(Q33535721)

27 July 2017

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title

Visualization of omics data for systems biology (English)

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27 July 2017

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7

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27 July 2017

11

Anne-Claude Gavin

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Nils Gehlenborg

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Nils Gehlenborg

1

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Alexander Goesmann

object named as

Alexander Goesmann

4

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Nitin S Baliga

3

object named as

Nitin S Baliga

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27 July 2017

Seán I O'Donoghue

2

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27 July 2017

Matthew A Hibbs

5

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27 July 2017

Hiroaki Kitano

6

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27 July 2017

Heiko Neuweger

8

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27 July 2017

Reinhard Schneider

9

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27 July 2017

Dan Tenenbaum

10

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27 July 2017

1 March 2010

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27 July 2017

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27 July 2017

7

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27 July 2017

S56-68

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27 July 2017

3 Suppl

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https://scigraph.springernature.com/pub.10.1038/nmeth.1436

27 July 2017

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cites work

Modulation of the TLR-mediated inflammatory response by the endogenous human host defense peptide LL-37.

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization

21 January 2018

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https://api.crossref.org/works/10.1038%2FNMETH.1436

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks

21 January 2018

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https://api.crossref.org/works/10.1038%2FNMETH.1436

The Pathway Tools software

21 January 2018

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https://api.crossref.org/works/10.1038%2FNMETH.1436

Graph-based analysis and visualization of experimental results with ONDEX

21 January 2018

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12 December 2020

Visualizing genomes: techniques and challenges

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12 December 2020

A generic algorithm for layout of biological networks

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12 December 2020

Reactome knowledgebase of human biological pathways and processes

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12 December 2020

An evaluation of human protein-protein interaction data in the public domain

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12 December 2020

Visual exploration of three-dimensional gene expression using physical views and linked abstract views

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12 December 2020

RNA-Seq: a revolutionary tool for transcriptomics

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12 December 2020

Integration of biological networks and gene expression data using Cytoscape

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12 December 2020

SpectralNET--an application for spectral graph analysis and visualization

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12 December 2020

Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example

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12 December 2020

Human Protein Reference Database and Human Proteinpedia as discovery tools for systems biology.

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12 December 2020

An insight-based methodology for evaluating bioinformatics visualizations

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12 December 2020

MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes

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12 December 2020

Browsing multidimensional molecular networks with the generic network browser (N-Browse)

1 reference

12 December 2020

VisANT 3.5: multi-scale network visualization, analysis and inference based on the gene ontology.

1 reference

12 December 2020

Cluster analysis and display of genome-wide expression patterns

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12 December 2020

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

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12 December 2020

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

1 reference

12 December 2020

Metabolic profiling of Medicago truncatula cell cultures reveals the effects of biotic and abiotic elicitors on metabolism

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12 December 2020

Tools for visually exploring biological networks.

1 reference

12 December 2020

KEGG Atlas mapping for global analysis of metabolic pathways

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12 December 2020

Announcing the worldwide Protein Data Bank

1 reference

12 December 2020

Graphle: Interactive exploration of large, dense graphs

1 reference

12 December 2020

Metabolic profiling, metabolomic and metabonomic procedures for NMR spectroscopy of urine, plasma, serum and tissue extracts

1 reference

12 December 2020

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

1 reference

12 December 2020

Computational analysis of microarray data

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12 December 2020

Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.

1 reference

12 December 2020

MetaboMiner--semi-automated identification of metabolites from 2D NMR spectra of complex biofluids

1 reference

12 December 2020

IPSEP-COLA: an incremental procedure for separation constraint layout of graphs.

1 reference

12 December 2020

Biochemistry. A postgenomic visual icon

1 reference

12 December 2020

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

1 reference

12 December 2020

Interaction techniques for selecting and manipulating subgraphs in network visualizations.

1 reference

12 December 2020

Caryoscope: an Open Source Java application for viewing microarray data in a genomic context

1 reference

12 December 2020

Presenting and exploring biological pathways with PathVisio

1 reference

12 December 2020

Medusa: a simple tool for interaction graph analysis

1 reference

12 December 2020

Java Treeview--extensible visualization of microarray data

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12 December 2020

NAViGaTOR: Network Analysis, Visualization and Graphing Toronto

1 reference

12 December 2020

The social network of a cell: recent advances in interactome mapping

1 reference

12 December 2020

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12 December 2020

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks

1 reference

12 December 2020

ArrayXPath: mapping and visualizing microarray gene-expression data with integrated biological pathway resources using Scalable Vector Graphics

1 reference

12 December 2020

The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

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12 December 2020

The Database of Interacting Proteins: 2004 update

1 reference

12 December 2020

Advanced computing for systems biology.

