🚨 New Assistant Professor Position 🚨 Come join the CPBM at Durham University! If you are interested in running a lab in AI-based biomolecular design and bionanotechnology please get in touch and apply! tinyurl.com/skwr65ua @cpbm-heddlelab.bsky.social @durham-university.bsky.social

Excited to share work with Zhidian Zhang, @milot.bsky.social, @martinsteinegger.bsky.social, and @sokrypton.org biorxiv.org/content/10.1... TLDR: We introduce MSA Pairformer, a 111M parameter protein language model that challenges the scaling paradigm in self-supervised protein language modeling🧵

Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!

I am super excited to announce that I will be starting my lab at the Department of Pharmacology of the University of Zurich in Switzerland next year!

Our paper on: A coarse-grained model for simulations of phosphorylated disordered proteins (aka parameters for phospho-serine and -threonine for CALVADOS) is now published in Biophysical Journal authors.elsevier.com/a/1lTcE1SPTB... @asrauh.bsky.social @giuliotesei.bsky.social & Gustav Hedemark

Protein structure alignment significance is often exaggerated https://www.biorxiv.org/content/10.1101/2025.07.17.665375v1

A few years ago, one could only dream of doing this. It so exciting seeing this work from the @adamrbentham.bsky.social lab. Of course, I am biased by the rice NLR pair and the Magnaporthe effector they chose 😁😁 #2025ISMPMI

AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues https://www.biorxiv.org/content/10.1101/2025.07.11.664327v1

Travelling to Köln for Heath's first MPMI! #2025ISMPMI

Thrilled to share our latest preprint! This work started during my PhD and was finished together with @jmadhuprakash.bsky.social. We found a Phytophthora infestans L-shaped effector that bridges a host TOL protein to activated NLRs to suppress immunity! www.biorxiv.org/content/10.1... 1/15

Ahn Lab is going to MPMI! #2025ISMPMI Hayden Burdett and myself will be attending the MPMI conference in Cologne ⛪ Check out poster P-073 for paired NLR biology, and let's chat about paired NLRs and more!🌱 See you in Cologne 😀 @instmolplantsci.bsky.social

Van der Weg et al. present TopEC, a 3D graph neural network for enzyme function classification. It integrates local structural details and achieves an F-score of 0.72 over 800 classes, outperforming conventional methods on both experimental and predicted structures www.nature.com/articles/s41...

Our new review in @theplantjournal.bsky.social on synthetic gene circuits is out! I am super proud of this. I hope that it acts as a useful resource for people new to gene circuits. The switch-liker's guide to plant synthetic gene circuits onlinelibrary.wiley.com/doi/10.1111/...

Pls repost 🚨I'm looking for someone excited about #proteindesign and #synbio to join my lab @Durham_Uni at the CPBM @cpbm-heddlelab.bsky.social to undertake a PhD using #synthetic knottins as novel #bioinsecticides. If you're interested please get in touch and check out the advert below 👇

📜 Plant pathogenic fungi hijack phosphate signaling with conserved enzymatic effectors 🧑‍🔬 Carl L. McCombe, Alex Wegner, Ely Oliveira-Garcia, Simon J. Williams, Ulrich Schaffrath, et al. 📔 @science.org 🔗 www.science.org/doi/10.1126/... #️⃣ #PlantScience #PlantImmunity #PlantNutrients

Out in @elife.bsky.social ! 🎉 Thank you @sohambio.bsky.social for your persistence! Also to @asimjaved.bsky.social & @jiaxuwu.bsky.social for your contributions! So excited to keep understanding gall-forming pathogens using these results as a starting point! elifesciences.org/reviewed-pre...

Plant Science Research Weekly Feb 21 plantae.org/plant-scienc.... Roles of large language models in science? Apoplastic pH modulates H2O2 redox potential; Balancing signal specificity in stomatal development and defense; Hydropatterning in maize inbred lines; Bacterial cellulose boosts regeneration

Hi all!!! 👋 New to Bluesky, but... I'm hiring a Postdoctoral Research Fellow at The Martin Luther University Halle-Wittenberg... www.verwaltung.uni-halle.de/dezern3/Auss... Please repost if you can!! Thank you!!!

Our study on #lichen #symbiosis is out in @currentbiology.bsky.social! How can multiple microbes create a large, 3D, and structurally complex organism? To answer this question, we used #metagenomics, #metatranscriptomics, and a bit of protein structure modeling 🧵1/7 🧬 🖥️ 🧪 🦠 🧫 #SymbioSky

From lesions to lessons: 2025 marks the 20th anniversary of filamentous plant pathogen genomics. In our new review, we present lessons we learned over the past 2 decades and discuss the future of plant pathogen genomics. Take a first look! apsjournals.apsnet.org/doi/10.1094/...

www.nature.com/articles/s41... See our new review in Cell Death and Differentiation led by Matthew Wengler on regulated cell death in Magnaporthe @thesainsburylab.bsky.social

Fast #protein #structure searching using structure graph embeddings biorxiv.org/cgi/content/...

www.nature.com/articles/s42... Paper on ASR protein ML published (congrats @danasmatthews.bsky.social and everyone else not on Bluesky). Some interesting bits - ASR can generate quality synthetic data, local sequence density important, and evo relationships can yield smoother fitness landscapes

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

An immune signalling holiday tale: A Poales-specific EXO70 clade doesn't fit in with the extended family. #PlantScience

Thrilled to share our work on an unusual EXO70 clade unique to grasses and grass-like species 🌾! (1/8) www.biorxiv.org/content/10.1... @thesainsburylab.bsky.social

5th person to be cured of HIV “Today, researchers announced the Dusseldorf patient still has no detectable virus in his body, even after stopping his HIV medication four years ago.”

