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Protocols

BEST specifications

Information


Unique identifier OMICS_29130
Name BEST
Alternative names Biomedical Education Skills and Training network, BEST Network
Restrictions to use None
Community driven No
Data access Browse
User data submission Allowed
Registration required Yes
Maintained Yes

Documentation


BEST citations

 (10)
library_books

Empirical Comparison of Visualization Tools for Larger Scale Network Analysis

2017
Adv Bioinformatics
PMCID: 5540468
PMID: 28804499
DOI: 10.1155/2017/1278932

[…] a great plethora of more than 200 plugins. Compared to Tulip, Gephi, and Pajek, it has the richest palette of predefined color styles, the most efficient collection of clustering algorithms, and the best network profiler for intranetwork comparison of topological features.Gephi clearly outperforms Cytoscape in terms of scalability and memory efficiency and, in our opinion, it is the best generic […]

library_books

Metabolome Dynamics of Smutted Sugarcane Reveals Mechanisms Involved in Disease Progression and Whip Emission

2017
Front Plant Sci
PMCID: 5450380
PMID: 28620397
DOI: 10.3389/fpls.2017.00882

[…] e (Tamura et al., ) with default settings. Maximum-likelihood algorithm was used to build the phylogenetic tree with the following settings: JTT model, 1000 replicates of bootstrap analyses, with the best network-network interface (NNI) topology search. […]

library_books

Embracing discordance: Phylogenomic analyses provide evidence for allopolyploidy leading to cryptic diversity in a Mediterranean Campanula (Campanulaceae) clade

2017
PMCID: 5413844
PMID: 28186341
DOI: 10.1111/evo.13203

[…] ulation assignments strongly supported a monophyletic octoploid C. erinus, and C. creutzburgii sister to C. simulans (Fig. , panel D).SNaQ analyses suggested a single hybridization event (Fig. ). The best network (–loglik = 129.62) included a single hybrid edge between C. creutzburgii and the tetraploid C. erinus, indicating these as the parental lineages of the octoploid C. erinus. A paraphyletic […]

library_books

Personalized Analysis by Validation of Monte Carlo for Application of Pathways in Cardioembolic Stroke

2017
PMCID: 5338568
PMID: 28232661
DOI: 10.12659/MSM.899690

[…] ere efficient in distinguishing differences among individual CES samples, and can provide broader carcinogenic insight in personalized medicine []. The final purpose of our approach was to detect the best network able to discriminate CES versus controls. We found that the 3 best networks were similar and had 22 common pairs of pathways. We tended to select network 10 to differentiate CES disease f […]

library_books

Modelling with ANIMO: between fuzzy logic and differential equations

2016
BMC Syst Biol
PMCID: 4962523
PMID: 27460034
DOI: 10.1186/s12918-016-0286-z

[…] rk, we would like to highlight the powerful tool CellNOpt []. CellNOpt is a software which can work with logic descriptions (Boolean, fuzzy) and differential equations, and automatically suggests the best network topologies to match a given data set. Thanks to the CytoCopteR plug-in for Cytoscape [], which provides an accessible user interface, CellNOpt can be used in tandem with ANIMO: after comp […]

library_books

Cis eQTL analysis and functional validation of candidate susceptibility genes for high grade serous ovarian cancer

2015
Nat Commun
PMCID: 4580986
PMID: 26391404
DOI: 10.1038/ncomms9234

[…] ultinet, InWeb, HINT and 252 KEGG pathways converted to binary format using the Bioconductor package graphite. Pathways from the Ingenuity Knowledge Base and KEGG significantly enriched in the single best network discovered by jActiveModules for the ovarian and fallopian gene lists were identified using a right-tailed Fisher's exact test with FDR control for multiple pathway comparisons by the Ben […]

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