iiinova — where your digital self keeps evolving

Adam Bentham @adamrbentham.bsky.social · 30/09/2026

🚨 Please share! 🚨 I'm recruiting a fully funded 4-year Gatsby Sainsbury PhD studentship at Durham! 🌱🤖 Designing plant immune receptors from scratch, combining AI protein design with structural biology and plant immunity. If you're interested please get in touch! benthamlab.org shorturl.at/U2PdV

benthamlab.org

Bentham Lab — Durham University

Bentham Lab, Centre for Programmable Biological Matter, Durham University. Structural biology and de novo protein design applied to host-pathogen interactions, plant immunity, and neglected tropical d...

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Adam Bentham @adamrbentham.bsky.social · 11/09/2026

This is an excellent open letter and probably the strongest argument I have read for not allowing the use of AI in Science. An answer received without the lesson does not allow for growth or development. terrytao.wordpress.com/2026/09/11/a...

terrytao.wordpress.com

A Severe Misalignment of AI in Mathematics

I am proud to be among the list of 25 initial signatories — all Fields Medallists — to the declaration below, which grew out of discussions between ourselves over the last week. We have…

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Nature Plants @natplants.nature.com · 02/09/2026

New News & Views: "Plant immune receptors built in silico and evolved in vivo" rdcu.be/Kh9wTHbDrKva Protein design & directed evolution in planta to build synthetic immune receptors that detect diverse pathogen proteins: on-demand design and refinement of resistance genes.

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Gabriel Renaud @gabrielylr.bsky.social · 23/08/2026

🧬 Ancient DNA → ancient proteins? We now have the computational toolkit to make this possible: CarpeDeam + AdDeam + AlphaFold + Foldseek. In our new preprint, we reconstruct an archaeal ATP synthase from ~2M-yo aeDNA from Greenland and predict its 3D structure. www.biorxiv.org/content/10.6...

biorxiv.org

Ancient Reconstructed Proteins: A Framework for Resurrecting Protein Structures from Million-Year-Old Metagenomes

DNA sequences derived from ancient samples provide insights into human history, paleoenvironments, and evolutionary biology. Advances in laboratory techniques and computational tools have established ...

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 07/08/2026

An immune receptor pair consisting of NLR and MLKL confers stable resistance against Pyricularia oryzae pathotype Eluesine on wheat by recognition of three effectors www.biorxiv.org/content/10.64898/20…

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Josh Bennett @joshwbennett.bsky.social · 07/08/2026

I am really excited to share the first chapter of my PhD, where we characterise a genetically linked NLR/MLKL pair underpinning the Rwt3 resistance locus in wheat! With yet another KFP involved in monocot immunity 🌾 www.biorxiv.org/content/10.6...

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 07/08/2026

A wheat immune receptor pair executes cell death through a helper MLKL www.biorxiv.org/content/10.64898/20…

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Juan Carlos De la Concepcion @delaconcepcionjc.bsky.social · 05/08/2026

PLEASE SHARE! New job openings in my lab @zmbp-tuebingen.bsky.social. We have a broad interest into the mechanistic basis of how molecular complexes are rewired during cellular development in plants and during invasion by pathogens. 🌱🍄🔬 See details below 👇 #PlantSciJobs

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Nick Talbot @talbotlabtsl.bsky.social · 24/07/2026

Worth a read www.science.org/content/blog...

science.org

The Assault On Science Funding Continues

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Nature Plants @natplants.nature.com · 24/07/2026

"Programmable design of synthetic plant immune receptors for pathogen protein recognition" www.science.org/doi/10.1126/...

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Tonni Andersen @tonnigrubeandersen.bsky.social · 22/07/2026

Read our new review: The life and legacy of the root endodermis: A spatiotemporal view of function and development - a very nice piece by @swatimahiwal.bsky.social www.sciencedirect.com/science/arti...

sciencedirect.com

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Nick Talbot @talbotlabtsl.bsky.social · 13/07/2026

Excited to preprint this collaborative study led by @adamrbentham.bsky.social in which computationally-designed protein binders were generated that recognise pathogen effectors leading to a plant immune response when deployed within NLR immune receptors. www.biorxiv.org/content/10.6...

biorxiv.org

Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.

The rapid evolution of plant pathogens poses a persistent threat to global agricultural sustainability, often outpacing the discovery and deployment of natural disease resistance genes. While bioengin...

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Adam Bentham @adamrbentham.bsky.social · 13/07/2026

Excited to see our new preprint on bioRxiv! 🌱🤖 We used AI protein design (RFdiffusion + ProteinMPNN) to build brand-new sensor domains from scratch and installed them in a rice NLR immune receptor engineering recognition of a Fusarium effector FoSSP17

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greg-knight.bsky.social @greg-knight.bsky.social · 13/07/2026

Happy to have taken part in this cool project! It's really exciting to see the potential that protein design has in plant science!

