next month 🎉 My group will work on context-aware deep learning for protein structure, interaction & design. Postdoc and PhD openings coming soon - keep an eye out!

compare, predict, design
Iris van Rooij 💭@irisvanrooij.bsky.social · 4w ago

If you read closely, it is clear that @chess.com indeed was referring to the game tree complexity, and not the positions, since they say "possible chess games". I assume M*sk used and LLM to, which ofc is unable to get pragmatics.

Iris van Rooij 💭@irisvanrooij.bsky.social · 4w ago

Possibly @chess.com meant to refer to game tree complexity (~10^120) not just # legal positions (~10^44), compared to the number of estimated atoms in universe (~10^80). Btw, even though ~10^44 << ~10^80 it's mindbogglingly large. Cf. number of seconds that passed since the Big Bang: ~10^27. 💥🧵

Needhi Bhalla 💅🏽@needhibhalla.bsky.social · last mo.

“Using research as an opportunity for learning-by-doing may produce seeming ‘inefficiencies,’ but that’s a feature, not a bug…the process of education is necessarily a productive struggle, and that the most important product of their education is not a GPA or a diploma but themselves“

Josh Eyler@josheyler.bsky.social · last mo.

Major kudos to MIT, who just put out a report about AI on their campus that lucidly explains the threat posed by AI to cognition and the student experience, while at the same time prioritizes learning, students, and the value of education. 1/x aiandeducation.mit.edu/report/

Antoine Taly@ataly.bsky.social · last mo.

🚨 🚨New preprint from the group 🚨🚨 "Can SMILES be fragmented into a concatenable ordered sequence of retrosynthetically interesting string block ? " E Reboul shows you can split SMILES into fragments that follow retrosynthetic analysis! with H Prabakaran J Waldispühl www.biorxiv.org/content/10.6...

Can SMILES be fragmented into a concatenable ordered sequence of retrosynthetically interesting string block ?

Molecules generated by deep learning models are often difficult to synthesize. Their synthetic accessibility can be improved with automated retrosynthetic analysis, which allows for identifying syntho...

biorxiv.org

Jessica Andreani@jessicaandreani.bsky.social · last mo.

🚨📣 Hiring a postdoc in bioinformatics 🧬🧑‍💻 Join our team at @i2bcparissaclay.bsky.social to explore biomolecular interactions and improve protein function prediction in bacteriophages! 📍 Gif-sur-Yvette, France ⏳ 13 months (+ possible extension) 📅 Apply here: emploi.cnrs.fr/Offres/CDD/U...

Portail Emploi CNRS - Job offer - Post-doctoral researcher in bioinformatics (M/F): exploring biomolecular interactions for bacteriophage protein function prediction

emploi.cnrs.fr

Chenxin Li, PhD@chenxinli2.bsky.social · 2mo ago

Arabidopsis Col-0 is not one thing "Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s". #PlantScience From: www.biorxiv.org/content/10.6...

Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s

The model plant Arabidopsis thaliana has been a workhorse of plant biology since the 1950s, when the Columbia-0 (Col-0) accession was widely adopted by the research community as a reference genotype. ...

biorxiv.org

vincentholst.bsky.social@vincentholst.bsky.social · 2mo ago

As promised, we now share some details why it took 32 months to get this Matters Arising published, and, since many asked, share some comments on the reply to our critique. All details can be found in this small FAQ vincentholst.github.io/the_curious_.... Below is a summary 🧵

The Curious Case of the Declining Disruption’s Disappearance

vincentholst.github.io

vincentholst.bsky.social@vincentholst.bsky.social · 2mo ago

In 2023, @nature.com published 'Papers and patents are becoming less disruptive over time', receiving world-wide media attention. Our Matters Arising, published after a 32 month delay (more on that soon), shows that the reported decline can largely be attributed to dataset artefacts. 🧵

The average CD_5 index per year for Web of Science. The original Park et al. decline (top curve) becomes essentially flat (bottom curve) when removing papers with CD_5=1. Those papers largely correspond to dataset artefacts.