(Q34156664)

31 July 2017

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

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31 July 2017

2

James R Faeder

1 reference

31 July 2017

3

Thierry Emonet

1 reference

31 July 2017

Michael W Sneddon

1

1 reference

31 July 2017

26 December 2010

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31 July 2017

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31 July 2017

8

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31 July 2017

2

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31 July 2017

177-183

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https://scigraph.springernature.com/pub.10.1038/nmeth.1546

31 July 2017

0 references

cites work

Executable cell biology

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Computational systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Cellular motility driven by assembly and disassembly of actin filaments

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Unlimited multistability in multisite phosphorylation systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Making sense of it all: bacterial chemotaxis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Rules for modeling signal-transduction systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Rule-based modeling of biochemical systems with BioNetGen

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

An analytical solution to the kinetics of breakable filament assembly

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Chemotaxis in Escherichia coli: a molecular model for robust precise adaptation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Stochastic severing of actin filaments by actin depolymerizing factor/cofilin controls the emergence of a steady dynamical regime

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Towards genome-scale signalling network reconstructions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

COPASI--a COmplex PAthway SImulator

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Bacterial chemoreceptors: high-performance signaling in networked arrays

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Automatic generation of cellular reaction networks with Moleculizer 1.0.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Simulation of large-scale rule-based models

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

RuleMonkey: software for stochastic simulation of rule-based models

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

A free-energy-based stochastic simulation of the Tar receptor complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

A general method for numerically simulating the stochastic time evolution of coupled chemical reactions

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Equilibrium theory for the clustering of bivalent cell surface receptors by trivalent ligands. Application to histamine release from basophils

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Global parameter estimation methods for stochastic biochemical systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Pathway of actin filament branch formation by Arp2/3 complex.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Direct real-time observation of actin filament branching mediated by Arp2/3 complex using total internal reflection fluorescence microscopy

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

An allosteric model for heterogeneous receptor complexes: understanding bacterial chemotaxis responses to multiple stimuli

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

How white noise generates power-law switching in bacterial flagellar motors.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

An ultrasensitive bacterial motor revealed by monitoring signaling proteins in single cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Design principles of biochemical oscillators

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Delay-induced degrade-and-fire oscillations in small genetic circuits.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1546

Input-output behavior of ErbB signaling pathways as revealed by a mass action model trained against dynamic data

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21186362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Defining the scientific method. Editorial

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21186362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Dizzy: stochastic simulation of large-scale genetic regulatory networks

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21186362

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NMETH.1546

1 reference

PubMed ID

21186362

Dimensions Publication ID

31 July 2017

0 references

1 reference

PubMed ID

21186362