It's up! bsky.app/profile/chen...

Our new paper is out in PNAS! We engineered bacteria to display enzymes that sea sponges use to mineralize their glass skeletons. These bacteria can self-assemble a bioglass coating around themselves, and focus light into bright, photonic nanojets. www.pnas.org/doi/10.1073/...

Nonuple atg8 mutant provides genetic evidence for functional specialization of #ATG8 isoforms in Arabidopsis thaliana #autophagy #proteomics www.biorxiv.org/content/10.1...

Back by popular demand, I present PPI Prediction Challenge #2. My claim: I AM SKEPTICAL COMPUTATIONAL APPROACHES CAN PREDICT WHETHER TWO PROTEINS INTERACT. Someone prove me wrong (take two). docs.google.com/forms/d/e/1F... 1/n

Artificial intelligence-guided #design of #lipid #nanoparticles for pulmonary gene therapy #synbio #biotech #AI www.nature.com/articles/s41...

Re docking: @workshopmlsb.bsky.social has been piloting a leaderboard for the PLINDER benchmark. It would be awesome to get submissions using existing methods, then everyone can see comparisons better 😁 leaderboard & instructions are on mlsb.io

Excited to present what we've been up to the last couple years. Introducing BioEmu, a Biomolecular Emulator of protein dynamics: www.biorxiv.org/content/10.1...

Chat with any open source repo easily. Gitingest (free online tool) turns any GitHub repository into a single markdown file for pasting. Claude artifacts makes this 300k token output pretty easy to work with.

Proud to have my updated work available on Biorxiv : ancestral function of LysM-RLK for AM establishment @lrsv-toulouse.bsky.social @malick-mbengue.bsky.social @pierremarcdelaux.bsky.social @melaniekrich.bsky.social @kellerjeanphd.bsky.social www.biorxiv.org/content/10.1...

Tim Minchin: ‘Maybe scrolling the traumas of the world is not in itself a moral act’

First paper of our lab today @natureportfolio.bsky.social by Nussi! We provide a real-time movie on how #transcription and #translation cooperate using #single-molecule FM: we find long-range #ribosome/ RNAP communication mediated by #RNA looping! @embl.org #RNAbiology #RNASky t.co/a24Xxcxdo0

Delighted to present an updated version of our LysM-RLK/AM symbiosis story in Marchantia! @lrsv-toulouse.bsky.social www.biorxiv.org/content/10.1...

1/🧬 Excited to share PLAID, our new approach for co-generating sequence and all-atom protein structures by sampling from the latent space of ESMFold. This requires only sequences during training, which unlocks more data and annotations: bit.ly/plaid-proteins 🧵

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science. www.biorxiv.org/content/10.1...

Even Microsoft Research AI for Science is out for protein science, and protein equilibrium. Love how things continue to unfold (like proteins...) right now on this field. www.biorxiv.org/content/10.1...

Rational #engineering of allosteric #protein #switches by #insilico #prediction of domain insertion sites. "Our work enables one-shot domain insertion engineering and substantially accelerates the #design of customized allosteric proteins" Exciting stuff! biorxiv.org/cgi/content/...

💪 A strong message from early-career scientists on the benefits of supporting & publishing in #SocietyJournals: "By choosing to support these journals [as authors, reviewers, & editors], we can reinforce our academic growth and benefit from their re-investment back into the scientific ecosystem."

New MRC-funded postdoc with me on comparative bacterial genomics/phylodynamics @roslininstitute.bsky.social university of Edinburgh. Great multidisciplinary team and collaboration with partners at Shanghai Jao Tong University. elxw.fa.em3.oraclecloud.com/hcmUI/Candid...

Perspective by Higman et al: deposition of data for titrations, relaxation rates, PREs, etc in a standardized way, e.g. the NEF format could help develop AI models to accurately predict the dynamic behaviour of a protein from the primary sequence alone. #NMRchat doi.org/10.1007/s108...

Crosslinks can sometimes improve AlphaFold3 models. Crosslinking is an experimental method often used as a source of distance restraints in modeling. In AlphaFold3, instead of using restraints, crosslinks can be included as covalent ligands. Thanks to Agnieszka Obarska-Kosinska for the idea.

We're hiring a PDRA in #proteindesign. If you're interested in developing #protein #cages for #vaccine therapeutics get in touch! #bionano #symbio #biochem

I'm thinking about organizing a conference about AI and non-AI approaches for protein design and computational structural biology in Oslo (Norway) next year. If this happens, would you be interested in attending or speaking there? P.S. Attached photos are the reason why Oslo 🏞️🌄

Come join us at the Centre Programmable Biological Matter 👇