(Q53556135)

15 May 2018

title

Network inference, analysis, and modeling in systems biology. (English)

1 reference

15 May 2018

1

Réka Albert

1 reference

15 May 2018

publication date

30 November 2007

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15 May 2018

number of pages

12

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inferred from page(s)

published in

The Plant Cell

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15 May 2018

volume

19

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15 May 2018

issue

11

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15 May 2018

page(s)

3327-3338

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15 May 2018

Combining classifiers to predict gene function in Arabidopsis thaliana using large-scale gene expression measurements

cites work

1 reference

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A novel method for signal transduction network inference from indirect experimental evidence.

7 September 2018

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A predicted interactome for Arabidopsis.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Experimental validation of a predicted feedback loop in the multi-oscillator clock of Arabidopsis thaliana

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Analysis of oncogenic signaling networks in glioblastoma identifies ASPM as a molecular target

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Data-driven modelling of signal-transduction networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Methods of robustness analysis for Boolean models of gene control networks.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

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

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

7 September 2018

Simulating cell biology.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Systematic identification of functional orthologs based on protein network comparison

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Identification of pathways regulating cell size and cell-cycle progression by RNAi

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

An auxin-driven polarized transport model for phyllotaxis

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The activity reaction core and plasticity of metabolic networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Elucidation of directionality for co-expressed genes: predicting intra-operon termination sites.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Exploration of the function and organization of the yeast early secretory pathway through an epistatic miniarray profile

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Dynamic properties of network motifs contribute to biological network organization

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Formation of regulatory patterns during signal propagation in a Mammalian cellular network

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Toward predictive models of mammalian cells

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Modelling genetic networks with noisy and varied experimental data: the circadian clock in Arabidopsis thaliana.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Quantitative inference of dynamic regulatory pathways via microarray data

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Global network analysis of phenotypic effects: protein networks and toxicity modulation in Saccharomyces cerevisiae

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Properties of metabolic networks: structure versus function

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A gene regulatory network model for cell-fate determination during Arabidopsis thaliana flower development that is robust and recovers experimental gene expression profiles.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Bayesian analysis of signaling networks governing embryonic stem cell fate decisions.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Advances to Bayesian network inference for generating causal networks from observational biological data

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Conserved network motifs allow protein-protein interaction prediction.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

PathBLAST: a tool for alignment of protein interaction networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Integrating high-throughput and computational data elucidates bacterial networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A dynamic mathematical model to clarify signaling circuitry underlying programmed cell death control in Arabidopsis disease resistance

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Functional and topological characterization of protein interaction networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The metabolic world of Escherichia coli is not small

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Network biology: understanding the cell's functional organization

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

NASCArrays: a repository for microarray data generated by NASC's transcriptomics service

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A protein interaction map of Drosophila melanogaster

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Structure and function of the feed-forward loop network motif

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The connectivity structure, giant strong component and centrality of metabolic networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Global protein function prediction from protein-protein interaction networks.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Thirteen years of building constraint-based in silico models of Escherichia coli

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Subnetwork hierarchies of biochemical pathways.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Computational approaches to cellular rhythms

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Control, exploitation and tolerance of intracellular noise

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Transcriptional regulatory networks in Saccharomyces cerevisiae

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Network motifs in the transcriptional regulation network of Escherichia coli

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Systems biology: a brief overview

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The small world inside large metabolic networks.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Lethality and centrality in protein networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Cis-regulatory logic in the endo16 gene: switching from a specification to a differentiation mode of control.

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Using Bayesian networks to analyze expression data

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The large-scale organization of metabolic networks

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A model for individual and collective cell movement in Dictyostelium discoideum

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Systematic determination of genetic network architecture

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Modeling gene expression with differential equations

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

Large-scale temporal gene expression mapping of central nervous system development

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

A connectionist model of development

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The war of the whorls: genetic interactions controlling flower development

7 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2174897

The logical analysis of continuous, non-linear biochemical control networks

7 September 2018

1 reference

12 December 2020

Dynamics of the genetic regulatory network for Arabidopsis thaliana flower morphogenesis

1 reference

12 December 2020

A model of the ethylene signaling pathway and its gene response in Arabidopsis thaliana: pathway cross-talk and noise-filtering properties

1 reference

12 December 2020

A probabilistic functional network of yeast genes

1 reference

12 December 2020

Topological and causal structure of the yeast transcriptional regulatory network

1 reference

12 December 2020

Evolutionary conservation of motif constituents in the yeast protein interaction network

1 reference

12 December 2020

Scale-rich metabolic networks

1 reference

12 December 2020

Identifiers

DOI

10.1105/TPC.107.054700

1 reference

15 May 2018

0 references

1 reference

15 May 2018