DNA motif discovery and, particularly, computational modeling of transcription factor binding motifs, has been a mecca of algorithmic bioinformatics for several decades. Here, we report the results of the largest open community challenge in Inferring BInding Specificities (IBIS), where participants all over the world w...
Nikita Gryzunov, Dmitry D. Penzar, V. Kamenets et al.· Cell Reports· 0 citations
The Botanic1 family of gLMs designed for plant research is presented, which operates reliably on sequences from hundreds of base pairs up to 128 kbp, and integrates Botanic1 as a specialised genomic layer callable by a generalist large language model (LLM) agent, illustrating how such hybrid systems could accelerate pl...
A. Barozet, V. Cabeli, Jean Ogier du Terrail et al.· bioRxiv· 0 citations
The development of climate-resilient crops would be greatly accelerated by models able to reason directly over plant genomic sequences and to pinpoint trait-associated regions or loci. Anticipating the impact of DNA base changes (variants) remains challenging, and understanding regulatory mechanisms is still an active...
A. Barozet, V. Cabeli, J. D. du Terrail et al.· bioRxiv· 0 citations
A biologically informed framework for classifying and interpreting chromatin interactions is developed and dual-state regulatory elements connected to these dual-state regulatory elements are enriched for developmental and signaling pathways and exhibit increased expression specificity across cell types, consistent wit...
