Yasushi Okuno

eSkip2 identifies effective exon-skipping ASO target regions by integrating genomic context and splicing perturbations, outperforming exon-restricted models in prioritizing active regions.

This study uses molecular dynamics simulations to show that longer amylose oligomers are more stable in hot water than shorter ones, with structural collapse observed in shorter chains.

The paper introduces intDesc-AbMut, a tool to automate the analysis of antibody mutations' effects on environmental interactions, achieving high accuracy in predicting crystal-like environments.

This paper introduces ChemGLaM, a chemical genomics language model for reliable and explainable compound-protein interaction predictions, achieving state-of-the-art performance and enabling drug/target exploration for ALS.

The paper converts an agonistic anti-TNFR2 biparatopic antibody into an antagonist by inserting peptide linkers into the hinge region, altering its immunocomplex formation.

The paper introduces cryoMDM, a method that estimates 3D atomic models from single cryoEM particle images by matching them to simulated structural models, revealing intermediate structures of the SARS-CoV-2 spike protein.

This study uses molecular dynamics to analyze inhibitor binding to DHFR, showing that reduced activity correlates with multiple-bound states on the protein surface.

This paper introduces Net-DMPred, a graph neural network-based method to predict cancer-specific driver missense mutations by incorporating molecular network structures.

This paper introduces a cancer subtyping method using patient-specific gene regulatory networks, identifying more clinically meaningful subtypes than existing methods.

This paper introduces PathoGN, a network-based method for predicting variant pathogenicity, which outperforms existing methods and identifies pathogenicity for 3,994 variants of uncertain significance.

This paper introduces DEFMap, a deep learning method that extracts dynamics information from cryo-EM maps, achieving results comparable to molecular dynamics simulations and experimental approaches.