(Q37952114)

25 August 2017

title

Software for systems biology: from tools to integrated platforms (English)

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25 August 2017

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2

Yukiko Matsuoka

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25 August 2017

Samik Ghosh

1

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25 August 2017

Yoshiyuki Asai

series ordinal

3

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25 August 2017

Kun-Yi Hsin

series ordinal

4

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25 August 2017

Hiroaki Kitano

series ordinal

5

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25 August 2017

publication date

3 November 2011

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25 August 2017

published in

Nature Reviews Genetics

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25 August 2017

volume

12

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25 August 2017

issue

12

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25 August 2017

page(s)

821-832

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Systems biology: a brief overview

25 August 2017

cites work

1 reference

Computational systems biology

31 March 2020

1 reference

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31 March 2020

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Network dynamics and cell physiology

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An ErbB3 antibody, MM-121, is active in cancers with ligand-dependent activation

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Therapeutically targeting ErbB3: a key node in ligand-induced activation of the ErbB receptor-PI3K axis.

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Big data: open-source format needed to aid wiki collaboration

31 March 2020

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Saving big pharma from drowning in the data pool

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Bioinformatics and data management support for environmental genomics

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Management of information in distributed biomedical collaboratories.

31 March 2020

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A structured overview of simultaneous component based data integration

31 March 2020

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Standards for systems biology

31 March 2020

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Minimum information about a microarray experiment (MIAME)-toward standards for microarray data

31 March 2020

1 reference

The minimum information about a proteomics experiment (MIAPE)

31 March 2020

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Data standards and controlled vocabularies for proteomics

31 March 2020

1 reference

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

31 March 2020

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caGrid: design and implementation of the core architecture of the cancer biomedical informatics grid

31 March 2020

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Taverna: a tool for the composition and enactment of bioinformatics workflows

31 March 2020

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Galaxy: a platform for interactive large-scale genome analysis

31 March 2020

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A network view of disease and compound screening

31 March 2020

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Gene expression profiling predicts clinical outcome of breast cancer

31 March 2020

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Genetic mapping in human disease

31 March 2020

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HTRA1 promoter polymorphism in wet age-related macular degeneration

31 March 2020

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A variant of the HTRA1 gene increases susceptibility to age-related macular degeneration

31 March 2020

1 reference

Complex trait analysis of gene expression uncovers polygenic and pleiotropic networks that modulate nervous system function

31 March 2020

1 reference

Genetic inheritance of gene expression in human cell lines

31 March 2020

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Genetic analysis of genome-wide variation in human gene expression

31 March 2020

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An integrative genomics approach to the reconstruction of gene networks in segregating populations.

31 March 2020

1 reference

Increasing the power to detect causal associations by combining genotypic and expression data in segregating populations

31 March 2020

1 reference

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

31 March 2020

1 reference

ARACNE: An Algorithm for the Reconstruction of Gene Regulatory Networks in a Mammalian Cellular Context

31 March 2020

1 reference

Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles

31 March 2020

1 reference

Network motifs in the transcriptional regulation network of Escherichia coli

31 March 2020

1 reference

Network motifs: theory and experimental approaches

31 March 2020

1 reference

Inferring the transcriptional network of Bacillus subtilis

31 March 2020

1 reference

The transcription unit architecture of the Escherichia coli genome

31 March 2020

1 reference

Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli

31 March 2020

1 reference

DISTILLER: a data integration framework to reveal condition dependency of complex regulons in Escherichia coli

31 March 2020

1 reference

Advantages and limitations of current network inference methods

31 March 2020

1 reference

Building Watson: An Overview of the DeepQA Project

31 March 2020

1 reference

A comprehensive map of the toll-like receptor signaling network

31 March 2020

1 reference

A comprehensive pathway map of epidermal growth factor receptor signaling

31 March 2020

1 reference

A comprehensive map of the mTOR signaling network

31 March 2020

1 reference

A comprehensive molecular interaction map of the budding yeast cell cycle

31 March 2020

1 reference

KEGG: kyoto encyclopedia of genes and genomes

31 March 2020

1 reference

Reactome: a knowledgebase of biological pathways

31 March 2020

1 reference

The PANTHER database of protein families, subfamilies, functions and pathways

31 March 2020

1 reference

Pathway Commons, a web resource for biological pathway data

31 March 2020

1 reference

Expansion of the BioCyc collection of pathway/genome databases to 160 genomes

31 March 2020

1 reference

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

31 March 2020

1 reference

The BioPAX community standard for pathway data sharing

31 March 2020

1 reference

The Systems Biology Graphical Notation

31 March 2020

1 reference

Minimum information requested in the annotation of biochemical models (MIRIAM)

