Introducing highly experimental localfold.org Building on @martinsteinegger.bsky.social af2 webgpu port, @milot.bsky.social optimizations & jax ports of af3-like models by @marielle.bsky.social, Choonghwan Lee, Julia Buhmann. WARNING: runs directly on your 💻, may drain 🪫 & eat data📱 & overheat 🔥💻

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 3w ago

Run AlphaFold2 locally in your browser via WebGPU, no installation needed, it's just a static webpage using your own GPU or CPU. Short proteins run in seconds. Larger ones are still slow: a 291-aa protein takes ~7 minutes on my M4 Pro. ❗It's just a PoC. 🌐 martin-steinegger.github.io/alphafold2-w...

www.biorxiv.org/content/10.6... Such important work. Systematic comparison of ATAC-seq, MNase-seq, ChIP-exo/seq reveals a special preference of Tn5 for chromatin remodeler/regulator bound chromatin.

ATAC-seq and MNase-seq Detect Distinct Modes of Chromatin Accessibility

Chromatin accessibility shapes the ability of transcription factors (TFs) and the transcriptional machinery to engage genomic DNA and therefore plays a central role in gene regulation. Two widely used...

biorxiv.org

Denatured ! 😂

Sergey Ovchinnikov@sokrypton.org · 3d ago

Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)

👋

CNRS Chimie@cnrschimie.bsky.social · 2d ago

📢 #Annonce CNRS Chimie arrive sur Bluesky ! 🧪 L’un des dix instituts du @cnrs.fr, CNRS Chimie anime et coordonne la recherche en chimie en s’appuyant sur près de 14 000 personnes, 150 laboratoires et une cinquantaine de partenaires industriels. #Chimie #CNRS #Fierd’êtrechimiste

😭 #RIP

La Voix du Nord@lavoixdunord.fr · 2d ago

Elle est décédée d’un cancer à l’âge de 68 ans ➡️ https://l.lavoixdunord.fr/oFOR

I'm trying, as best I can, to keep up with the literature on my favorite topic: interactions between TFs and Mediator subunits. It's often tedious & I must have missed some papers covering 25y. An AI did it for me in 2 minutes. A few things to check, but it really makes a difference & saves me time

paging @marnieblewitt.bsky.social @heardlab.bsky.social @heard65.bsky.social 🫣

Joy Jeongyoon Choi@joyjoychoi.bsky.social · 3d ago

Excited to share our new preprint on in situ chromatin structure of the inactive X chromosome in differentiated female mouse embryonic stem cells. www.biorxiv.org/content/10.6... 🧵1/8

It's just awesome ! I'm totally rediscovering my favorite protein.

Martin Steinegger 🇺🇦@martinsteinegger.bsky.social · 4d ago

Fold Spacer lets you fly through protein structures (Weekend project #2). It’s my first game: I originally set out to build a racer with structures as the tracks, but was a little too crazy. So it became this instead. You can upload your own structures. 🌐 martin-steinegger.github.io/Fold-Spacer/

AtlasFold: Protein structure prediction with metagenomic-scale language models https://www.biorxiv.org/content/10.64898/2026.09.04.749352v1

AlphaFold can now predict protein complexes at unprecedented scale. But once we have a predicted complex, the core question of how much we should trust the interface remains. Existing confidence scores are useful, but their meaning is not always obvious. #alphafold

My lab at the Center for Gene Expression (CGEN), University of Copenhagen is looking for a motivated Postdoc interested in cohesin biology, 3D chromatin, and super-resolution microscopy. 📩 Please email your CV and letter of intent to fena.ochs(at)sund.ku.dk.

🧬🔬 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... 🧵👇

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 ...

science.org

www.nature.com/articles/s41... “By mining millions of AlphaFold2 models, we identify two human families of ‘superdark’ seven-transmembrane proteins—TM184 and PRRT—with structural homology to G-protein-coupled receptors (GPCRs).”

TM184C is a GPCR-like regulator of intercellular exchange and autophagy - Nature

TM184C—an ancient G-protein-coupled receptor-like superdark protein involved in regulation of autophagy, intercellular connectivity and material exchange—underscores the promise of exploring the under...

nature.com

We are thrilled to share that our GPN-Star manuscript is now published and freely available: doi.org/10.1038/s415... (1/n)

Predicting genome-wide functional constraints with GPN-Star - Nature

GPN-Star, a genomic language model with a phylogeny-aware architecture for whole-genome alignment data, is shown to be a scalable and flexible tool for genetic variant effect prediction across species...

doi.org

la maternelle dès 1 an, l'apprentissage à 14 ans #makesense

💯 active learning !

