Yu Sugihara

🎉 Exciting news during #2025ISMPMI Our AlphaFold 3 sensor vs helper NLR paper is now published in @NewPhyt! Big thanks to the reviewers for their constructive feedback 🙏 📖 Check out the peer-reviewed version here 👇 🔗 nph.onlinelibrary.wiley.com/doi/10.1111/np… x.com/YuSugiharaY/st…

With the genetic color palette unlocked, I look forward to creating gradients of complementing colors I’m prototyping on paper. The capacity to rewire petals to paint themselves with natures pigments is a profound advancement in design that will soon be recognized 🌼 🎨 🧬

Dear Takashi, I hope you get a chance to see this. I am a flower genetic designer inspired by your work and have engineered flowers with DNA to look like yours in real life. I would love to tell you more about it sometime :) -Nick

[PlsRT] We are recruiting a Tenure-Track Assistant Professor in my laboratory at the IPSR, Okayama Univ. Those who are interested are highly encouraged to apply. * The previous link was incorrect, so I am resending the correct link. jrecin.jst.go.jp/seek/SeekJorDe…

Are Fungal Disease Outbreaks Instigated by Starship Transposons? - Urquhart - 2025 - Molecular Plant Pathology - Wiley Online Library bsppjournals.onlinelibrary.wiley.com/doi/10.1111/mp…

After our lab retreat to the #ISMPMI conference in Cologne, we are sharing our posters! At Plant Breeding @WUR, we study disease resistance in #potato and wild Solanum (plantbreeding.wur.nl/SolRgenes/ ) against a range of #plantpathogens @EPSGradSchool

Plasmids aren't just passengers; they're drivers of bacterial evolution 🧬 Mutation rate scales with plasmid copy number, boosting adaptability 💥 Check out our latest preprint! 🚨 biorxiv.org/content/10.110…

Introducing @PLOS is our speaker today Nonia @npariente — advancing open science. Hosted by no one other than our own #openscience champion @mpcontreras4

Had an awesome time at ISMPMI and the honour to present some of our work! Greatful for the oppurtunity to meet new people, catch up with friends, and see and discuss some great science! If you want to learn more the poster is up online: zenodo.org/records/158817…

Excited to preprint work mainly by former postdocs Li Feng, Yingnan Hou @Cerhou, and the phylogenomics genius @amiralito_ @TheSainsburyLab. We found a plant defense gene family enabling pathogen gene silencing & explored engineering this pathway to boost disease resistance!

I just published: Stop displaying journal names on your slides A mentoring event at a Congress called for better support of early-career scientists - but what followed sent mixed signals. This blog reflects on those moments and ends with a pledge. medium.com/p/stop-display…

Detecting Foldback Artifacts in Long Reads biorxiv.org/content/10.110… #biorxiv_bioinfo

Can AI structural modelling distinguish between sensor and helper NLR immune receptors? Toghani et al. @amiralito_ @Tolga_Bzkrt @ryoheiterauchi @KamounLab @YuSugiharaY 📖 nph.onlinelibrary.wiley.com/doi/10.1111/np…

FAMSA2 enables accurate multiple sequence alignment at protein-universe scale biorxiv.org/content/10.110… #biorxiv_bioinfo

New preprint on Taka's work! We analyzed feeding responses in two independently evolved carnivorous pitcher plants and found both convergence and divergence in gene regulation, including divergent expression in genes whose proteins evolved convergently. biorxiv.org/content/10.110…

Second, work from @EunyoungChae on autoimmunity mediated by the NLR DM2 and DM3 "Dangerous mix". CryoEM structures show a shift in hexamer stability to be the trigger for DM2. @DiWu96569752 highlights that Alphafold can't predict this structural shift cell.com/molecular-cell…

First, work from Chang-Bao Li and Chuanyou Li (Shandong Ag U) on regulation of SYR1 receptor. The paralog SYR2 is an induced negative regulator w/ lower binding affinity. @nataliagupa highlighted that the SYR1-SYR2 module is only found in Solanoideae sciencedirect.com/science/articl…

We have a new version of OrthoFinder: biorxiv.org/content/10.110… Faster scaling to larger species sets, phylogenetically resolved orthogroups, reduced RAM usage. Thanks to @dr_belcher, Yi Liu & Jonathan Holmes who have joined the team, and as ever OrthoFinder's PI @Steve__Kelly!

New publication: Can AI modeling of protein structures distinguish between sensor and helper NLR immune receptors? (2025) tsl.ac.uk/publications/1…

I'm very happy that this paper is now published in PNAS! Isochorismate-based SA biosynthesis appears to have emerged in the Brassicales after the divergence of C. papaya, likely within the timeframe between the divergence of B. maritima and R. odorata. pnas.org/doi/10.1073/pn…

Great reunion of (part of) the PERU receptor team at #2025ISMPMI 🙌🥳 Joining forces to improve PRR-mediated immunity against Late Blight 🥔🌱🧬 @adnroide @VivianneTwit @Yerisf_TA @LishaZhang2 @amiralito_