This paper shows how SHAPE-guided RNA folding is implemented in the ViennaRNA Package, comparing three widely used strategies for turning nucleotide reactivities into soft constraints that improve thermodynamic structure prediction.
This paper revisits the earlier flooding-based landscape methods and adapts them to RNA secondary structures with a local, memory-efficient enumeration strategy.
TSSAR introduced statistically grounded, automated annotation of bacterial transcription start sites from dRNA-seq data and packaged it as both a RESTful web service and a standalone tool.
This paper develops an efficient flooding-style algorithm for exploring the low-energy part of discrete polymer landscapes, making barrier-tree analysis feasible without exhaustive enumeration.
This paper develops the barrier-tree formalism for degenerate landscapes and helped establish a general language for analyzing basins, saddle points, and transition barriers in complex discrete systems.