Julia Sero@cellmorphosero.bsky.social · last wk.

Right?!?! This drives me crazy. New predictions have to bw tested, and new models have to be updated with *actual data*. There's no way around doing the work.

👀 #alphagenome deepmind.google/blog/alphage...

We are hiring! Start at a #MaxPlanckInstitute with your own independent Max Planck Research Group. This position is equivalent to a W2 Professorship at a German university, or Associate Professor internationally. 🔗Apply until October 14th! www.mpg.de/career/max-p... #ScienceCareer #MPRG #TenureTrack

Good morning

PIC-Med SWI/SNF 🤯 #CryoEM

Cell - a Cell Press journal@cp-cell.bsky.social · last wk.

Now online! Structural basis of a SWI/SNF-associated transcription pre-initiation complex

⚡Preprint alert⚡ So proud of @amohamed98.bsky.social! Abdallah determined the cryo-EM structure of BRD4 bound to the kinase P-TEFb, defining the molecular basis of this key transcription interaction — and revealing that BRD4 and AFF4 binding are mutually exclusive to P-TEFb. Lots more inside 👇

Abdallah Mohamed@amohamed98.bsky.social · last wk.

New preprint: in the last bit of my graduate work in the @voslab.org, we describe the mechanism for how BRD4 engages with P-TEFb in the context of regulating early RNA Pol II elongation. Read more here: www.biorxiv.org/content/10.6...

It was great working with students Kun and Ryan and @hannahlong.bsky.social, combing the literature to try and find examples of bona fide disease-causing variants in non-coding elements - promoters, enhancers and silencers. www.nature.com/articles/s41...

Mechanisms underlying disease-causing variants in promoters and enhancers - Nature Genetics

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

nature.com

#alphafold

Elmo Surrounded by Intense Fire

ALT: Elmo Surrounded by Intense Fire

static.klipy.com

Magnus Bauer@kinasekid.bsky.social · 2w ago

AlphaFold Server’s ligand menu just got a lot bigger and I almost missed it! You can now add any ligand from the wwPDB Chemical Component Dictionary. Just enter its CCD code 🥳

New preprint from our lab: PathFold, an AI framework that predicts protein-folding pathways directly from amino acid sequences. Beyond static str prediction, PathFold models intermediate states and the sequence of events along the folding pathway. www.biorxiv.org/content/10.6...

J'ai Mistral AI Emmy (et le CNRS) qui me propose Pubmed comme unique extension vs Claude Science AI déjà connecté à plus de 60 bases de données scientifiques et un paquet de plugin (chembl, biorxiv, pubmed, etc...) du coup, je ne sais vraiment pas quel AI utiliser 😏

A triptych of reviews on the transcription cycle @natrevmcb.nature.com 1️⃣ Initiation Chen & Xu 2️⃣ Elongation @camimoso.bsky.social @isaacfianu.bsky.social @adelmanlab.bsky.social 3️⃣ Termination Song et al. www.nature.com/articles/s41... www.nature.com/articles/s41... www.nature.com/articles/s41...

Big review by Xizi Chen & Yanhui Xu in @natrevmcb.nature.com The molecular basis of transcription initiation by RNA polymerase II www.nature.com/articles/s41...

The molecular basis of transcription initiation by RNA polymerase II - Nature Reviews Molecular Cell Biology

Recent technological breakthroughs have transformed our understanding of how transcription initiation in eukaryotes is regulated. This Review discusses the dynamics and roles of initiation-relevant pr...

nature.com

Effet matilda, invisibilisation ou mentrification, je connaissais Je découvre aujourd'hui le mot cryptogynie #womeninstem #womeninscience olivia.science/cryptogyny/ fr.wikipedia.org/wiki/Effacem...

Cryptogyny

On the systematic obfuscation of women's contributions.

olivia.science

and why not 😋☕ www.nature.com/articles/s41...

Direct electrochemical appraisal of black coffee quality using cyclic voltammetry - Nature Communications

Coffee flavor is primarily determined by the bean roast color and concentration of the beverage. Here, the authors show that both of these characteristics are reflected in the coffee’s cyclic voltammo...

nature.com

wait, wait, what ????? protein-coding chimeric mRNAs 🤯 www.nature.com/articles/s41...

Functional chimeric mRNAs encode proteins in mammalian immunity - Nature

Inflammation induces interchromosomal DNA interactions that bring parent genes into close proximity, facilitating the formation of chimeric mRNAs that encode physiologically relevant, functional prote...

nature.com