Iowa State University

Cis-regulatory network reconstruction from DNA sequence, epigenomic tracks, and Hi-C priors, constrained by gene expression. 0.84 zero-shot auROC.

Enzyme function prediction model that uses contrastive learning to assign the first three EC digits to enzymes with functions unseen during training.

Conditional variational autoencoder for antimicrobial peptide design that disentangles sequence, function, and length for independent control.

Protein-protein binding affinity and interface hotspot prediction from sequence alone, using protein language models fine-tuned on SKEMPI 2.0.

Protein melting temperature prediction from sequence, pairing frozen ESM2 embeddings with growth-temperature and thermophilicity features.

Enzyme kcat and KM prediction from sequence and substrate SMILES, binned by order of magnitude so catalytic-site mutations shift the prediction.