1 reference

12 December 2020

ManyEyes: a site for visualization at internet scale

1 reference

12 December 2020

Genesis: cluster analysis of microarray data

1 reference

12 December 2020

An automated method for finding molecular complexes in large protein interaction networks

1 reference

12 December 2020

TOPPView: an open-source viewer for mass spectrometry data

1 reference

12 December 2020

VitaPad: visualization tools for the analysis of pathway data

1 reference

12 December 2020

KaPPA-view: a web-based analysis tool for integration of transcript and metabolite data on plant metabolic pathway maps

1 reference

12 December 2020

KEGG for linking genomes to life and the environment

1 reference

12 December 2020

GenMAPP 2: new features and resources for pathway analysis

1 reference

12 December 2020

A survey of visualization tools for biological network analysis

1 reference

12 December 2020

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

1 reference

12 December 2020

TM4: a free, open-source system for microarray data management and analysis

1 reference

12 December 2020

High-quality binary protein interaction map of the yeast interactome network

1 reference

12 December 2020

BiologicalNetworks: visualization and analysis tool for systems biology

1 reference

12 December 2020

Gene regulatory networks for development

1 reference

12 December 2020

Visualization methods for statistical analysis of microarray clusters

1 reference

12 December 2020

BNDB - the Biochemical Network Database

1 reference

12 December 2020

Proteome survey reveals modularity of the yeast cell machinery

1 reference

12 December 2020

Expression Profiler: next generation--an online platform for analysis of microarray data

1 reference

12 December 2020

Microarray data normalization and transformation

1 reference

12 December 2020

Control of yeast filamentous-form growth by modules in an integrated molecular network

1 reference

12 December 2020

Proteome organization in a genome-reduced bacterium

1 reference

12 December 2020

Current challenges and developments in GC-MS based metabolite profiling technology

1 reference

12 December 2020

Visualization of multiple alignments, phylogenies and gene family evolution

1 reference

12 December 2020

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization

1 reference

12 December 2020

Visualization of macromolecular structures.

1 reference

12 December 2020

VANTED: a system for advanced data analysis and visualization in the context of biological networks

1 reference

12 December 2020

PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways

1 reference

12 December 2020

Osprey: a network visualization system

1 reference

12 December 2020

Visualization of image data from cells to organisms

1 reference

12 December 2020

Statistical Issues in cDNA Microarray Data Analysis

1 reference

12 December 2020

Pathguide: a pathway resource list

1 reference

12 December 2020

Analysis and validation of proteomic data generated by tandem mass spectrometry

1 reference

12 December 2020

The Pathway Tools cellular overview diagram and Omics Viewer

1 reference

12 December 2020

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

1 reference

12 December 2020

BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data

1 reference

12 December 2020

The role of protein kinase C in cell surface signal transduction and tumour promotion

2 references

12 December 2020

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

STITCH 2: an interaction network database for small molecules and proteins

1 reference

12 December 2020

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

1 reference

12 December 2020

Mayday--a microarray data analysis workbench

1 reference

12 December 2020

Comparative assessment of large-scale data sets of protein-protein interactions

1 reference

12 December 2020

iPath: interactive exploration of biochemical pathways and networks

1 reference

12 December 2020

Towards zoomable multidimensional maps of the cell

1 reference

12 December 2020

Probability-based protein identification by searching sequence databases using mass spectrometry data

1 reference

12 December 2020

Spectroscopic and statistical techniques for information recovery in metabonomics and metabolomics

1 reference

12 December 2020

The IntAct molecular interaction database in 2010

1 reference

12 December 2020

Exploration of networks using overview+detail with constraint-based cooperative layout

1 reference

12 December 2020

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways

1 reference

12 December 2020

VistaClara: an expression browser plug-in for Cytoscape

1 reference

12 December 2020

Genome Expression Pathway Analysis Tool--analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context

1 reference

12 December 2020

EXPANDER--an integrative program suite for microarray data analysis

1 reference

12 December 2020

Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

1 reference

12 December 2020

A tool to visualize and evaluate data obtained by liquid chromatography-electrospray ionization-mass spectrometry

1 reference

12 December 2020

Dynamic Complex Formation During the Yeast Cell Cycle

1 reference

12 December 2020

Network integration and graph analysis in mammalian molecular systems biology

1 reference

12 December 2020

Construction, visualisation, and clustering of transcription networks from microarray expression data

1 reference

12 December 2020

SetupX--a public study design database for metabolomic projects

1 reference

12 December 2020

CellML: its future, present and past

1 reference

12 December 2020

Coexpression analysis of human genes across many microarray data sets

1 reference

12 December 2020

BicOverlapper: a tool for bicluster visualization.

1 reference

12 December 2020

Arena3D: visualization of biological networks in 3D.

1 reference

12 December 2020

Cerebral: visualizing multiple experimental conditions on a graph with biological context

1 reference

12 December 2020

WikiPathways: pathway editing for the people

1 reference

12 December 2020

Caleydo: connecting pathways and gene expression

1 reference

12 December 2020

Quantitative mass spectrometry in proteomics: a critical review

1 reference

12 December 2020

Graph drawing by force-directed placement

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

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

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

Metabolomics: Current analytical platforms and methodologies

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

The Systems Biology Graphical Notation

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

Analysis of a complex of statistical variables into principal components

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

Multidimensional scaling by optimizing goodness of fit to a nonmetric hypothesis

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

The plane with parallel coordinates

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

The History of the Cluster Heat Map

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.1436

7 January 2021

Identifiers

DOI

10.1038/NMETH.1436

1 reference

Dimensions Publication ID

27 July 2017

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