PathVisio 3: an extendable pathway analysis toolbox (Q25296662)

1

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Alexander R. Pico

6

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Anwesha Bohler

3

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Thomas Kelder

4

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Martijn P van Iersel

2

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Nuno Nunes

PLOS Computational Biology

5

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language of work or name

English

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publication date

February 2015

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number of pages

13

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published in

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volume

11

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page(s)

e1004085

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issue

2

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copyright license

Creative Commons Attribution 4.0 International

start time

23 February 2015

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

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describes a project that uses

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Presenting and exploring biological pathways with PathVisio

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

KEGG Atlas mapping for global analysis of metabolic pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

MAPPFinder: using Gene Ontology and GenMAPP to create a global gene-expression profile from microarray data

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Molecular pathways involved in prostate carcinogenesis: insights from public microarray datasets

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

The BioPAX community standard for pathway data sharing

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

WikiPathways: building research communities on biological pathways

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Cytoscape 2.8: new features for data integration and network visualization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Ten years of pathway analysis: current approaches and outstanding challenges

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

The Systems Biology Graphical Notation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

WikiPathways App for Cytoscape: Making biological pathways amenable to network analysis and visualization

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

A Network Map of FGF-1/FGFR Signaling System

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Integrated visualization of a multi-omics study of starvation in mouse intestine

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

ProfileDB: a resource for proteomics and cross-omics biomarker discovery

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

PathVisio-Faceted Search: an exploration tool for multi-dimensional navigation of large pathways

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

The immediate early gene product EGR1 and polycomb group proteins interact in epigenetic programming during chondrogenesis

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Into the eye of the cytokine storm

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

PathVisio-Validator: a rule-based validation plugin for graphical pathway notations

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs)

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Eu.Gene Analyzer a tool for integrating gene expression data with pathway databases

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Whole blood transcriptome comparison of pigs with extreme production of in vivo dsRNA-induced serum IFN-a.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4338111

Proteome-based systems biology analysis of the diabetic mouse aorta reveals major changes in fatty acid biosynthesis as potential hallmark in diabetes mellitus-associated vascular disease

31 May 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004085

Brain-Computer Interfaces for Communication and Control

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25706687

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Integrated visualization of a multi-omics study of starvation in mouse intestine.

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25706687

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PCBI.1004085

1 reference

journals/ploscb/KutmonIBKNPE15

1482183

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1482183

1 reference

0 references

1 reference

1 reference