SIB Swiss Institute of Bioinformatics

Protein sequence encoder that maps ESM2 embeddings to a learned 20-letter alphabet for structure-quality remote homology detection at MMseqs2 speed.

Bacterial genomics foundation model reading whole genomes as ordered protein sequences. Predicts operons, gene essentiality, and phenotypic traits.

Protein binder design that inverts the frozen Boltz-1 all-atom predictor, targeting small molecules, nucleic acids, metals, and modified residues.

Enhancer-promoter interaction prediction from DNA sequence and ATAC-seq alone. Spearman above 0.90 on cell types unseen during training.

Per-residue classifiers fine-tuned from ESM-2 and ProtT5 that label 20 UniProt protein features and read out what a missense variant disrupts.

De novo protein binder design pipeline that hallucinates binders through frozen AlphaFold2 weights, averaging a 46% experimental success rate.

Homology-aware but alignment-free protein language model using the Mamba state space architecture to condition on hundreds of unaligned homologs.

Virtual staining model that generates 11-marker spatially resolved protein multiplexes from routine H&E histopathology whole-slide images.

Cryo-electron tomography membrane analysis pipeline pairing generalizable U-Net membrane segmentation with mesh-based particle localization.