209-scooby: modeling multimodal profiles from DNA sequence

Paper Talk · Nov 5, 2025 · 20m

The paper introduces scooby, a novel computational framework that utilizes deep learning to model multimodal genomic profiles-specifically single-cell RNA-sequencing (scRNA-seq) coverage and chromatin accessibility (scATAC-seq insertions)-directly from DNA sequence at single-cell resolution. scooby builds upon the existing bulk multiomics model Borzoi by integrating a cell-specific decoder and employing parameter-efficient fine-tuning (LoRA) to adapt it for single-cell data, effectively capturing cellular heterogeneity. The authors demonstrate that scooby accurately predicts…