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Adam Bentham @adamrbentham.bsky.social · Sep 3

🚨 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

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Reposted by Adam Bentham

Yo Akiyama @yoakiyama.bsky.social · Aug 5

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

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Reposted by Adam Bentham

MLSB (in San Diego + Copenhagen) @workshopmlsb.bsky.social · Jul 28

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

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!🌟

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Reposted by Adam Bentham

Martin Pacesa @martinpacesa.bsky.social · Jul 25

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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Adam Bentham @adamrbentham.bsky.social · Jul 22

There's not enough zigging or zagging the prequels.

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Reposted by Adam Bentham

Kresten Lindorff-Larsen @lindorfflarsen.bsky.social · Jul 22

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

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Adam Bentham @adamrbentham.bsky.social · Jul 22

a man in a blue shirt is sitting on a couch and making a funny face .

ALT: a man in a blue shirt is sitting on a couch and making a funny face .

media.tenor.com

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Reposted by Adam Bentham

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 20

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

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Reposted by Adam Bentham

Juan Carlos De la Concepcion @delaconcepcionjc.bsky.social · Jul 17

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

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.

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Adam Bentham @adamrbentham.bsky.social · Jul 15

Definitely keen!

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Reposted by Adam Bentham

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 14

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

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Adam Bentham @adamrbentham.bsky.social · Jul 11

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

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Reposted by Adam Bentham

Mauricio Contreras @mpcontreras.bsky.social · Jul 9

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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Reposted by Adam Bentham

Hee-Kyung Ahn @hee-kyung-ahn.bsky.social · Jul 11

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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Reposted by Adam Bentham

Jorge Bravo Abad @bravo-abad.bsky.social · Mar 20

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

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Reposted by Adam Bentham

James Lloyd 🧬 @jamespblloyd.bsky.social · Mar 9

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

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Adam Bentham @adamrbentham.bsky.social · Feb 28

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

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

Adam Bentham @adamrbentham.bsky.social · Feb 28

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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Reposted by Adam Bentham

Marc Somssich @somssich.bsky.social · Feb 28

📜 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

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Reposted by Adam Bentham

Edel Pérez-López 🇨🇦 @edelplopez.bsky.social · Feb 21

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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Reposted by Adam Bentham

Mary Williams @PlantTeaching @plantteaching.bsky.social · Feb 21

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

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Reposted by Adam Bentham

Marc Knight Lab @marcknightcalcium.bsky.social · Feb 14

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

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Reposted by Adam Bentham

Gulnara Tagirdzhanova @metalichen.bsky.social · Jan 31

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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Reposted by Adam Bentham

Thorsten Langner @thorstenlangner.bsky.social · Jan 20

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

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Reposted by Adam Bentham

Nick Talbot @talbotlabtsl.bsky.social · Jan 10

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

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