Assistant Professor (Research %26 Education) Click the link provided to see the complete job description.

🚨 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

Scaling down protein language modeling with MSA Pairformer Recent efforts in protein language modeling have focused on scaling single-sequence models and their training data, requiring vast compute resources that limit accessibility. Although models that use ...

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!

There's not enough zigging or zagging the prequels.

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 www.biorxiv.org/content/10.1101/2025.07....

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

Definitely keen!

AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues www.biorxiv.org/content/10.1101/2025.07....

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

TopEC: prediction of Enzyme Commission classes by 3D graph neural networks and localized 3D protein descriptor - Nature Communications TopEC, a 3D graph neural network, predicts enzyme functions from local structural features achieving high accuracy (F-score: 0.72) across >800 Enzyme Commission classes. It is robust to binding sit...

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...

The switch‐liker's guide to plant synthetic gene circuits Synthetic gene circuits have the potential to revolutionise how plants can be engineered by allowing highly customised gene expression patterns to be designed. Gene circuits can sense and integrate m....

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/...

Synthetic knottins as new sources of insecticides. at Durham University on FindAPhD.com PhD Project - Synthetic knottins as new sources of insecticides. at Durham University, listed on FindAPhD.com

www.findaphd.com/phds/project...

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 Inorganic phosphate (Pi) is essential for life, and plant cells monitor Pi availability by sensing inositol pyrophosphate (PP-InsP) levels. In this work, we describe the hijacking of plant phosphate s...

📜 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

promotional figure

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: February 21, 2025 | Plantae Perspective: How should the advancement of large language models affect the practice of science? In this thought-provoking Perspective, four sets of authors express their opinions about the use of…

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!!!

A meme with 4 panels showing a lichen with a cartoonish face drawn on it. The text says: “A lichen sits in a community. Is the community made of lichen? Or is the lichen made of community? It screams, for it does not know”.

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: Two Decades of Filamentous Plant Pathogen Genomics | Molecular Plant-Microbe Interactions® Filamentous plant pathogens pose a severe threat to food security. Current estimates suggest up to 23% yield losses to pre- and post-harvest diseases and these losses are projected to increase due to ...

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/...

Mechanisms of regulated cell death during plant infection by the rice blast fungus Magnaporthe oryzae - Cell Death & Differentiation Cell Death & Differentiation - Mechanisms of regulated cell death during plant infection by the rice blast fungus Magnaporthe oryzae

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 Comparing and searching protein structures independent of primary sequence has proved useful for remote homology detection, function annotation and protein classification. Fast and accurate methods to...

Fast #protein #structure searching using structure graph embeddings

biorxiv.org/cgi/content/...

Leveraging ancestral sequence reconstruction for protein representation learning - Nature Machine Intelligence Matthews et al. present a protein sequence embedding based on data from ancestral sequences that allows machine learning to be used for tasks where training data are scarce or expensive.

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

Putative neofunctionalization of a Poales-specific EXO70 clade EXO70s are uniquely expanded in land plants compared to all other eukaryotic lineages. The functional implications of this expansion and diversification on the conserved role of EXO70 as a subunit of ...

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