Predicting fluorescence lifetimes and spectra of biopolymers / Modeling of regulatory networks : theory and applications in the study of the Drosophila circadian clock / Strategies for articulated multibody-based adaptive coarse grain simulation of RNA / Modeling loop entropy / Inferring functional relationships and causal network structure from gene expression profiles / Numerical solution of the chemical master equation : uniqueness and stability of the stationary distribution for chemical networks, and mRNA bursting in a gene network with negative feedback regulation / How molecular should your molecular model be? / Computational modeling of biological pathways by executable biology / Computing molecular fluctuations in biochemical reaction systems based on a mechanistic, statistical theory of irreversible processes / Probing the input-output behavior of biochemical and genetic systems : system idenitification methods from control theory / Biochemical pathway modeling tools for drug target detection in cancer and other complex diseases / Deterministic and stochastic simulation and analysis of biochemical reaction networks : the lactose operon example / Multivariate neighborhood sample entropy : a method for data reduction and prediction of complex data / Scaling differences of heartbeat excursions between wake and sleep periods / Changepoint analysis for single-molecule polarized total internal reflection fuorescence microscopy experiments / Inferring mechanisms from dose-response curves / Spatial aspects in biological system simulations / Computational approaches to modeling viral structure and assembly / Rosetta3 : an object-oriented software suite for the simulation and design of macromolecules / Computational design of intermolecular stability and specificity in protein self-assembly / Differential analysis of 2D gel images