Goro Terai

PKProbDesign optimizes thermodynamic folding probability for pseudoknotted RNA targets, achieving high pseudo-joint folding probability on most tested targets.

The paper introduces ID3, a framework for optimizing mRNA sequences using gradient-based methods, balancing multiple properties while preserving amino acid sequences.

LinearCapR computes per-nucleotide structural-context probabilities for RNA in linear time without span limits, outperforming existing methods on long-range structures and large RNAs.

StateMap integrates CRISPR fitness and gene expression data to map cancer pathway states, identifying therapeutic vulnerabilities in the Hippo pathway.

The paper introduces a method to detect readthrough downstream-of-gene transcripts by semi-extractable RNA-seq and identifies stress-inducible, semi-extractable transcripts.

The paper shows that lncRNA-dependent nuclear stress bodies promote intron retention via SR protein phosphorylation during thermal stress recovery.