(Q30821850)

10 September 2017

R-based software for the integration of pathway data into bioinformatic algorithms (English)

1 reference

10 September 2017

0 references

0 references

0 references

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

author name string

Michaela Bayerlová

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

Tim Beißbarth

series ordinal

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

publication date

7 February 2014

1 reference

10 September 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

volume

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

page(s)

85-100

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

3 June 2020

copyright license

start time

7 February 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

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

limma

object named as

limma

2 references

22 June 2022

https://europepmc.org/article/PMC/4009765

based on heuristic

inferred from PubMed Central ID database lookup

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

cites work

RCytoscape: tools for exploratory network analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Pathview: an R/Bioconductor package for pathway-based data integration and visualization

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Supporting SBML as a model exchange format in software applications

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

A new reference implementation of the PSICQUIC web service

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Graphite Web: Web tool for gene set analysis exploiting pathway topology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Precise generation of systems biology models from KEGG pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

CePa: an R package for finding significant pathways weighted by multiple network centralities.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

rBiopaxParser--an R package to parse, modify and visualize BioPAX data.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

PathNet: a tool for pathway analysis using topological information

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Along signal paths: an empirical gene set approach exploiting pathway topology.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Qualitative translation of relations from BioPAX to SBML qual

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Camera: a competitive gene set test accounting for inter-gene correlation

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Joint Bayesian inference of condition-specific miRNA and transcription factor activities from combined gene and microRNA expression data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

RedeR: R/Bioconductor package for representing modular structures, nested networks and multiple levels of hierarchical associations.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

graphite - a Bioconductor package to convert pathway topology to gene network.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Graph based fusion of miRNA and mRNA expression data improves clinical outcome prediction in prostate cancer

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

WikiPathways: building research communities on biological pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

From sets to graphs: towards a realistic enrichment analysis of transcriptomic systems

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Sig2BioPAX: Java tool for converting flat files to BioPAX Level 3 format

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

HTSanalyzeR: an R/Bioconductor package for integrated network analysis of high-throughput screens.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

SPIKE: a database of highly curated human signaling pathways

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Reactome: a database of reactions, pathways and biological processes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

The BioPAX community standard for pathway data sharing

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Dynamic deterministic effects propagation networks: learning signalling pathways from longitudinal protein array data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

A novel signaling pathway impact analysis.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

PID: the Pathway Interaction Database

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Presenting and exploring biological pathways with PathVisio

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Analyzing gene perturbation screens with nested effects models in R and bioconductor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

LibSBML: an API library for SBML.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Estimating large-scale signaling networks through nested effect models with intervention effects from microarray data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Tools for visually exploring biological networks.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Interpreting experimental results using gene ontologies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

The Gaggle: an open-source software system for integrating bioinformatics software and data sources

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Pathguide: a pathway resource list

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Discovering statistically significant pathways in expression profiling studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Pathway information for systems biology

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

A two-way interface between limited Systems Biology Markup Language and R

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Bioconductor: open software development for computational biology and bioinformatics

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Network structures and algorithms in Bioconductor

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

The KEGG resource for deciphering the genome

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

Integration of pathway knowledge into a reweighted recursive feature elimination approach for risk stratification of cancer patients.

14 July 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOLOGY3010085

BoolNet--an R package for generation, reconstruction and analysis of Boolean networks

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOLOGY3010085

Representations of molecular pathways: an evaluation of SBML, PSI MI and BioPAX.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOLOGY3010085

Integrating BioPAX pathway knowledge with SBML models.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOLOGY3010085

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOLOGY3010085

The Comprehensive R Archive Network

21 January 2018

1 reference

https://api.crossref.org/works/10.3390%2FBIOLOGY3010085

miRNApath: a database of miRNAs, target genes and metabolic pathways.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4009765

25 November 2018

Identifiers

DOI

10.3390/BIOLOGY3010085

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json

3 June 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24833336%20AND%20SRC:MED&resulttype=core&format=json