Masaki Tagashira

ConsAlign: simultaneous RNA structural aligner based on rich transfer learning and thermodynamic ensemble model of alignment scoring

The paper introduces ConsAlign, a simultaneous RNA structural aligner that uses transfer learning and an ensemble model to improve alignment quality while maintaining computational efficiency.

Consistent Consideration of RNA Structural Alignments Improves Prediction Accuracy of RNA Secondary Structures

This paper introduces ConsHomfold and ConsAlifold, which improve RNA secondary structure prediction by consistently considering global pairwise structural alignments, achieving better accuracy with comparable speed to conventional methods.

PhyloFold: Precise and Swift Prediction of RNA Secondary Structures to Incorporate Phylogeny among Homologs

PhyloFold predicts RNA secondary structures of homologs by incorporating phylogenetic information, achieving high accuracy with efficient runtime.

RNAfamProb Plus NeoFold: Estimations of Posterior Probabilities on RNA Structural Alignment and RNA Secondary Structures with Incorporating Homologous-RNA Sequences

The paper introduces RNAfamProb and NeoFold to estimate pseudo-probabilities for RNA structural alignment and secondary structures, showing improved accuracy over existing methods.

CRAST Leads to Homologous-ncRNA Search in Genomic Scale

The paper introduces CRAST, a tool for homologous ncRNA search that uses adaptive seeds and secondary structure context, achieving efficient alignment comparable to BLAST-like tools.