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BioNetGen 2.2: advances in rule-based modeling
: BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and… Expand
An Automated Phenotype-Driven Approach (GeneForce) for Refining Metabolic and Regulatory Models
Integrated constraint-based metabolic and regulatory models can accurately predict cellular growth phenotypes arising from genetic and environmental perturbations. Challenges in constructing such… Expand
Exploring higher-order EGFR oligomerisation and phosphorylation--a combined experimental and theoretical approach.
The epidermal growth factor receptor (EGFR) kinase is generally considered to be activated by either ligand-induced dimerisation or a ligand-induced conformational change within pre-formed dimers.… Expand
Structure-based kinetic models of modular signaling protein function: focus on Shp2.
We present here a computational, rule-based model to study the function of the SH2 domain-containing protein tyrosine phosphatase, Shp2, in intracellular signal transduction. The two SH2 domains of… Expand
Computational Models of Tandem Src Homology 2 Domain Interactions and Application to Phosphoinositide 3-Kinase*
Intracellular signal transduction proteins typically utilize multiple interaction domains for proper targeting, and thus a broad diversity of distinct signaling complexes may be assembled.… Expand
A Bipolar Clamp Mechanism for Activation of Jak-Family Protein Tyrosine Kinases
Most cell surface receptors for growth factors and cytokines dimerize in order to mediate signal transduction. For many such receptors, the Janus kinase (Jak) family of non-receptor protein tyrosine… Expand
Metal oxide thin films deposited from metal organic precursors in supercritical CO2 solutions
This work demonstrates a novel method for deposition of metal oxide thin films, including Al2O3, ZrO2, MnOx, and RuOx where the metal−organic precursors and oxidizing agents are delivered in liquid… Expand
Modeling the Effect of APC Truncation on Destruction Complex Function in Colorectal Cancer Cells
In colorectal cancer cells, APC, a tumor suppressor protein, is commonly expressed in truncated form. Truncation of APC is believed to disrupt degradation of β—catenin, which is regulated by a… Expand
A Multiscale Algorithm for Spatiotemporal Modeling of Multivalent Protein-Protein Interaction
This article introduces a multiscale framework for spatiotemporal modeling of protein-protein interaction. Cellular protein molecules represent multivalent species that contain modular features, such… Expand
Multicellular Models Bridging Intracellular Signaling and Gene Transcription to Population Dynamics
Cell signaling and gene transcription occur at faster time scales compared to cellular death, division, and evolution. Bridging these multiscale events in a model is computationally challenging. We… Expand