RNA Design

Sequence design for RNA-RNA interactions.- Sequence design using RNAStructure.- Riboswitch design using MODENA.- Complex in-silico RNA design with MoiRNAiFold.- Machine learning for RNA design – LEARNA.- Simulated Annealing for RNA design with SIMARD.- RNA design using incaRNAfbinv demonstrated with the identification of functional RNA motifs in hepatitis delta virus.- gRNAde: a geometric deep learning pipeline for 3D RNA inverse design.- Towards increasing the credibility of RNA design.- 3D-based RNA function prediction tools in rnaglib.- Generative modeling of RNA sequence families with restricted Boltzmann  machines.- SHAPE probing to screen computationally designed RNA.- A computational approach for designing synthetic riboswitches for next-generation RNA therapeutics.- Monte Carlo inverse RNA folding.- Generating artificial ribozymes using sparse coevolutionary models.- Datasets for benchmarking RNA design algorithms.- The evolution of nucleic acid-based diagnosis methods from (pre-)CRISPR to CRISPR era and the associated machine/deep leaning approaches in relevant RNA design.