Hugo Talibart

GitHub - Benoitdw/warnme: Library / CLI to communicate with me Library / CLI to communicate with me. Contribute to Benoitdw/warnme development by creating an account on GitHub.

It's easy to receive an email when a job finishes on a computer cluster, but setting that up on a single machine is a little less straightforward. Thanks to my colleague Benoît I discovered you can very easily send yourself messages via a Telegram bot from Python!

github.com/Benoitdw/war...

GitHub - pola-rs/polars: Dataframes powered by a multithreaded, vectorized query engine, written in Rust Dataframes powered by a multithreaded, vectorized query engine, written in Rust - pola-rs/polars

This week I discovered the python library polars, it's like pandas but based on Rust so it's much faster. I was working with a big dataframe (around 100 million rows) and I was blown away by its speed. Highly recommend you try it!

github.com/pola-rs/polars

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale We introduce FAMSA2, an algorithm that produces high-accuracy multiple protein sequence alignments with unprecedented speed. Across structural, phylogenetic, and functional benchmarks, FAMSA2 matches ...

Interested in a tool that aligns millions of proteins in minutes with quality similar to or better than the state-of-the-art utilities? Please take a look at our FAMSA2 paper: www.biorxiv.org/content/10.1...
and GH repo: github.com/refresh-bio/...

A simple flow of gas over water may have helped kickstart life on early Earth.

Research shows how evaporation and fluid flow in a narrow channel can drive isothermal DNA replication, offering a plausible, low-temp setting for early molecular evolution.
buff.ly/ADgyeFk

Matsvei Tsishyn will also be there at poster A-063 to present our work (mostly his): StructureDCA, "Inferring Protein Mutational Landscape with Structure-Informed Direct Coupling Analysis"

#ISMBECCB2025 #3DSIG

See you tomorrow, poster B-443! #ISMBECCB2025

Evaluating Deep Learning Based Structure Prediction Methods on Antibody-Antigen Complexes Motivation: AlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without co-evolutionary signals, such as host-pathogen and a...

A paper thar took too long to finish. We show that AlphaFold3 its clearly better than AlphaFold2 (and Boltz-1 and Chai-1) to predict the structure of antibody-Antigens, but only for cases with (har to detect) similarity in the training set.

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

Graphical abstract of our VAE. The encoder inputs a SELFIES string representing a molecule and encodes into an embedding vector in a structured latent space. The decoder can decode this embedding vector into the original molecule.

Two weeks from now I'll be at ISMB 2025 in Liverpool with a poster presenting our Transformer-based small molecule VAE with a chemistry-aware latent space. In the meantime, if you're attending, you can already see it online: iscb.junolive.co/ISMB/live/ex...

Looking forward to seeing you there!

Rare ‘ambidextrous’ protein breaks rules of handedness Most proteins are left-handed, but scientists have found an ancient molecule that works in both mirror-image forms.

Most proteins are left-handed, but scientists have found an ancient molecule that works in both mirror-image forms

https://go.nature.com/4mCImRm

1/n
Looking through this. Will pull tidbits out and put them in this thread.

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.

And that's the goal of my current research: design new molecules that target some specific olfactory receptors.

And that's a challenge... more on that later! :)

Interestingly, olfactory receptors aren’t limited to the nose: they’re also expressed in various tissues where they regulate different functions (blood pressure, glucose metabolism, hair growth, even play a role in prostate cancer...)...

which makes them promising drug targets!

Illustration of the olfactory combinatorial code, by C. Trimmer, J.D. Mainland, in "Chapter 17 - The Olfactory System", 2017

Olfaction works like a combinatorial code: there are various types of olfactory receptors, each can be activated by multiple molecules, and some molecules can activate multiple receptors. The brain interprets these unique activation patterns as distinct smells.

Olfactory receptor activation mechanism. Figure from https://doctorlib.org/physiology/ganong-review-medical-physiology/13.html

Did you know smell detection relies on specialized proteins called "olfactory receptors"?

Located in olfactory neuron membranes inside the nose, they change shape when a molecule binds, triggering reactions that ultimately open ion channels, depolarize the membrane and send a signal to the brain.

Hi! I'm a little late to the party, but glad to be finally joining BlueSky! I'll be posting a little bit about the work I do as a postdoctoral researcher at ULB, also probably random fun facts I learn here and there, because biology never ceases to amaze me.