Reposted by AmirAli Toghaniioannamor.bsky.social @ioannamor.bsky.social · 15/10/2026I'm new on Bluesky, and happy to share that this paper finally came out while I was on maternity leave! It contains the main body of work of my PhD research, and it's much improved compared to the bioRxiv version thanks to our reviewers. 1239 23
Reposted by AmirAli ToghaniPLOS Biology @plosbiology.org · 08/07/2026#Mosquito gene drives for #malaria control can be undermined by rare, hard to detect genetic resistance alleles. This study by @ioannamor.bsky.social @drew-hammond.bsky.social &co reveals how #CRISPR resistance emerges and how to overcome it, advancing vector control 🧪 #AcademicSky plos.io/3R0ggEQ 0103 10
Reposted by AmirAli ToghaniHassan Salem @hassansalem.bsky.social · 12/10/2026Beetles secrete jelly to embed & sustain symbionts with impossibly tiny genomes🪲 But what is this jelly made of? And how does it help maintain a partnership that has lasted over 62 million years? Thrilled to share our latest, out now in @natcomms.nature.com! www.nature.com/articles/s41...nature.comYellow protein co-opted to sustain obligate symbiosis in leaf beetles - Nature CommunicationsInsects have evolved diverse strategies to protect their genome-reduced symbionts during vertical transmission. Here, authors show that tortoise beetles have co-opted a Yellow protein to form spheres ... 511152 111
Reposted by AmirAli ToghaniYu Sugihara @yusugihara.bsky.social · 08/10/2026Excited to share our latest work! 🍅 Two evolutionarily distinct immune receptors recognize the same viral target, yet differ in their recognition spectra. A fascinating example of convergent evolution in plant immunity! 02210 22
Reposted by AmirAli ToghaniJogi Madhuprakash @jmadhuprakash.bsky.social · 08/10/2026🍅 Tomato brown rugose fruit virus spread worldwide. For >60 years, one resistance gene protected tomatoes. This virus broke through. A second gene confers resistance. The same viral target? Convergent evolution? Preprint: www.biorxiv.org/content/10.6... #EvoMPMI #NLRbiology (1/9) 🧵 12611 26
Reposted by AmirAli ToghaniSophien Kamoun @kamounlab.bsky.social · 27/09/2026I just published: How do we recognize world-class science? Not by the journal it appeared in What I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs. kamounlab.medium.com/how-do-we-re...kamounlab.medium.comHow do we recognize world-class science? Not by the journal it appeared inWhat I told early-career researchers about prediction, rigour, failure, priors — and the tyranny of bar graphs. 27738 77
Reposted by AmirAli ToghaniSophien Kamoun @kamounlab.bsky.social · 22/09/2026Two seemingly unrelated sides of our lab collided today in the AWESOME new Angiosperm Phylogeny Group system poster: flowers 🌸 and phylogenomics 🧬 Need a new genome? Just pick up the phone and “dial-a-genome” 📞🧬 @getgenome.bsky.social www.tudelft.nl/en/hortus-bo... 1278 27
Reposted by AmirAli ToghaniMartin Pacesa @martinpacesa.bsky.social · 21/09/2026ʙɪɴᴅᴄʀᴀꜰᴛ2 is out, and we're not waiting for the paper. The full code drops today, free for academic and industry use. We're releasing it early so you can start designing right now, and bring its full power to the current Adaptyv competition. github.com/PacesaLab/Bi... 4293142 293
Reposted by AmirAli ToghaniNick Talbot @talbotlabtsl.bsky.social · 14/09/2026Latest preprint from our group. We found the Bip1 transcription factor is phosphorylated in a Pmk1-dependent manner & with Mst12 co-regulates appressorium-specific functions, as well as acting on genes associated with invasive growth. @camilla-moli.bsky.social www.biorxiv.org/content/10.6...biorxiv.orgA Pmk1-Regulated Mst12-Bip1 Network Coordinates Appressorium Function, Effector Deployment, and Invasive Growth by Magnaporthe oryzaeTo cause rice blast disease, the filamentous fungus Magnaporthe oryzae develops a specialised infection cell called an appressorium, which generates enormous turgor to breach the rice leaf cuticle. Al... 01911 19
