Vladimir Reinharz

FASTiso is an exact subgraph isomorphism algorithm that improves efficiency and scalability across graph sizes and structures, outperforming existing solvers in speed and memory usage.

The paper presents parallel algorithms to find maximal common subgraphs between RNA 3D structures and evaluates them on a non-redundant dataset.

The paper develops an integer programming framework to predict RNA secondary structures with pseudoknots and local 3D motifs, showing improved accuracy when integrating motif information.

The paper develops a stochastic agent-based model to explain multiphasic HBV kinetics in humanized mice by simulating intracellular virion production cycles.

The paper introduces an algorithm to find recurrent RNA structural modules spanning multiple secondary structure elements, identifying a module common to bacterial ribosomes.

The paper investigates how the RNA chaperone StpA interacts with group I introns, revealing a mechanism involving specific disruption and non-specific binding governed by charge patterns.

RNAmigos predicts small molecule ligands for RNA binding sites using augmented base pairing networks, showing improved performance over baselines and highlighting the importance of non-canonical base pairs.

The paper introduces BayesPairing 2, a sequence search algorithm for RNA 3D module identification, showing improved speed and accuracy over its predecessor.