(Q34060651)

30 July 2017

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

1 reference

30 July 2017

3

Antonio A Alonso

1 reference

30 July 2017

2

Julio R Banga

1 reference

30 July 2017

Gábor Szederkényi

1

1 reference

30 July 2017

28 October 2011

1 reference

30 July 2017

1 reference

30 July 2017

5

1 reference

30 July 2017

177

1 reference

https://scigraph.springernature.com/pub.10.1186/1752-0509-5-177

30 July 2017

0 references

cites work

Mathematical modeling of gene expression: a guide for the perplexed biologist

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

A unique transformation from ordinary differential equations to reaction networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Optimization meets systems biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Classic and contemporary approaches to modeling biochemical reactions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

A software tool to model genetic regulatory networks. Applications to the modeling of threshold phenomena and of spatial patterning in Drosophila.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Revealing strengths and weaknesses of methods for gene network inference

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Towards a rigorous assessment of systems biology models: the DREAM3 challenges

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Examples of testing global identifiability of biological and biomedical models with the DAISY software.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Systems biology: parameter estimation for biochemical models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Gene regulatory network inference: data integration in dynamic models-a review

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Small-scale copy number variation and large-scale changes in gene expression.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Network inference using informative priors

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Parameter estimation and optimal experimental design.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Subnetwork analysis reveals dynamic features of complex (bio)chemical networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Dialogue on reverse-engineering assessment and methods: the DREAM of high-throughput pathway inference

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

DAISY: a new software tool to test global identifiability of biological and physiological systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

A model-based optimization framework for the inference of regulatory interactions using time-course DNA microarray expression data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Reconstructing gene regulatory networks with bayesian networks by combining expression data with multiple sources of prior knowledge

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

How to infer gene networks from expression profiles

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Metabolic networks in motion: 13C-based flux analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Predicting essential components of signal transduction networks: a dynamic model of guard cell abscisic acid signaling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

A methodology for the structural and functional analysis of signaling and regulatory networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Mathematical models in microbial systems biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Mathematical and computational techniques to deduce complex biochemical reaction mechanisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Metabolomics and systems biology: making sense of the soup

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Network component analysis: reconstruction of regulatory signals in biological systems

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Computational systems biology

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Metabolic network structure determines key aspects of functionality and regulation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Linking the genes: inferring quantitative gene networks from microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Modeling and simulation of genetic regulatory systems: a literature review

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Reverse engineering of biological complexity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Systems biology: the reincarnation of systems theory applied in biology?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

The large-scale organization of metabolic networks

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Identifiability and indistinguishability of nonlinear pharmacokinetic models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3305990

Structural identifiability analysis of some highly structured families of statespace models using differential algebra.

5 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-177

Differential algebra methods for the study of the structural identifiability of rational function state-space models in the biosciences.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-177

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-177

Linking data to models: data regression

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-177

A generalized model of the repressilator.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-177

Inference of gene networks from temporal gene expression profiles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1752-0509-5-177

Structural identifiability and indistinguishability of compartmental models

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22034917

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1752-0509-5-177

1 reference

journals/bmcsb/SzederkenyiBA11

30 July 2017

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

30 July 2017

1 reference

PubMed ID

22034917