Reposted by AmirAli ToghaniCamilla Molinari @camilla-moli.bsky.social · 14/09/2026Excited to share this pre-print from my PhD work! We explore a Pmk1-Mst12-Bip1 network required for appressorium-mediated infection by the blast fungus 🌾 www.biorxiv.org/content/10.6... Thread 👇biorxiv.orgA Pmk1-Regulated Mst12-Bip1 Network Coordinates Appressorium Function, Effector Deployment, and Invasive Growth by Magnaporthe oryzaeTo cause rice blast disease, the filamentous fungus Magnaporthe oryzae develops a specialised infection cell called an appressorium, which generates enormous turgor to breach the rice leaf cuticle. Al... 33528 35
Reposted by AmirAli ToghaniSophien Kamoun @kamounlab.bsky.social · 14/09/2026We just published: Fold on Tight — 10 lessons on AI structure prediction Andy Posbe @adnroide.bsky.social turned our ten lessons on AI structure prediction into a thread. Here it is, one lesson at a time. kamounlab.medium.com/fold-on-tigh...kamounlab.medium.comFold on Tight — 10 lessons on AI structure predictionAndy Posbe turned our ten lessons on AI structure prediction into a thread. Here it is, one lesson at a time. 01210 12
Reposted by AmirAli ToghaniAndy Posbe @adnroide.bsky.social · 11/09/2026No one remembers authorising this firmware update 063 6
Reposted by AmirAli ToghaniJack Rhodes @jackrhodes.bsky.social · 10/09/2026An embryo-derived peptide signal directs endosperm polarity in Arabidopsisscience.orgAn embryo-derived peptide signal directs endosperm polarity in ArabidopsisAngiosperm seed formation requires the coordinated development of the products of double fertilization—the embryo and the endosperm. The endosperm mediates efficient nutrient transfer from surrounding... 04722 47
Reposted by AmirAli ToghaniAlex McClelland @alexjmcclelland.bsky.social · 11/09/2026Very pleased to have contributed to this concise, digestible overview of AI structure prediction! I think this is a great resource for newbies and experienced AlphaFold users alike. Happy Folding! 043 4
Reposted by AmirAli ToghaniRemco Stam @rstam.bsky.social · 11/09/2026New preprint! There have been quite a few papers about RLP and RLK receptors, but none of them have a truly reproducible annotation pipeline (including my own...)... We finally made such a pipeline and look more systematically at RLPs within tomato. www.biorxiv.org/content/10.6...biorxiv.orgPlantLRR-PRR:A Reproducible Annotation Pipeline Reveals Contrasting Evolution of Developmental and Defense Receptor-Like Proteins in TomatoPlants perceive external and internal signals via receptors to modulate their growth, development, and defenses. Leucine-rich-repeat receptor-like-kinase (RLKs) and receptor-like-proteins (RLPs) are t... 13824 38
Reposted by AmirAli ToghaniBuzz Baum @buzzbaum.bsky.social · 11/09/2026If you thought you understood how one cell becomes two (and imagined studying the problem using an organism that lives in deep sea volcanic vents was impossible), read Florian’s paper and think again! 25020 50
Reposted by AmirAli ToghaniAndy Posbe @adnroide.bsky.social · 10/09/2026Excited to share Fold on Tight! 🎉 We distil recent advances in plant immunity into 10 lessons for using AI structure prediction critically and effectively, in plants and beyond. 📝 zenodo.org/records/2210... 13217 32
Reposted by AmirAli ToghaniSophien Kamoun @kamounlab.bsky.social · 10/09/2026You saw the poster—now hear the talk! Mauricio Contreras @mpcontreras.bsky.social with Maian @maigarro.bsky.social and AmirAli @amiralito.bsky.social reveal the hidden handshake between sensors and helpers in the NRC network 🤝🌱 #BSPP26 #PPATH2026 062 6
