BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology (Q35127856)

6 August 2017

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology (English)

1 reference

6 August 2017

11

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Alejandro Fernández Villaverde

6 August 2017

Anton Crombach

7

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Alejandro F Villaverde

1

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Eva Balsa-Canto

Eva Balsa-Canto

10

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Johannes Jäger

Johannes Jaeger

12

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Julio R. Banga

Julio R Banga

13

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author name string

David Henriques

2

1 reference

6 August 2017

Kieran Smallbone

3

1 reference

6 August 2017

Sophia Bongard

4

1 reference

6 August 2017

Joachim Schmid

5

1 reference

6 August 2017

Damjan Cicin-Sain

6

1 reference

6 August 2017

Julio Saez-Rodriguez

8

1 reference

6 August 2017

Klaus Mauch

9

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6 August 2017

20 February 2015

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6 August 2017

1 reference

6 August 2017

9

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6 August 2017

8

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Creative Commons Attribution 4.0 International

6 August 2017

start time

20 February 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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exact match

https://scigraph.springernature.com/pub.10.1186/s12918-015-0144-4

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cites work

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28 July 2018

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Kinetic models in industrial biotechnology - Improving cell factory performance

28 July 2018

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Advancing metabolic models with kinetic information.

28 July 2018

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Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach

28 July 2018

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Reverse engineering and identification in systems biology: strategies, perspectives and challenges

28 July 2018

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Reverse-engineering post-transcriptional regulation of gap genes in Drosophila melanogaster

28 July 2018

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Incremental parameter estimation of kinetic metabolic network models

28 July 2018

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State-time spectrum of signal transduction logic models

28 July 2018

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Efficient reverse-engineering of a developmental gene regulatory network

28 July 2018

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A cooperative strategy for parameter estimation in large scale systems biology models.

28 July 2018

1 reference

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Yeast 5 – an expanded reconstruction of the Saccharomyces cerevisiae metabolic network

28 July 2018

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Structural identifiability of systems biology models: a critical comparison of methods

28 July 2018

1 reference

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Sustainable model building the role of standards and biological semantics

28 July 2018

1 reference

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ON IDENTIFIABILITY OF NONLINEAR ODE MODELS AND APPLICATIONS IN VIRAL DYNAMICS.

28 July 2018

1 reference

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GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods

28 July 2018

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AMIGO, a toolbox for advanced model identification in systems biology using global optimization

28 July 2018

1 reference

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BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

28 July 2018

1 reference

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Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation

28 July 2018

1 reference

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Bacterial adaptation through distributed sensing of metabolic fluxes

28 July 2018

1 reference

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An iterative identification procedure for dynamic modeling of biochemical networks

28 July 2018

1 reference

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Gene circuit analysis of the terminal gap gene huckebein

28 July 2018

1 reference

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Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling

28 July 2018

1 reference

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Systems biology: parameter estimation for biochemical models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Benchmarking regulatory network reconstruction with GRENDEL.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Benchmarks for identification of ordinary differential equations from time series data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Parameter estimation and optimal experimental design.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Comparison of reverse-engineering methods using an in silico network

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

COPASI--a COmplex PAthway SImulator

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Iterative approach to model identification of biological networks

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Production of recombinant protein therapeutics in cultivated mammalian cells

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

A benchmark for methods in reverse engineering and model discrimination: problem formulation and solutions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Parameter estimation in biochemical pathways: a comparison of global optimization methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Artificial gene networks for objective comparison of analysis algorithms

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

A connectionist model of development

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Parameter uncertainty in biochemical models described by ordinary differential equations.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

On the identifiability of metabolic network models.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Benchmarking of continuous black box optimization algorithms.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Conclusions via unique predictions obtained despite unidentifiability--new definitions and a general method.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Inference of complex biological networks: distinguishability issues and optimization-based solutions

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

GenSSI: a software toolbox for structural identifiability analysis of biological models

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Parameter identifiability of power-law biochemical system models

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Flux balance analysis: a geometric perspective.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Generating realistic in silico gene networks for performance assessment of reverse engineering methods

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Optimization in computational systems biology

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Conservation laws and unidentifiability of rate expressions in biochemical models

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Dynamic modeling of the central carbon metabolism of Escherichia coli.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Insights into the behaviour of systems biology models from dynamic sensitivity and identifiability analysis: a case study of an NF-kappaB signalling pathway.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Linking data to models: data regression

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Dynamic control of positional information in the early Drosophila embryo.

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

Mechanism of eve stripe formation

27 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4342829

10.1186/S12918-015-0144-4

27 September 2018

Identifiers

DOI

1 reference

journals/bmcsb/VillaverdeHSB0C15

6 August 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

1008164526

0 references

Fatcat ID

release_kpionivsk5h2rnuc7vcczo6wy4

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/kpionivsk5h2rnuc7vcczo6wy4

mapped directly with Wikidata item

24 November 2022

based on heuristic

PMCID

4342829

1 reference

6 August 2017

1 reference