ArticleF1000Research2014
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks.
Article in F1000Research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- Comparative Transcriptome Analysis of Sexual Differentiation in Male and Female Gonads of Nao-Zhou Stock Large Yellow Croaker (Animals : an open access journal from MDPI · 2024Article
- Comparative transcriptomic analysis provides insights into the genetic networks regulating oil differential production in oil crops.BMC biology · 2024Article
- Healthspan pathway maps inAging · 2020Review
- Proteomic analysis for identifying the differences in molecular profiling between fanconi anaemia and aplastic anaemia.American journal of translational research · 2019Article
- Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.BMC bioinformatics · 2017Article
- CompNet: a GUI based tool for comparison of multiple biological interaction networks.BMC bioinformatics · 2016Article
- GreedyPlus: An Algorithm for the Alignment of Interface Interaction Networks.Scientific reports · 2015Article
- NetMatchStar: an enhanced Cytoscape network querying app.F1000Research · 2015Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm. GASOLINE starts with the identification of sets of similar nodes, called seeds of the alignment. Alignments are then extended in a greedy manner and finally refined. Both the identification of seeds and the extension of alignments are performed through an iterative Gibbs sampling strategy. GASOLINE is a Cytoscape app for computing and visualizing local alignments, without requiring any post-processing operations. GO terms can be easily attached to the aligned proteins for further functional analysis of alignments. GASOLINE can perform the alignment task in few minutes, even for a large number of input networks.
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Registered trials
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.