Reposted by AmirAli ToghaniJosh Bennett @joshwbennett.bsky.social · 07/08/2026I am really excited to share the first chapter of my PhD, where we characterise a genetically linked NLR/MLKL pair underpinning the Rwt3 resistance locus in wheat! With yet another KFP involved in monocot immunity 🌾 www.biorxiv.org/content/10.6... 33520 35
Reposted by AmirAli ToghanibioRxiv Plant Bio @biorxiv-plants.bsky.social · 07/08/2026A wheat immune receptor pair executes cell death through a helper MLKL www.biorxiv.org/content/10.64898/20… 01711 17
Reposted by AmirAli ToghaniIsabel Monte @isabelmonte.bsky.social · 17/07/2026Deadline extended 📢 Submit your abstract for the #PPRM2026 by July 29th! Check our fantastic lineup of invited speakers and come join us discuss all things #plant peptide receptors 🌱 Please spread the word and see you in Freising (Germany) from September 14 to 16 😊 www.events.tum.de/frontend/ind... 02928 29
Reposted by AmirAli ToghanibioRxiv Plant Bio @biorxiv-plants.bsky.social · 10/07/2026Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors. www.biorxiv.org/content/10.64898/20… 01612 16
Reposted by AmirAli ToghaniJuan Carlos De la Concepcion @delaconcepcionjc.bsky.social · 24/06/2026Our latest work on immune receptor engineering for enhanced pathogen recognition is out in @theplantcell.bsky.social academic.oup.com/plcell/artic... #NLRs #Effectors #Exo70academic.oup.comEngineering an Exo70 integrated domain of a barley NLR for improved blast resistanceEngineering the barley NLR RGH2 enhances recognition of blast pathogen effectors from rice and wheat, leading to improved disease resistance. 15127 51
Reposted by AmirAli ToghaniMauricio Contreras @mpcontreras.bsky.social · 09/06/2026As seen on @biorxivpreprint.bsky.social: our story on how the dreaded late blight pathogen hijacks a helper NLR pathway is now out in its final form! 🎉 Meet AVRcap1b: the two-faced effector 🧵👇 www.science.org/doi/10.1126/...science.orgA potato late blight pathogen effector interacts with ENTH-domain protein TOL9a and an activated helper NLR to suppress immunityA plant pathogen effector suppresses an activated helper NLR via a host ENTH domain–containing protein, NbTOL9a. 13719 37
Reposted by AmirAli ToghaniSophien Kamoun @kamounlab.bsky.social · 05/06/2026You saw them first on @bioRxiv. Now they’re out in print—back-to-back. Meet AVRcap1b: the two-faced immunosuppressor from the potato blight pathogen Phytophthora infestans. www.science.org/doi/10.1126/...science.orgA potato late blight pathogen effector interacts with ENTH-domain protein TOL9a and an activated helper NLR to suppress immunityA plant pathogen effector suppresses an activated helper NLR via a host ENTH domain–containing protein, NbTOL9a. 14020 40
Reposted by AmirAli ToghaniMarion Clavel @thevirusmc.bsky.social · 29/05/2026Our work is out now! (www.science.org/doi/10.1126/...). We discover a selective autophagy pathway that protects plants from the mess caused by RNA viruses. Intrigued? Follow the spaghetti trail for a summary of our findings🧵-->science.orgSelective autophagy fine-tunes plant immunity to promote cell survival during viral infectionRNA viruses co-opt host endomembranes to form replication complexes, often triggering cellular stress and immune responses. Here, we show that Arabidopsis thaliana activates selective autophagy to res... 98140 81
Reposted by AmirAli ToghaniElenor Kennedy @ebkennedy.bsky.social · 22/05/2026@khongsamchia.bsky.social Extremely excited to share the first pre-print from my PhD project in the Carella lab, co-first authored with @khongsamchia.bsky.social 🎉 (Thread below ⬇️) www.biorxiv.org/content/10.6... Huge thanks to all co-authors and the #CarellaCapybaras for all the support 😊biorxiv.org 13519 35
