100% agree. Especially with how much money is spent a year toward pub fees (10-30K+) that could go to other career opportunities. Plus, I can get high quality reviews from peers without a formal journal system. Sadly as a postdoc, I feel like my hands are tied, but I would love to help the cause.

Many times, we come back to traditional journals in the end because like NIH grants, preprints don't hold the same weight/merit in trainee fellowships, tenure process, etc. It is still a challenge, though I'd like to think that if established groups move away from trad pubs, others will follow.

Yes, @kseniakrasileva.bsky.social have moved to an increasingly open science model where we not only preprint early, sometimes far before journal submission, but even make datasets open before preprinting (wheat genome example: zenodo.org/records/1021...). We welcome feedback from our community.

Sweet! Those look beautiful. I wish sharing pymol/chimeraX scripts were as common as other computational work and languages.

This is quite interesting, especially since myself and others have found the opposite (ROS, no MAPK)! If I were to $$ on it, my guess is the binding interaction in-complex is causing different PTM modifications on the kinase domain, leading to a bimodal signaling cascade. 🤔 Can't wait to read more!

GitHub - DanielleMStevens/mamp-ml: mamp-ml: Prediction of immunogenic outcomes of LRR-PRRs and protein ligands in plants using pLM ESM-2 mamp-ml: Prediction of immunogenic outcomes of LRR-PRRs and protein ligands in plants using pLM ESM-2 - DanielleMStevens/mamp-ml

While there's lots of work to be done, mamp-ml is a critical advancement in plant immunology for accelerating receptor-epitope characterization and engineering resistance. Mamp-ml is on Github and we implemented a version on Google Colab for easy use. Please check it out!
github.com/DanielleMSte...

Finally, we also tested its ability to predict outcomes for convergently evolved receptors. SCORE, a csp22 receptor found in Citrus and relatives, was recently discovered by @brunongou.bsky.social. We preliminarily found mamp-ml can zero-shot predict immunogenic outcomes!

Compared to other state-of-the-art models such as AlphaFold3, mamp-ml can predict these outcomes with higher confidence, even when a solved structure is not available. We anticipate users can now screen for immunogenic outcomes of receptor-ligand variants before spending time and $$ in the lab.

Mamp-ml harnesses the power of protein language models (ESM-2) to build a classifier model for immunogenic outcomes.

Previously immunogenicity was primarily characterized in the lab but was a expensive bottleneck considering the variation captured computationally!

We then generated a pipeline that combines AlphaFold2 and LRR-Annotation to precisely extract the LRR ectodomain as well as generated features to improve model training. This even includes tracking which residues interface with the ligand!

Mamp-ml was built upon two decades of foundational research. To generate the training data required, I manually pulled receptor and epitope sequences from every paper I could find, small or large. In total, we were able to capture over 1,300+ combinations across 11 receptors and 91 plant species.

mamp-ml: A deep learning approach to epitope immunogenicity in plants Eukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...

#2025ISMPMI 📣 In silico screening of PRR-epitope interactions is now possible!

Here, we developed mamp-ml to predict their immunogenic outcomes without structural context. Let's accelerate engineering plant receptors for robust resistance! 🚀🌱 Small 🧵

www.biorxiv.org/content/10.1...

Great presentation from @gittacoaker.bsky.social on kinase mediated defense responses and harnessing the power of language models for receptor/ ligand prediction. These LMs will help us in engineering more resilient crops #2025ISMPMI

While I'm not going to be at #2025ISMPMI this year (🥲),
@kseniakrasileva.bsky.social will be there presenting on some of our latest work that was submitted to BioRxiv today. Teaser: Plant immunity + large language models will transform receptor discovery and engineering for disease resistance. 🌱🚀

Microsoft AI predicts protein conformations The open-source tool goes beyond AlphaFold by finding proteins’ multiple equilibrium states and free energies

An artificial intelligence tool developed by @microsoft.com researchers can predict the multiple conformational states of proteins in minutes with a fraction of the resources required by other techniques. cen.acs.org/biological-c... #chemsky 🧪

The Resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops Plants are natural bioengineers, and we illustrate how the stunning diversity in plant immune receptors can be translated into engineering efforts from Ara

The Resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to crops 🧬🌱 💫🚀

by Chandler Sutherland @danimstevens.bsky.social @weiweibio.bsky.social Kyungyong Seong

academic.oup.com/plcell/advan...

It was great to catch up with so many people! Super thankful to Grey Monroe for the invite and enjoyed all the engaging questions. Can’t wait to wrap up this project and get it out there! 😁

2025 has been quite a whirlwind. Learned of good funding news, had my first faculty (zoom) interview, will give my first dept. seminar on Monday at Davis all while trying to keep cool with the current news events. 😆😬🫠

To UC Davis folks, if anyone wants to meet up on Monday, feel free to reach out.

This was such a fun review to be part of and truly a group effort! 😄please feel free to check it out. 🌱

Subtilase SBT5.2 inactivates flagellin immunogenicity in the plant apoplast - Nature Communications Plants recognize bacteria by perceiving a 22-residue epitope in flagellin. Plant-secreted SBT5.2 subtilases are found to inactivate this epitope, leading to elicitor removal and reducing costly immuni...

🌿 Excited to share our latest research on how host proteases regulate immune activation!

Read more about how SBT5.2 releases and inactivates flg22: www.nature.com/articles/s41...
rdcu.be/d1UsT

Congratulations to all involved!
#PlantImmunity #PlantPathology #PlantChemeticsLab

Diversification of molecular pattern recognition in bacterial NLR-like proteins - Nature Communications Avs proteins are bacterial anti-phage pattern recognition receptors evolutionarily related to eukaryotic NLRs. Here, Béchon et al show that a single bacterial Avs can recognize different phage protein...

One bacterial NLR recognizing three different phage proteins vis direct interaction! How cool is that?

www.nature.com/articles/s41...

This is the one I would suggest! Was one of the first papers read as part of a phylogenetics journal club/class I took several years ago.

Sometimes the smallest things warm the soul ❤️ so thankful to be part of such a great lab group!

Tomato roots exhibit distinct, development-specific responses to bacterial-derived peptides ### Competing Interest Statement The authors have declared no competing interest.

Interested in how immune responses change over different stages of root development? 🍅🌱 Check out the preprint lead by @bleuschenkohl.bsky.social! 🥳

www.biorxiv.org/content/10.1...