Rule-based multi-level modeling of cell biological systems

Hierarchical graphs for rule-based modeling of biochemical systems

(2011) Nathan W Lemons et al.   BMC BIOINFORMATICS

Reactive Oxygen Species Production by Forward and Reverse Electron Fluxes in the Mitochondrial Respiratory Chain

(2011) Vitaly A. Selivanov et al.   PLoS Computational Biology

Snoopy--a unifying Petri net framework to investigate biomolecular networks

(2010) C. Rohr et al.   BIOINFORMATICS

Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes

(2010) Dominic P Tolle et al.   BMC Systems Biology

Flexible experimentation in the modeling and simulation framework JAMES II--implications for computational systems biology

(2010) R. Ewald et al.   BRIEFINGS IN BIOINFORMATICS

Stochastic Modeling of Naïve T Cell Homeostasis for Competing Clonotypes via the Master Equation

(2010) Shev MacNamara et al.   MULTISCALE MODELING & SIMULATION

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

(2010) Michael W Sneddon et al.   NATURE METHODS

Detailed Simulations of Cell Biology with Smoldyn 2.1

(2010) Steven S. Andrews et al.   PLoS Computational Biology

Cell division brought down to size

(2009) Kenneth E. Sawin   NATURE

A spatial gradient coordinates cell size and mitotic entry in fission yeast

(2009) James B. Moseley et al.   NATURE

Exploring the roles of noise in the eukaryotic cell cycle

(2009) S. Kar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Location, Location, Location

(2009) S. Hurtley   SCIENCE

Multiscale modeling for biologists

(2009) Martin Meier-Schellersheim et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases

(2009) Dipak Barua et al.   PLoS Computational Biology

Programming with models: modularity and abstraction provide powerful capabilities for systems biology

(2008) A. Mallavarapu et al.   Journal of the Royal Society Interface