AmirAli Toghani @amiralito.bsky.social · 20/05/2026Started off as convergent observations in the lab with Mau and led to one of my favorite works so far! Gotta love molecular evolution and receptor biology 😊🧬💻 Huge effort from @maigarro.bsky.social @mpcontreras.bsky.social for pushing this together to the end. 🤘🏻 0177 17
Reposted by AmirAli ToghaniMauricio Contreras @mpcontreras.bsky.social · 20/05/2026Huge team effort together with the two legends @amiralito.bsky.social & Maián! Thanks to Raoul Frijters from @rijkzwaan.bsky.social for inspiration and to @kamounlab.bsky.social for the constant support. It was a pleasure to put this story together! Check it out now👇 www.biorxiv.org/content/10.6...biorxiv.org 271 7
Reposted by AmirAli ToghaniMauricio Contreras @mpcontreras.bsky.social · 20/05/2026Check out our updated activation-and-release model. This one image condenses over 10 years of work from many legendary @kamounlab.bsky.social members 🤯 Big shoutout to Chih-Hang, @tolgaboz.bsky.social, Lida, Aki, Selvaraj, @jmadhuprakash.bsky.social, @hsuanpai.bsky.social, Ben and many more! 1229 22
Reposted by AmirAli ToghaniSophien Kamoun @kamounlab.bsky.social · 20/05/2026This is the culmination of >10 years of work by generations of students and postdocs. Many false starts. And we know that others have tried too. Structural insights into the activate-and-release mechanism of NLR activation. And we can engineer it too! Kudos Team 🙏🔥 0218 21
Reposted by AmirAli ToghaniMauricio Contreras @mpcontreras.bsky.social · 20/05/2026Check out our latest work! AlphaFold 3 revealed a transient immune receptor complex that eluded biochemical studies for almost a decade 🤯 We describe a conserved structural logic underlying sensor–helper communication in an NLR immune receptor network 🧵👇 19843 98
Reposted by AmirAli ToghanibioRxiv Plant Bio @biorxiv-plants.bsky.social · 19/05/2026A conserved structural logic underlies sensor-helper NLR communication in the NRC immune receptor network www.biorxiv.org/content/10.64898/20… 01711 17
AmirAli Toghani @amiralito.bsky.social · 19/05/2026Glad to see we're starting to work on Giraffes 👌🏻 020 2
Reposted by AmirAli ToghaniJuan Carlos De la Concepcion @delaconcepcionjc.bsky.social · 13/05/2026Excited to have started my group @zmbp-tuebingen.bsky.social through the @dfg.de Emmy Noether program. In this project we will be looking at the mechanisms of host invasion by fungal pathogens 🍄🌱 Check it out and drop me a line if you are interested! uni-tuebingen.de/en/universit...uni-tuebingen.deNew Emmy Noether research group on fungal infections in plants 09428 94
Reposted by AmirAli ToghaniAndrew Roger @andrewjroger.bsky.social · 06/05/2026IQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary Models academic.oup.com/mbe/article/...academic.oup.comIQ-TREE 3: Phylogenomic Inference Software using Complex Evolutionary ModelsAbstract. IQ-TREE (https://iqtree.github.io/) is a widely used open-source software tool for efficiently inferring phylogenetic trees under maximum likelih 2210105 210
Reposted by AmirAli ToghaniLarry Hunter @proflhunter.bsky.social · 06/05/2026Fun thread. Cool work, and make sure to read all the way to the end! 0103 10
Reposted by AmirAli ToghaniThe Sainsbury Laboratory @thesainsburylab.bsky.social · 06/05/2026New Preprint in collaboration with GoogleDeepMind: AI-guided discovery of atypical protein assemblies The @kamounlab.bsky.social discovered an 11-protomer complex thanks to the Structural Novelty Index , a new way to use AlphaFold to find protein assemblies that break the pattern.tsl.ac.ukAI-guided discovery of atypical protein assembliesArtificial intelligence (AI) systems such as AlphaFold have transformed structural biology by enabling accurate prediction of protein structures. However, their capacity to uncover new classes of… 0128 12
