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machine.learning.bio
🏳️‍🌈 NVIDIA & Duke. Was Allianz, VantAI, TUM. BioCS+ML dude. Lab page: https://machine.learning.bio GScholar: https://scholar.google.com/citations?user=4q0fNGAAAAAJ
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With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp

submitted 16 days ago • 1 comment

The final program is now online for the 5th Virtual @chembiotalks.bsky.social: web.cvent.com/event/60e9f3... Looking forward to talks by Sarah O'Connor, Chengqi Yi, @machine.learning.bio, @cathleenzeymer.bsky.social, @kellychibale.bsky.social, Jennifer Prescher and @craigmcrews.bsky.social.

submitted 21 days ago • 0 comments

@michael-heinzinger.bsky.social and I are seeking talented postdocs to support for the Marie Skłodowska-Curie Fellowship! Join our international AI+biology team, collaborate on protein design, and access top labs in the US & EU. Interested? Apply by July 15! Details: machine.learning.bio/news/msca

submitted 27 days ago • 0 comments

Save the date for the Helmholtz Munich AI for Health Symposium 2025, devoted to the topic of Generative AI in Molecule Discovery! July 4, 2025 Helmholtz Munich Campus in Neuherberg, Germany What now? Register and submit abstracts (deadline May 2, 2025!) events.hifis.net/event/2015/r...

submitted 85 days ago • 1 comment

📢📢 "Proteina: Scaling Flow-based Protein Structure Generative Models" #ICLR2025 (Oral Presentation) 🔥 Project page: research.nvidia.com/labs/genair/... 📜 Paper: arxiv.org/abs/2503.00710 🛠️ Code and weights: github.com/NVIDIA-Digit... 🧵Details in thread... (1/n)

submitted 118 days ago • 1 comment

Big time

submitted 170 days ago • 0 comments

A DNA language model based on multispecies alignment predicts the effects of genome-wide variants | Nature Biotechnology www.nature.com/articles/s41...

submitted 178 days ago • 0 comments

Two major life updates: - I'm moving to Senior Applied Research Scientist in Digital Biology at NVIDIA (Jan '25) - I'm starting a new lab at Duke as Visiting Assistant Prof (early '25) Both roles focus on tackling hard problems in biological machine learning through collaborative research. Long 🧵

submitted 189 days ago • 16 comments

After a busy CASP/CAPRI year we resume our rolling CAPRI rounds, announcing the 1st target of 2025. It consists of an antibody-glycan complex. The glycan is heptyl α-D-mannopyranoside. Registration for this target is now open. pdbe.org/capri

submitted 194 days ago • 0 comments

We've a postdoc opening for our lab at the Broad: Cambridge MA! Must have experience in toxicology + data science Work on the wonderful OASIS dataset we are producing... Cell Painting, transcriptomics, proteomics in various liver cell and tissue models! broad.io/mlcbpostdoc

submitted 194 days ago • 1 comment

CDC just confirmed the first severe case of #H5N1 in the US in a patient in Louisiana. This virus seems to be the same genotype D1.1 that is spreading in birds at the moment (so not the cattle genotype B3.13) that severely sickened the teenager in Canada.

submitted 194 days ago • 3 comments

Protein language models excel at generating functional yet remarkably diverse artificial sequences. They however fail to naturally sample rare datapoints, like very high activities. In our new preprint, we show that RL can solve this without the need for additional data: arxiv.org/abs/2412.12979

submitted 194 days ago • 1 comment

Starting the new BSC IA factory. Financed by Europe, Spanish & Catalan governments + contributions from Portugal, Turkey, Romania New HPC and AI resources at the service of companies (hospitals included) With Juan Cruz Sec Estado Núria Montserrat Consellera Mateo Valero Dir @bsc-cns.bsky.social

submitted 202 days ago • 0 comments

We trained a model to co-generate protein sequence and structure by working in the ESMFold latent space, which encodes both. PLAID only requires sequences for training but generates all-atom structures! Really proud of @amyxlu.bsky.social 's effort leading this project end-to-end!

submitted 203 days ago • 2 comments

AF3 BEST METHOD followed by cluspro but also some conversion errors

submitted 209 days ago • 2 comments

Assessors’ conclusions of the 3D category (individual protein chains) of #CASP16 🧪

submitted 211 days ago • 0 comments

NVIDIA people working in digital biology product, research and sci comm starter pack 🦋🧪✨ go.bsky.app/GZJuvs2

submitted 211 days ago • 3 comments

submitted 212 days ago • 1 comment

#CASP16 results are in! Template-based VFold seems to be lead method for nucleic acid structure prediction! AlphaFold2 and 3 still seem to be best methods for protein monomer and complex prediction.

submitted 212 days ago • 2 comments

#CASP16 program is posted (so you can guess the "winners". Congratulations to Yang and Kihara who seems to have done well in RNA+Proteins. Also congratulations to AF3-server (i.e. me) who was selected to talk (i.e. most people did worse than the server). predictioncenter.org/casp16/doc/C... .

submitted 215 days ago • 2 comments

Chai-1, the open source AF3 clone, is now available with an Apache 2 license github.com/chaidiscover...

submitted 215 days ago • 0 comments

Wow! 🤩 This may be the most carefully documented dataset on @polarishq.bsky.social. Great work by @roman-bushuiev.bsky.social! Do I have any #MassSpec researchers in my 🦋 network yet? I would love to hear what you think! github.com/polaris-hub/... #mass #spectrometry #dataset #benchmark

submitted 216 days ago • 2 comments

MMseqs2 Release 16 Highlights: GPU-accelerated search📄, ORF or new 6-frame translated search modes, contig taxonomy always keeps the longest ORF, bug fixes (reduced memory and higher sensitivity) and relicensed as MIT 📄 biorxiv.org/content/10.1... 💾 mmseqs.com and 🐍Bioconda 🖥️🧬🧶

submitted 216 days ago • 0 comments