sequence-to-function modeling

Learning Strand-Equivariant Tokenizations of DNA with MirrorDNA

This paper introduces MirrorDNA, a DNA language model with a strand-equivariant tokenizer that improves prediction consistency across DNA strands.

pLM-bVAE: protein language model-enhanced binary representation improves quantum annealing-based protein sequence design

This paper introduces pLM-bVAE, a binary variational autoencoder enhanced with protein language model representations, showing improved sequence reconstruction and design performance in quantum annealing-based protein sequence design.

Physiological mapping and prediction reveal stress-responsive translation initiation landscapes

This study introduces TISCA2 and IncepTIS to map and predict stress-responsive translation initiation sites, revealing tissue-specific patterns and enabling engineered mRNA 5' leaders.

Translating chemical reactions into enzyme sequences enables formate dehydrogenase engineering

This paper introduces REXzyme, a model translating chemical reactions into enzyme sequences, and demonstrates its ability to generate active formate dehydrogenases for CO2 reduction.

Massively parallel quantification and prediction of monomeric protein yield in Escherichia coli

The paper develops a scalable assay and a protein language model to predict monomeric yield of proteins in E. coli, showing it can be learned and designed.

AlphaFold 3 Prediction Accuracy and Reliability across RNA Structures and Protein-RNA Interfaces

This study evaluates AlphaFold 3's accuracy and reliability in predicting RNA structures and protein-RNA interfaces, finding that confidence scores do not always correlate with correct predictions.

Comparative genomics of canonical antifungal dsRNA target genes across fungal plant pathogens: conserved siRNA-length windows define the scope for broad-spectrum spray-induced gene silencing

This study evaluates the conservation of antifungal dsRNA target genes across fungal plant pathogens at siRNA-length resolution, finding limited conservation beyond closely related species.

De novo design of mini-proteins as specific binders to PACAP-38, a key mediator of migraine

This study designs mini-proteins that bind PACAP-38 with high affinity, showing improved potency and stability compared to earlier versions.

GLOM TGITO: multiscale protein modelling and multiview landscape-guided sequence discovery

The paper introduces GLOM-TGITO, a method for protein design that combines multiscale modeling with multiview landscape-guided optimization, achieving high accuracy and novel sequence discovery.

ChAI-Net learns a regulatory code for chromatin co-accessibility

The paper introduces ChAI-Net, a deep learning model that predicts chromatin co-accessibility from DNA sequences in mouse embryonic stem cells, revealing sequence motifs that govern coordinated TF binding.