Resources for integrative systems biology: from data through databases to networks and dynamic system models (Q31066861)

28 June 2017

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title

Resources for integrative systems biology: from data through databases to networks and dynamic system models (English)

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28 June 2017

Borisas Bursteinas

2

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Marketa J Zvelebil

object named as

Marketa Zvelebil

5

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author name string

Aylwin Ng

1

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PubMed ID

17040977

28 June 2017

Qiong Gao

3

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PubMed ID

17040977

28 June 2017

Ewan Mollison

4

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28 June 2017

13 October 2006

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Briefings in Bioinformatics

28 June 2017

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28 June 2017

7

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28 June 2017

4

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28 June 2017

318-330

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Computational systems biology

28 June 2017

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https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

From molecular to modular cell biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

ArrayExpress--a public repository for microarray gene expression data at the EBI

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Gene-Expression Omnibus integration and clustering tools in SeqExpress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

CIBEX: center for information biology gene expression database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Design and implementation of microarray gene expression markup language (MAGE-ML)

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The Stanford Microarray Database accommodates additional microarray platforms and data formats

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

ONCOMINE: a cancer microarray database and integrated data-mining platform

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The mouse Gene Expression Database (GXD): updates and enhancements

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Options available--from start to finish--for obtaining expression data by microarray.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Gene expression informatics--it's all in your mine.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

SWISS-2DPAGE, ten years later

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

GELBANK: a database of annotated two-dimensional gel electrophoresis patterns of biological systems with completed genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Presentation of differentially regulated proteins within a web-accessible proteome database system of microorganisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The need for a public proteomics repository.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Role of accurate mass measurement (+/- 10 ppm) in protein identification strategies employing MS or MS/MS and database searching.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

TANDEM: matching proteins with tandem mass spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

PRIDE: a public repository of protein and peptide identifications for the proteomics community

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

21 January 2018

The PeptideAtlas project

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The Biomolecular Interaction Network Database and related tools 2005 update

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The Database of Interacting Proteins: 2004 update

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

IntAct: an open source molecular interaction database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

MINT: a Molecular INTeraction database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The MIPS mammalian protein-protein interaction database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

pSTIING: a 'systems' approach towards integrating signalling pathways, interaction and transcriptional regulatory networks in inflammation and cancer.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

STRING: known and predicted protein-protein associations, integrated and transferred across organisms

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

A map of the interactome network of the metazoan C. elegans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Global analysis of protein activities using proteome chips

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Functional organization of the yeast proteome by systematic analysis of protein complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

A physical and functional map of the human TNF-alpha/NF-kappa B signal transduction pathway

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

A gene network for navigating the literature

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Human protein reference database as a discovery resource for proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Reactome: a knowledgebase of biological pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

BioLayout(Java): versatile network visualisation of structural and functional relationships

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Discovering regulatory and signalling circuits in molecular interaction networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Osprey: a network visualization system

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

VisANT: data-integrating visual framework for biological networks and modules

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Community structure in social and biological networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Network motifs: simple building blocks of complex networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Protein complexes and functional modules in molecular networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

A network-based analysis of systemic inflammation in humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

METLIN: a metabolite mass spectral database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

GMD@CSB.DB: the Golm Metabolome Database

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

RNAiDB and PhenoBlast: web tools for genome-wide phenotypic mapping projects

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

FlyBase: anatomical data, images and queries

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

FlyRNAi: the Drosophila RNAi screening center database.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

FLIGHT: database and tools for the integration and cross-correlation of large-scale RNAi phenotypic datasets

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

PhenomicDB: a multi-species genotype/phenotype database for comparative phenomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

MetaCyc: a multiorganism database of metabolic pathways and enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The KEGG resource for deciphering the genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Ultrasensitivity in the mitogen-activated protein kinase cascade

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Computational physiology and the Physiome Project

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Web-based kinetic modelling using JWS Online.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

MathSBML: a package for manipulating SBML-based biological models

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Computational representation of developmental genetic regulatory networks

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Grid cellware: the first grid-enabled tool for modelling and simulating cellular processes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

STOCKS: STOChastic Kinetic Simulations of biochemical systems with Gillespie algorithm.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

E-Cell 2: multi-platform E-Cell simulation system.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Integrating biological databases

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

AGML Central: web based gel proteomic infrastructure.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Common interchange standards for proteomics data: Public availability of tools and schema

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

PAX of mind for pathway researchers

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Molecular interaction maps of bioregulatory networks: a general rubric for systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Systems biology markup language: Level 2 and beyond

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

CellML: its future, present and past

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

CellML2SBML: conversion of CellML into SBML.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4.

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Understanding 'Global' Systems Biology: Metabonomics and the Continuum of Metabolism

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

Barriers to progress in systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBL036

21 January 2018

Identifiers

DOI

10.1093/BIB/BBL036

1 reference

28 June 2017

journals/bib/NgBGMZ06

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

PubMed ID

17040977