AmirAli Toghani @amiralito.bsky.social · 06/05/2026Breaking the Pattern with AlphaFold: Introducing the Structural Novelty Index by @KamounLab medium.com/p/breaking-t...medium.comBreaking the Pattern with AlphaFold: Introducing the Structural Novelty IndexThe AI system AlphaFold has transformed how we predict protein structures. But sometimes the most interesting discoveries come from asking… 031 3
Reposted by AmirAli ToghaniDaniel Lüdke @danielluedke.bsky.social · 06/05/2026Some predictions are high-confidence. These go to eleven! Huge congrats to the whole team ❤️ Such a privilege to work with you all. 12312 23
Reposted by AmirAli ToghaniMauricio Contreras @mpcontreras.bsky.social · 05/05/2026📢 The next @mpmijournal.bsky.social Focus Issue is now open for submissions: "Plant Immune Receptors in the Spotlight" 🌱🔬 Edited by @dinglab.bsky.social @clemmar.bsky.social @marischuster.bsky.social Rich Wilson and myself! Submit your best work by 31/10/26! 👇 apsjournals.apsnet.org/mpmireceptorsapsjournals.apsnet.orgPlant Immune Receptors in the Spotlight 01715 17
AmirAli Toghani @amiralito.bsky.social · 05/05/2026One last thing...These go to eleven! 1️⃣1️⃣😃 Spinal Tap knew it all along… (10/10) youtu.be/4xgx4k83zzc?...youtu.beSpinal Tap - "These go to eleven...."YouTube video by goto11tv 0100 10
AmirAli Toghani @amiralito.bsky.social · 05/05/2026Huge thanks to an incredible team for making this happen! And to @googledeepmind.zpravobot.news.ap.brid.gy for the co-scientist collaboration. (9/n) doi.org/10.64898/202...doi.org 142 4
AmirAli Toghani @amiralito.bsky.social · 05/05/2026SNI is a scalable way to discover atypical protein assemblies. Works on any family with prior structural knowledge. Working on a complex? Give it a try. We’d love to see what you find! Happy to discuss collaborations as well :) (8/n) 💻 github.com/amiralito/So... 192 9
AmirAli Toghani @amiralito.bsky.social · 05/05/2026We asked @googledeepmind.zpravobot.news.ap.brid.gy AI co-scientist to propose SNI parameters based on priors. It rediscovered 4 of our expert-defined ones, added 3 of its own — and on its own would have flagged NRC7 as atypical. Agentic AI coming to structural biology. (7/n) 131 3
AmirAli Toghani @amiralito.bsky.social · 05/05/2026One-off, or a clade feature? We grabbed NRC7 orthologs from tomato and Nicotiana benthamiana. Expressed them, imaged them, counted protomers. Both: 11. It is indeed a feature of the NRC7 clade. 1️⃣1️⃣ (6/n) 161 6
AmirAli Toghani @amiralito.bsky.social · 05/05/2026UP TO ELEVEN - We expressed potato NRC7, imaged it by negative-stain EM, ran 2D classification. 🔬💥 Rings ~250 Å across — way bigger than canonical hexamers (~150 Å). 11 protomers. (5/n) 1114 11
AmirAli Toghani @amiralito.bsky.social · 05/05/2026Phylogeny and SNI parameters further highlight clades that deviate from canonical hexamers. SNI flagged NRC7 as the largest, atypical clade in the family. A telltale clue of an unconventional assembly? 🗯️ (4/n) 141 4
AmirAli Toghani @amiralito.bsky.social · 05/05/2026We scaled SNI to 637 non-redundant NRCs from 346 genomes across 85 Solanaceae species. Most clustered with canonical hexamers. Five clades didn’t. (3/n) doi.org/10.5281/zeno... 141 4
AmirAli Toghani @amiralito.bsky.social · 05/05/2026SNI quantifies AlphaFold models based on features that define canonical protein complexes, incorporating prior knowledge. We applied it to NRC-type NLR immune receptors—typically hexameric—and it cleanly separates canonical hexamers from structural outliers. (2/n) 162 6