Dani Stevens, Ph.D.

Dani Stevens, Ph.D.

@danimstevens.bsky.social

Plant Immunologist x Machine Learning, occasional biochemist | 🌱-🧫 interactions | UC Berkeley Postdoc | 2 x USDA NIFA Fellow

951 followers560 following19 posts

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Dani Stevens, Ph.D.
@danimstevens.bsky.social

#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...

biorxiv.orgmamp-ml: A deep learning approach to epitope immunogenicity in plantsEukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...
Dani Stevens, Ph.D.
@danimstevens.bsky.social

#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...

biorxiv.orgmamp-ml: A deep learning approach to epitope immunogenicity in plantsEukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...
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Dani Stevens, Ph.D.
@danimstevens.bsky.social

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...

github.comGitHub - DanielleMStevens/mamp-ml: mamp-ml: Prediction of immunogenic outcomes of LRR-PRRs and protein ligands in plants using pLM ESM-2mamp-ml: Prediction of immunogenic outcomes of LRR-PRRs and protein ligands in plants using pLM ESM-2 - DanielleMStevens/mamp-ml
Dani Stevens, Ph.D.
@danimstevens.bsky.social

#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...

biorxiv.orgmamp-ml: A deep learning approach to epitope immunogenicity in plantsEukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...
View full thread
Dani Stevens, Ph.D.
@danimstevens.bsky.social

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!

Dani Stevens, Ph.D.
@danimstevens.bsky.social

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.

Dani Stevens, Ph.D.
@danimstevens.bsky.social

#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...

biorxiv.orgmamp-ml: A deep learning approach to epitope immunogenicity in plantsEukaryotes detect biomolecules through surface-localized receptors, key signaling components. A subset of receptors survey for pathogens, induce immunity, and restrict pathogen growth. Comparative gen...
Dani Stevens, Ph.D.
@danimstevens.bsky.social

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.

Dani Stevens, Ph.D.
@danimstevens.bsky.social

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!

Dani Stevens, Ph.D. reposted

C&EN (Chemical & Engineering News)
@cenmag.bsky.social

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 🧪

cen.acs.orgMicrosoft AI predicts protein conformationsThe open-source tool goes beyond AlphaFold by finding proteins’ multiple equilibrium states and free energies

Dani Stevens, Ph.D. reposted

Ksenia Krasileva
@kseniakrasileva.bsky.social

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...

academic.oup.comThe Resistance awakens: Diversity at the DNA, RNA, and protein levels informs engineering of plant immune receptors from Arabidopsis to cropsPlants are natural bioengineers, and we illustrate how the stunning diversity in plant immune receptors can be translated into engineering efforts from Ara
Dani Stevens, Ph.D.
@danimstevens.bsky.social

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.

Dani Stevens, Ph.D.
@danimstevens.bsky.social

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

Ksenia Krasileva@kseniakrasileva.bsky.social

Several Jedis in our lab joined forces to review the rise of the plant immune resistance at DNA, RNA, and protein levels 💫🚀 check out the preprinted review here: zenodo.org/records/1420...

zenodo.orgThe Resistance Awakens: Natural diversity informs engineering of plant immune receptors at the DNA, RNA, and protein levelsPlants rely on germline-encoded, innate immune receptors to sense pathogens and initiate the defense response. The exponential increase in quality and quantity of genomes, RNA-seq datasets, and protei...

Dani Stevens, Ph.D. reposted

Pierre Buscaill
@pierrebuscaill.bsky.social

🌿 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

nature.comSubtilase SBT5.2 inactivates flagellin immunogenicity in the plant apoplast - Nature CommunicationsPlants 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...

Dani Stevens, Ph.D. reposted

Mauricio Contreras
@mpcontreras.bsky.social

One bacterial NLR recognizing three different phage proteins vis direct interaction! How cool is that? www.nature.com/articles/s41...

nature.comDiversification of molecular pattern recognition in bacterial NLR-like proteins - Nature CommunicationsAvs 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...

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