31 March 2020

1 reference

Using process diagrams for the graphical representation of biological networks

31 March 2020

1 reference

Systems biology standards—the community speaks

31 March 2020

1 reference

Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration

31 March 2020

1 reference

Presenting and exploring biological pathways with PathVisio

31 March 2020

1 reference

Cytoscape: a software environment for integrated models of biomolecular interaction networks

31 March 2020

1 reference

Pathway databases and tools for their exploitation: benefits, current limitations and challenges

31 March 2020

1 reference

A comprehensive modular map of molecular interactions in RB/E2F pathway

31 March 2020

1 reference

Reconstruction annotation jamborees: a community approach to systems biology

31 March 2020

1 reference

A protocol for generating a high-quality genome-scale metabolic reconstruction

31 March 2020

1 reference

Reconstruction of biochemical networks in microorganisms

31 March 2020

1 reference

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

31 March 2020

1 reference

A comprehensive molecular interaction map for rheumatoid arthritis

31 March 2020

1 reference

Payao: a community platform for SBML pathway model curation

31 March 2020

1 reference

WikiPathways: pathway editing for the people

31 March 2020

1 reference

Resources, standards and tools for systems biology

31 March 2020

1 reference

Irreversibility of mitotic exit is the consequence of systems-level feedback.

31 March 2020

1 reference

Stochastic mechanisms in gene expression

31 March 2020

1 reference

Regulation of noise in the expression of a single gene

31 March 2020

1 reference

AgentCell: a digital single-cell assay for bacterial chemotaxis

31 March 2020

1 reference

BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains

31 March 2020

1 reference

Enzyme kinetics informatics: from instrument to browser

31 March 2020

1 reference

Minimum Information About a Simulation Experiment (MIASE)

31 March 2020

1 reference

SBRML: a markup language for associating systems biology data with models

31 March 2020

1 reference

COPASI--a COmplex PAthway SImulator

31 March 2020

1 reference

Metabolic stability and epigenesis in randomly constructed genetic nets

31 March 2020

1 reference

SimBoolNet--a Cytoscape plugin for dynamic simulation of signaling networks

31 March 2020

1 reference

Genetic basis and molecular mechanism for idiopathic ventricular fibrillation

31 March 2020

1 reference

Modeling the heart--from genes to cells to the whole organ

31 March 2020

1 reference

Toward integration of biological and physiological functions at multiple levels.

31 March 2020

1 reference

NeuroML: a language for describing data driven models of neurons and networks with a high degree of biological detail

31 March 2020

1 reference

Specifications of insilicoML 1.0: a multilevel biophysical model description language

31 March 2020

1 reference

Can we trust docking results? Evaluation of seven commonly used programs on PDBbind database.

31 March 2020

1 reference

Docking ligands into flexible and solvated macromolecules. 4. Are popular scoring functions accurate for this class of proteins?

31 March 2020

1 reference

Beyond standardization: dynamic software infrastructures for systems biology

31 March 2020

1 reference

PANTHER pathway: an ontology-based pathway database coupled with data analysis tools

31 March 2020

1 reference

PathText: a text mining integrator for biological pathway visualizations

31 March 2020

1 reference

LitMiner and WikiGene: identifying problem-related key players of gene regulation using publication abstracts

31 March 2020

1 reference

The Gene Wiki: community intelligence applied to human gene annotation

31 March 2020

1 reference

No rest for the bio-wikis

31 March 2020

1 reference

Social engineering for virtual 'big science' in systems biology

31 March 2020

1 reference

How will bioinformatics influence metabolic engineering?

31 March 2020

1 reference

In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data

31 March 2020

1 reference

Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos.

31 March 2020

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22048662

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Quantitative modeling of biochemical networks.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22048662

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22048662

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NRG3096

1 reference

25 August 2017

1 reference