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List of works by James Faeder

'On-the-fly' or 'generate-first' modeling?

scientific article published in November 2005

A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases

scientific article

A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity

scientific article published on 17 October 2005

Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 system

scientific article published on April 2009

Analysis and verification of the HMGB1 signaling pathway

scientific article

Automated visualization of rule-based models

scientific article published on 13 November 2017

BioNetGen 2.2: advances in rule-based modeling. ⬇️

scientific article published on 8 July 2016

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

scientific article

Carbon-fate maps for metabolic reactions.

scientific article published on 12 October 2007

Combination treatment optimization using a pan-cancer pathway model

scientific article published on 28 December 2021

Combinatorial complexity and dynamical restriction of network flows in signal transduction

scientific article published in March 2005

Computational models of tandem SRC homology 2 domain interactions and application to phosphoinositide 3-kinase.

scientific article published on 20 January 2008

Cutting Edge: Differential Regulation of PTEN by TCR, Akt, and FoxO1 Controls CD4+ T Cell Fate Decisions

scientific article published on 8 April 2015

Demystifying the cytokine network: Mathematical models point the way.

scientific article published on 2 December 2016

Depicting signaling cascades

scientific article published on 01 February 2006

Domain-oriented reduction of rule-based network models.

scientific article published on September 2008

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

scientific article

Efficient stochastic simulation of chemical kinetics networks using a weighted ensemble of trajectories

scientific article published on September 2013

Exact hybrid particle/population simulation of rule-based models of biochemical systems

scientific article (publication date: April 2014)

GetBonNie for building, analyzing and sharing rule-based models.

scientific article published on 25 March 2009

Heterogeneities in Axonal Structure and Transporter Distribution Lower Dopamine Reuptake Efficiency.

scientific article published in January 2018

In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoes

scientific article published on 11 June 2013

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

scientific article

Kinetic proofreading model.

scientific article published on January 2008

MOSBIE: a tool for comparison and analysis of rule-based biochemical models.

scientific article

Memory of Germinant Stimuli in Bacterial Spores

scientific article

Modeling for (physical) biologists: an introduction to the rule-based approach

scientific article (publication date: July 2015)

Modeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates

scientific article

Modeling the T cell immune response: a fascinating challenge

scientific article

Modeling the early signaling events mediated by FcepsilonRI.

scientific article

NF-κB Dynamics Discriminate between TNF Doses in Single Cells

scientific article published on 7 November 2017

Parallel Tempering with Lasso for model reduction in systems biology

scientific article published on 09 March 2020

Q-bio 2007: a watershed moment in modern biology

scientific article published on 4 December 2007

Rapid community-driven development of a SARS-CoV-2 tissue simulator ⬇️

scientific article published on 06 April 2020

Reductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist Experiments

scientific article published on April 2016

Regulatory network analysis acceleration with reconfigurable hardware

scientific article published in January 2011

Rule-based modeling of biochemical systems with BioNetGen

scientific article

Rule-based modeling of signal transduction: a primer.

scientific article published on January 2012

Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.

scientific article published on 30 September 2013

RuleBender: a visual interface for rule-based modeling

scientific article

Rules for modeling signal-transduction systems

scientific article

SBML Level 3: an extensible format for the exchange and reuse of biological models

scientific article published on 01 August 2020

Selected papers from the First q-bio Conference on Cellular Information Processing

scientific article published on 01 September 2008

Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing

scientific article published on 10 August 2011

Shaping the response: the role of FcεRI and Syk expression levels in mast cell signaling

scientific article

Simulation of large-scale rule-based models

scientific article

Simulations of ICl-(CO2)n photodissociation: effects of structure, excited state charge flow, and solvent dynamics

scientific article published on 01 January 2010

Solvation dynamics in reverse micelles: the role of headgroup-solute interactions

scientific article

Special section dedicated to The Sixth q-bio Conference: meeting report and preface

scientific article published on 4 June 2013

Structure-based kinetic models of modular signaling protein function: focus on Shp2.

scientific article published on 5 January 2007

Synergism between different germinant receptors in the germination of Bacillus subtilis spores.

scientific article published on July 2011

Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2

scientific article published on 06 July 2020

The Seventh q-bio Conference: meeting report and preface

scientific article published on 30 July 2014

The complexity of cell signaling and the need for a new mechanics

scientific article

The complexity of complexes in signal transduction.

scientific article

The duration of T cell stimulation is a critical determinant of cell fate and plasticity.

scientific article published on 5 November 2013

The eighth q-bio conference: meeting report and special issue preface

scientific article published on 30 December 2015

The interplay of double phosphorylation and scaffolding in MAPK pathways

scientific article

The mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases

scientific article

Toward a comprehensive language for biological systems ⬇️

scientific article published on October 17, 2011

Toward a quantitative theory of intrinsically disordered proteins and their function

scientific article

Translational systems approaches to the biology of inflammation and healing

scientific article

Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patient

scientific article published on March 2008

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

scientific article

Workshop report: modeling the molecular mechanism of bacterial spore germination and elucidating reasons for germination heterogeneity

scientific article

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