Junichi Iwakiri

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

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.

This paper evaluates blind predictions of dynamic water and ion ensembles around RNA using cryo-EM densities from CASP16, finding that molecular dynamics approaches perform best.

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 derives nearest-neighbor parameters for inosine-cytosine RNA pairs using experimental and computational methods, showing their stability compared to canonical base pairs.

The paper introduces RintC, a method for efficiently and accurately decomposing RNA secondary structure probability distributions, validated on 16S rRNA data.

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

reactIDR evaluates the statistical reproducibility of high-throughput RNA structural analyses to classify RNA reactivity into stem, loop, and unmapped categories with high accuracy.