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adamrbentham.bsky.social
Adam Bentham
@adamrbentham.bsky.social
440 followers 580 following 27 posts
Assistant Prof @ Durham University
Centre for Programmable Biological Matter: @cpbm-heddlelab.bsky.social

Structural biologist
Protein design in plant systems
Engineering disease resistance

Views are my own

He / Him 🇦🇺🇬🇧
Posts Replies Media Videos
adamrbentham.bsky.social
🚨 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
Assistant Professor (Research %26 Education)
Click the link provided to see the complete job description.
durham.taleo.net
September 3, 2025 at 12:05 PM
Reposted by Adam Bentham
yoakiyama.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🧵
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 ...
biorxiv.org
August 5, 2025 at 6:31 AM
Reposted by Adam Bentham
workshopmlsb.bsky.social
Stay tuned for details on the 6th edition of MLSB, officially happening this December in downtown San Diego, CA!
ginaelnesr.bsky.social Gina El Nesr @ginaelnesr.bsky.social · Jul 28
The MLSB workshop will be in San Diego, CA (co-located with NeurIPS) this year for its 6th edition in December 🧬🔬

Stay tuned @workshopmlsb.bsky.social as we share details about the stellar lineup of speakers, the official call for papers, and other announcements!🌟
July 28, 2025 at 3:41 PM
Reposted by Adam Bentham
martinpacesa.bsky.social
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!
July 25, 2025 at 7:48 AM
Reposted by Adam Bentham
lindorfflarsen.bsky.social
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
July 22, 2025 at 5:58 AM
Reposted by Adam Bentham
biorxiv-bioinfo.bsky.social
Protein structure alignment significance is often exaggerated https://www.biorxiv.org/content/10.1101/2025.07.17.665375v1
July 20, 2025 at 4:46 AM
Reposted by Adam Bentham
delaconcepcionjc.bsky.social
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
effectomics.bsky.social Armin Djamei @effectomics.bsky.social · Jul 17
#2025ISMPMI Agnus Bucknell of the Talbot lab gives an exciting presentation to engineer fungal effectors recognizing immune sensors based on Pik1. Great and clear talk.
July 17, 2025 at 1:51 PM
Reposted by Adam Bentham
biorxiv-bioinfo.bsky.social
AlphaFlex: Accuracy modeling of protein multiple conformations via predicted flexible residues https://www.biorxiv.org/content/10.1101/2025.07.11.664327v1
July 14, 2025 at 4:47 PM
adamrbentham.bsky.social
Travelling to Köln for Heath's first MPMI! #2025ISMPMI
July 11, 2025 at 3:38 PM
Reposted by Adam Bentham
mpcontreras.bsky.social
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
July 9, 2025 at 1:03 PM
Reposted by Adam Bentham
hee-kyung-ahn.bsky.social
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
July 11, 2025 at 3:01 PM
Reposted by Adam Bentham
bravo-abad.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...
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...
www.nature.com
March 20, 2025 at 10:51 AM
Reposted by Adam Bentham
jamespblloyd.bsky.social
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/...
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....
onlinelibrary.wiley.com
March 9, 2025 at 1:15 AM
adamrbentham.bsky.social
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 👇
February 28, 2025 at 10:23 AM
Reposted by Adam Bentham
somssich.bsky.social
📜 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
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...
www.science.org
February 28, 2025 at 6:03 AM
Reposted by Adam Bentham
edelplopez.bsky.social
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...
promotional figure
February 21, 2025 at 4:34 PM
Reposted by Adam Bentham
plantteaching.bsky.social
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
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…
plantae.org
February 21, 2025 at 7:35 AM
Reposted by Adam Bentham
marcknightcalcium.bsky.social
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!!!
www.verwaltung.uni-halle.de
February 14, 2025 at 10:35 PM
Reposted by Adam Bentham
metalichen.bsky.social
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”.
January 31, 2025 at 4:35 PM
Reposted by Adam Bentham
thorstenlangner.bsky.social
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/...
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 ...
apsjournals.apsnet.org
January 20, 2025 at 9:51 AM
Reposted by Adam Bentham
talbotlabtsl.bsky.social
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
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
January 10, 2025 at 6:39 PM
adamrbentham.bsky.social
Fast #protein #structure searching using structure graph embeddings

biorxiv.org/cgi/content/...
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...
biorxiv.org
December 31, 2024 at 4:56 PM
Reposted by Adam Bentham
cjjackson.bsky.social
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
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
December 19, 2024 at 4:54 AM
Reposted by Adam Bentham
noeliaferruz.bsky.social
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
December 18, 2024 at 9:06 PM
Reposted by Adam Bentham
pdchristine.bsky.social
An immune signalling holiday tale: A Poales-specific EXO70 clade doesn't fit in with the extended family. #PlantScience
biorxiv-plants.bsky.social bioRxiv Plant Bio @biorxiv-plants.bsky.social · Dec 17
Putative neofunctionalization of a Poales-specific EXO70 clade https://www.biorxiv.org/content/10.1101/2024.12.13.628418v1
December 17, 2024 at 11:12 PM