ArticleBMC systems biology2013
BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.
Article in BMC systems biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 57 citations in OpenAlex.
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- Comprehensive Map of the Regulated Cell Death Signaling Network: A Powerful Analytical Tool for Studying Diseases.Cancers · 2020Article
- A multiscale signalling network map of innate immune response in cancer reveals cell heterogeneity signatures.Nature communications · 2019Article
- PathMe: merging and exploring mechanistic pathway knowledge.BMC bioinformatics · 2019Article
- Metabolic and signalling network maps integration: application to cross-talk studies and omics data analysis in cancer.BMC bioinformatics · 2019Article
- Community-driven roadmap for integrated disease maps.Briefings in bioinformatics · 2019Review
- Inferring hidden causal relations between pathway members using reduced Google matrix of directed biological networks.PloS one · 2018Article
- Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.NPJ systems biology and applications · 2018Article
- Signalling maps in cancer research: construction and data analysis.Database : the journal of biological databases and curation · 2018Article
- Modeling of the jasmonate signaling pathway in Arabidopsis thaliana with respect to pathophysiology of Alternaria blight in Brassica.Scientific reports · 2017Article
- Identification of clinically predictive metagenes that encode components of a network coupling cell shape to transcription by image-omics.Genome research · 2017Article
- NaviCom: a web application to create interactive molecular network portraits using multi-level omics data.Database : the journal of biological databases and curation · 2017Article
- Qualitative dynamics semantics for SBGN process description.BMC systems biology · 2016Article
- MapMaker and PathTracer for tracking carbon in genome-scale metabolic models.Biotechnology journal · 2016Article
- Sexual Dimorphism and Aging in the Human Hyppocampus: Identification, Validation, and Impact of Differentially Expressed Genes by Factorial Microarray and Network Analysis.Frontiers in aging neuroscience · 2016Article
- DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.BMC systems biology · 2015Article
- Atlas of Cancer Signalling Network: a systems biology resource for integrative analysis of cancer data with Google Maps.Oncogenesis · 2015Article
- NaviCell Web Service for network-based data visualization.Nucleic acids research · 2015Article
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPublic repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the formulation of new biological hypotheses to be tested, a fundamental principle of the systems biology approach. However, large-scale molecular maps are not always easy to mine and interpret.
resultsWe have developed BiNoM (Biological Network Manager), a Cytoscape plugin, which provides functions for the import-export of some standard systems biology file formats (import from CellDesigner, BioPAX Level 3 and CSML; export to SBML, CellDesigner and BioPAX Level 3), and a set of algorithms to analyze and reduce the complexity of biological networks. BiNoM can be used to import and analyze files created with the CellDesigner software. BiNoM provides a set of functions allowing to import BioPAX files, but also to search and edit their content. As such, BiNoM is able to efficiently manage large BioPAX files such as whole pathway databases (e.g. Reactome). BiNoM also implements a collection of powerful graph-based functions and algorithms such as path analysis, decomposition by involvement of an entity or cyclic decomposition, subnetworks clustering and decomposition of a large network in modules.
conclusionsHere, we provide an in-depth overview of the BiNoM functions, and we also detail novel aspects such as the support of the BioPAX Level 3 format and the implementation of a new algorithm for the quantification of pathways for influence networks. At last, we illustrate some of the BiNoM functions on a detailed biological case study of a network representing the G1/S transition of the cell cycle, a crucial cellular process disturbed in most human tumors.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.