Efficient modeling, simulation and coarse-graining of biological complexity with NFsim

Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates

(2010) Michael I. Monine et al.   BIOPHYSICAL JOURNAL

RuleMonkey: software for stochastic simulation of rule-based models

(2010) Joshua Colvin et al.   BMC BIOINFORMATICS

Global parameter estimation methods for stochastic biochemical systems

(2010) Suresh Poovathingal et al.   BMC BIOINFORMATICS

Towards genome-scale signalling-network reconstructions

(2010) Daniel R. Hyduke et al.   NATURE REVIEWS GENETICS

Simulation of large-scale rule-based models

(2009) Joshua Colvin et al.   BIOINFORMATICS

Unlimited multistability in multisite phosphorylation systems

(2009) Matthew Thomson et al.   NATURE

Defining the scientific method

(2009)   NATURE METHODS

Delay-Induced Degrade-and-Fire Oscillations in Small Genetic Circuits

(2009) William Mather et al.   PHYSICAL REVIEW LETTERS

An Analytical Solution to the Kinetics of Breakable Filament Assembly

(2009) T. P. J. Knowles et al.   SCIENCE

Design principles of biochemical oscillators

(2008) Béla Novák et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Kinetic Monte Carlo method for rule-based modeling of biochemical networks

(2008) Jin Yang et al.   PHYSICAL REVIEW E

Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation

(2008) Clinton H. Hansen et al.   PLoS Computational Biology

Bacterial chemoreceptors: high-performance signaling in networked arrays

(2008) Gerald L. Hazelbauer et al.   TRENDS IN BIOCHEMICAL SCIENCES

Stochastic Severing of Actin Filaments by Actin Depolymerizing Factor/Cofilin Controls the Emergence of a Steady Dynamical Regime

(2007) Jeremy Roland et al.   BIOPHYSICAL JOURNAL