Takumi Otagaki

LinearKnot approximates CParty's hierarchical pseudoknot analysis with linear time complexity, achieving comparable accuracy for RNA structure prediction and ensemble calculations.

LinearRaccess computes RNA accessibility for long windows in linear time without base-pair span limits, achieving high accuracy and efficiency.

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.

The paper introduces Mountain Centroid, a method for representing RNA structural ensembles as single secondary structures, showing improved performance over existing methods in certain metrics.

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.