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Josh Bennett @joshwbennett.bsky.social · 11/07/2026

Awesome to see this bioRxiv out, after lots of great work from @yuxuan-xi.bsky.social to integrate de novo binders into a plant immune receptor! It's a very exciting time to be working on protein engineering in this field 🧬🌱

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Angus Bucknell @ahbucknell.com · 11/07/2026

This has been a great project to work on and I’m very excited to see where this technology is headed within plant pathology. Big thanks to all the contributors, especially @yuxuan-xi.bsky.social and @adamrbentham.bsky.social!

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yuxuan-xi.bsky.social @yuxuan-xi.bsky.social · 11/07/2026

Our new preprint is out! Using AI-guided design (RFdiffusion + ProteinMPNN), we engineered a plant immune receptor to recognise non-cognate pathogen effectors. Huge thanks to our amazing co-authors for making this possible! doi.org/10.64898/202...

doi.org

Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors.

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bioRxivpreprint @biorxivpreprint.bsky.social · 10/07/2026

Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors. www.biorxiv.org/content/10.64898/20…

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 10/07/2026

Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors. www.biorxiv.org/content/10.64898/20…

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The Plant Journal @theplantjournal.bsky.social · 13/06/2026

📚 𝐅𝐨𝐜𝐮𝐬𝐞𝐝 𝐑𝐞𝐯𝐢𝐞𝐰 "How to frustrate a plant pathogen" 🐛 From structural genomics to AI-driven protein design, this review explores new strategies for engineering broad-spectrum resistance against plant pathogen effectors. ✍️ Knight, Heddle and @adamrbentham.bsky.social 👉 doi.org/10.1111/tpj....

doi.org

How to frustrate a plant pathogen

Plant pathogens deploy large families of structurally related but sequence-diverse effector proteins to manipulate host cells, allowing them to evade immune recognition whilst maintaining the capacit...

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Mauricio Contreras @mpcontreras.bsky.social · 09/06/2026

As seen on @biorxivpreprint.bsky.social: our story on how the dreaded late blight pathogen hijacks a helper NLR pathway is now out in its final form! 🎉 Meet AVRcap1b: the two-faced effector 🧵👇 www.science.org/doi/10.1126/...

science.org

A potato late blight pathogen effector interacts with ENTH-domain protein TOL9a and an activated helper NLR to suppress immunity

A plant pathogen effector suppresses an activated helper NLR via a host ENTH domain–containing protein, NbTOL9a.

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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 19/05/2026

Colletotrichum higginsianum effector ChEC108 binds a plasmodesmal HMA protein and elicits plant defence www.biorxiv.org/content/10.64898/20…

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Adam Bentham @adamrbentham.bsky.social · 03/09/2025

🚨 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

durham.taleo.net

Assistant Professor (Research %26 Education)

Click the link provided to see the complete job description.

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Yo Akiyama @yoakiyama.bsky.social · 05/08/2025

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🧵

biorxiv.org

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 ...

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MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · 28/07/2025

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

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Martin Pacesa @martinpacesa.bsky.social · 25/07/2025

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!

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Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · 22/07/2025

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

authors.elsevier.com

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 20/07/2025

Protein structure alignment significance is often exaggerated www.biorxiv.org/content/10.1101/202…

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Juan Carlos De la Concepcion @delaconcepcionjc.bsky.social · 17/07/2025

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

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 14/07/2025

AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues www.biorxiv.org/content/10.1101/202…

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Adam Bentham @adamrbentham.bsky.social · 11/07/2025

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

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Mauricio Contreras @mpcontreras.bsky.social · 09/07/2025

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

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Hee-Kyung Ahn @hee-kyung-ahn.bsky.social · 11/07/2025

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

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Jorge Bravo Abad @bravo-abad.bsky.social · 20/03/2025

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...

nature.com

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...

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James Lloyd 🧬 @jamespblloyd.bsky.social · 09/03/2025

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/...

onlinelibrary.wiley.com

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....

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Adam Bentham @adamrbentham.bsky.social · 28/02/2025

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 👇

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Marc Somssich @somssich.bsky.social · 28/02/2025

📜 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

science.org

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...

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Edel Pérez-López 🇨🇦 @edelplopez.bsky.social · 21/02/2025

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...

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Mary Williams @PlantTeaching @plantteaching.bsky.social · 21/02/2025

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

plantae.org

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…

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Marc Knight Lab @marcknightcalcium.bsky.social · 14/02/2025

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!!!

verwaltung.uni-halle.de

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Gulnara Tagirdzhanova @metalichen.bsky.social · 31/01/2025

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

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”.

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Thorsten Langner @thorstenlangner.bsky.social · 20/01/2025

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/...

apsjournals.apsnet.org

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 ...

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Colin Jackson @cjjackson.bsky.social · 19/12/2024

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

nature.com

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.

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Noelia Ferruz @noeliaferruz.bsky.social · 18/12/2024

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

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Christine Faulkner @pdchristine.bsky.social · 17/12/2024

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

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