Models (7)
Transformer framework that models protein-protein interactions at residue resolution, generalizing zero-shot to unseen MHC alleles and sequence-neutral PTMs from one fixed checkpoint.
Channel-adaptive autoregressive generative model that synthesizes in-silico fluorescence microscopy of protein subcellular localization from amino-acid sequence and cellular landmark stains.
Long-context (64 kb) RNA foundation model using the Striped-Hyena architecture for zero-shot prediction of transcriptome architecture from unspliced pre-mRNA sequence.
Scooby
Technical University of Munich / Helmholtz Munich / Harvard Medical School / Broad Institute / Harvard University
Released October 1, 2025
Predicts single-cell-resolution scRNA-seq coverage and scATAC-seq insertion profiles directly from DNA sequence by adapting the Borzoi predictor with a cell-specific decoder.
Multimodal foundation model predicting genome-wide binding of chromatin-associated proteins from protein sequence, DNA sequence, and cell-type chromatin state.
A rigorous benchmarking study of scBERT and scGPT for cell type annotation, comparing foundation models against logistic regression baselines.
Transformer-based foundation model pretrained on ~30 million single-cell transcriptomes for context-aware gene network predictions and therapeutic target discovery.