The scikit-bio paper in online in Nature Methods! Many thanks to our collaborators, community contributors and reviewers! We couldn’t have done it without you. www.nature.com/articles/s41... #Bioinformatics #OpenSource

Wishing you all happy holidays. 🎄🎁 Greetings from the Environmental Genomics Group. 🇲🇽🇫🇷🇧🇷🇵🇹🇵🇪🇷🇸🇮🇷🇩🇰🇩🇪🤗

🎉 Our new paper is out! We assembled a telomere-to-telomere genome 🧬 of Sporisorium scitamineum and showed how two smut strains with contrasting virulence deploy distinct early-infection programs on resistant and susceptible sugarcane genotypes. DOI: doi.org/10.1186/s128...

Had a great time organizing & teaching the MadFungi transcriptomics workshop. We spent three amazing days on RNA-seq for plant–microbe interactions and had great conversations with brilliant MSc/PhD students! 🌱🍄 #RNAseq #PlantMicrobeInteractions #Bioinformatics #PlantPathology

Important read if you use LLMs for science knowledge discovery around plants "What Large Language Models Know About Plant Molecular Biology" www.biorxiv.org/content/10.1.... As per usual LLMs appear to propagate biases.

Really happy this is out in preprint - Congratulations to @graemekettles.bsky.social @zymohaider.bsky.social, and everyone involved for their hard work completing this study! It examines a Z. tritici effector that is a molecular mimic of plant LRRs, and suppresses PTI www.biorxiv.org/content/10.1...

Dolly (@dollymehta.bsky.social‬) developed a pipeline to screen for conserved #RNA structures across genomes. She then applied it ~14,000 #plastid genomes and identified nearly 60 conserved structures. doi.org/10.1101/2025...

Great talk this afternoon by Joy Bergelson at #ESEB2025! 🌱 She showed how a small number of NLRs in Arabidopsis can recognize P. syringae, and how a protein interaction model can help explain ETI responses.

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

In #GENETICS, @3rdreviewer.bsky.social‬ and @smishra677.bsky.social‬ show it is possible to estimate recombination solely using the allele frequency spectrum and provide a genealogical interpretation of the results, showing how #MachineLearning can provide insights into biology. buff.ly/emixz9W

#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...

New online! A genomic perspective on fungal diversity and evolution

Admixture’s impact on Brazilian population evolution and health | Science www.science.org/doi/10.1126/...

FYI: New online! Transcriptomics in the era of long-read sequencing

The rest of Mendel's alleles characterized! So, out of 7 traits, 3 caused by TE insertions!!! (though apparently there are two different green alleles, one cause by a TE insertion, but another a promoter deletion allele) www.nature.com/articles/s41...

Comparative genomics needs to use phylogenetic methods: why, how and common questions www.nature.com/articles/s41... @annadewar.bsky.social @lauriebelch.bsky.social