Discrete energy landscapes provide a valuable means for analyzing non-equilibrium properties of biopolymers. In this study we propose a memory-efficient approach for local flooding of the lower portion of an RNA folding landscape
A RESTful web service and standalone application for automated de-novo annotation of bacterial transcription start sites from dRNA-seq data
In this paper, we introduce a novel approach to exploring the energy landscapes of discrete polymer models, with a particular emphasis on the lower-energy regions that play a critical role in understanding biopolymer folding behavior
This method paper introduces the concept of barrier trees, a convenient approach to describe the landscape of an optimization function. Barrier trees represent the toplogical characteristics of an energy landscape, such as a unique partitioning into local minima as leaves of the tree and saddle points as internal nodes connecting different minima.