about
Modeling for (physical) biologists: an introduction to the rule-based approachExact hybrid particle/population simulation of rule-based models of biochemical systemsUnbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of TrajectoriesToward a quantitative theory of intrinsically disordered proteins and their functionMOSBIE: a tool for comparison and analysis of rule-based biochemical models.Solvation dynamics in reverse micelles: the role of headgroup-solute interactions.A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinasesModeling multivalent ligand-receptor interactions with steric constraints on configurations of cell-surface receptor aggregates.Analysis and verification of the HMGB1 signaling pathway.Toward a comprehensive language for biological systemsThe mitogen-activated protein kinome from Anopheles gambiae: identification, phylogeny and functional characterization of the ERK, JNK and p38 MAP kinases.Efficient modeling, simulation and coarse-graining of biological complexity with NFsim.The complexity of complexes in signal transduction.BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains.Rules for modeling signal-transduction systems.Shaping the response: the role of FcεRI and Syk expression levels in mast cell signalingModeling the early signaling events mediated by FcepsilonRI.Kinetic Monte Carlo method for rule-based modeling of biochemical networks.Simulation of large-scale rule-based modelsRule-based modeling of biochemical systems with BioNetGen.RuleBender: a visual interface for rule-based modeling.Translational systems approaches to the biology of inflammation and healing.Structure-based kinetic models of modular signaling protein function: focus on Shp2.The interplay of double phosphorylation and scaffolding in MAPK pathwaysMemory of Germinant Stimuli in Bacterial Spores.Translational systems biology: introduction of an engineering approach to the pathophysiology of the burn patientReductionism Is Dead: Long Live Reductionism! Systems Modeling Needs Reductionist ExperimentsDomain-oriented reduction of rule-based network models.In vivo, in vitro, and in silico studies suggest a conserved immune module that regulates malaria parasite transmission from mammals to mosquitoesGetBonNie for building, analyzing and sharing rule-based models.Aggregation of membrane proteins by cytosolic cross-linkers: theory and simulation of the LAT-Grb2-SOS1 systemThe Seventh q-bio Conference: meeting report and preface.Kinetic proofreading model.Rule-based modeling: a computational approach for studying biomolecular site dynamics in cell signaling systems.Rule-based modeling of signal transduction: a primer.Modeling the T cell immune response: a fascinating challenge.Synergism between different germinant receptors in the germination of Bacillus subtilis spores.Carbon-fate maps for metabolic reactions.Demystifying the cytokine network: Mathematical models point the way.BioNetGen 2.2: advances in rule-based modeling.
P50
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P50
description
hulumtues
@sq
onderzoeker
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researcher
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հետազոտող
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name
James Faeder
@ast
James Faeder
@en
James Faeder
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James Faeder
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James Faeder
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type
label
James Faeder
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James Faeder
@en
James Faeder
@es
James Faeder
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James Faeder
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prefLabel
James Faeder
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James Faeder
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James Faeder
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James Faeder
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James Faeder
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P106
P1153
6602183658
P21
P2456
P31
P496
0000-0001-8127-609X