Dani Stevens, Ph.D.
@danimstevens.bsky.social
Plant Immunologist x Machine Learning, occasional biochemist | 🌱-🧫 interactions | UC Berkeley Postdoc | 2 x USDA NIFA Fellow
Pinned
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...
www.biorxiv.org
#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...
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...
#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...
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...
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...
www.biorxiv.org
July 15, 2025 at 11:28 PM
#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...
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...
Reposted by Dani Stevens, Ph.D.
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
July 14, 2025 at 2:06 PM
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. 🌱🚀
@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. 🌱🚀
July 12, 2025 at 12:00 AM
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. 🌱🚀
@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. 🌱🚀
Reposted by Dani Stevens, Ph.D.
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 🧪
Microsoft AI predicts protein conformations
The open-source tool goes beyond AlphaFold by finding proteins’ multiple equilibrium states and free energies
cen.acs.org
July 11, 2025 at 3:44 PM
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 🧪
Reposted by Dani Stevens, Ph.D.
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...
by Chandler Sutherland @danimstevens.bsky.social @weiweibio.bsky.social Kyungyong Seong
academic.oup.com/plcell/advan...
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
academic.oup.com
May 15, 2025 at 11:37 PM
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...
by Chandler Sutherland @danimstevens.bsky.social @weiweibio.bsky.social Kyungyong Seong
academic.oup.com/plcell/advan...
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.
To UC Davis folks, if anyone wants to meet up on Monday, feel free to reach out.
February 1, 2025 at 6:28 PM
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.
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. 🌱
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...
The Resistance Awakens: Natural diversity informs engineering of plant immune receptors at the DNA, RNA, and protein levels
Plants 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...
zenodo.org
December 6, 2024 at 4:34 AM
This was such a fun review to be part of and truly a group effort! 😄please feel free to check it out. 🌱
Reposted by Dani Stevens, Ph.D.
🌿 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
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
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...
www.nature.com
December 2, 2024 at 2:05 PM
🌿 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
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
Reposted by Dani Stevens, Ph.D.
One bacterial NLR recognizing three different phage proteins vis direct interaction! How cool is that?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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...
www.nature.com
November 14, 2024 at 9:25 PM
One bacterial NLR recognizing three different phage proteins vis direct interaction! How cool is that?
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Sometimes the smallest things warm the soul ❤️ so thankful to be part of such a great lab group!
November 13, 2024 at 6:10 PM
Sometimes the smallest things warm the soul ❤️ so thankful to be part of such a great lab group!
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...
www.biorxiv.org/content/10.1...
Tomato roots exhibit distinct, development-specific responses to bacterial-derived peptides
### Competing Interest Statement
The authors have declared no competing interest.
www.biorxiv.org
November 12, 2024 at 8:01 PM
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...
www.biorxiv.org/content/10.1...