October 2025
New preprint! 🌱💻
Wei W, Wu X, Sutherland CA, Lin Y, Lunde C, Exposito-Alonso M, Krasileva K. Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes. bioRxiv [Preprint]. 2025 Oct 28:2025.10.27.684862. doi: 10.1101/2025.10.27.684862. PMID: 41280085; PMCID: PMC12636352.
September 2025
Graduate student Nicole Dubs has been award the prestigious Center for Computational Biology NIH T32 fellowship! 🔥💻
New preprint: Seong K, Kumar R, Prigozhin DM, Lunde C, Ribeiro THC, Bélanger S, Hsieh JWA, Tang M, Meyers BC, Krasileva KV The Annotated Blueprint: Integrated Functional Genomic Resources for a model Tetraploid Wheat Triticum turgidum cv. Kronos bioRxiv [Preprint]. 2025. doi: https://doi.org/10.1101/2025.09.12.675711 🧬
July 2025
New preprint from the lab! 🚀💻
Stevens DM, Yang D, Liang TJ, Li T, Vega B, Coaker G, Krasileva K. Mamp-ml: A deep learning approach to epitope immunogenicity in plants. bioRxiv [Preprint]. 2025. doi: 10.1101/2025.07.11.664399
This work has been presented at International Congress for Molecular Plant Microbe Interactions in Cologne July 2025 and will be presented in September 2025 at the Machine Learning for Computational Biology in New York. Link to recording on YouTube.
If you are in industry and want to use mamp-ml, get in touch: dmstev@berkeley.edu, kseniak@berkeley.edu
February 2025
Frances Grace Stark’s work on establishing molecular system to study fungal-bacterial interactions with two model organisms, Neurospora crassa – Pseudomonas syringae and its application to discover fungal genes required for growth in the presence of bacteria is now available on bioRxiv
Stark FG, Torii-Karch M, Yuvaraj S, Bonometti L, Gladieux P, Glass NL, Krasileva K. Molecular Insights into Fungal Innate Immunity Using the Neurospora crassa – Pseudomonas syringae Model. bioRxiv [Preprint]. 2025 Jan 24:2025.01.22.633611. doi: 10.1101/2025.01.22.633611