Babelomics statistics

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Citations per year

Number of citations per year for the bioinformatics software tool Babelomics
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Tool usage distribution map

This map represents all the scientific publications referring to Babelomics per scientific context
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Associated diseases

This word cloud represents Babelomics usage per disease context
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Popular tool citations

chevron_left Gene set enrichment analysis Gene expression clustering Driver mutation prioritization Protein-protein interaction prediction Variant detection Differential expression Over-representation analysis Gene expression classification Normalization Differential expression detection Bioinformatics workflows Normalization chevron_right
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Protocols

Babelomics specifications

Information


Unique identifier OMICS_00748
Name Babelomics
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 5.0
Stability Stable
Registration required Yes
Maintained Yes

Subtools


  • FatiGO
  • FatiScan
  • SNOW

Versioning


No version available

Maintainer


  • person_outline Joaquín Dopazo

Information


Unique identifier OMICS_00748
Name Babelomics
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 5.0
Stability Stable
Maintained Yes

Subtools


  • FatiGO
  • FatiScan
  • SNOW

Maintainer


  • person_outline Joaquín Dopazo

Publications for Babelomics

Babelomics citations

 (416)
library_books

Ehrlichia chaffeensis TRP75 Interacts with Host Cell Targets Involved in Homeostasis, Cytoskeleton Organization, and Apoptosis Regulation To Promote Infection

2018
PMCID: 5909120
PMID: 29643078
DOI: 10.1128/mSphere.00147-18

[…] logy analysis of the 90 identified TRP75-interacting targets (, ). Proteins were classified in the human gene ontology database of biological processes that may be affected by TRP75, and results of a FatiGO single enrichment analysis performed for the rest of the human genome (P < 0.05) indicated that most of the target proteins were involved in major biological processes, including multicellular […]

call_split

Combining targeted panel based resequencing and copy number variation analysis for the diagnosis of inherited syndromic retinopathies and associated ciliopathies

2018
Sci Rep
PMCID: 5869593
PMID: 29588463
DOI: 10.1038/s41598-018-23520-1
call_split See protocol

[…] .nih.gov/variation/tools/1000genomes/), Exome Variant Server (EVS) (http://evs.gs.washington.edu/EVS/), ExAC Browser (http://exac.broadinstitute.org/), and CIBERER Spanish Variant Server (http://csvs.babelomics.org/); iv) missense SNV and in-frame deletions that induced an alteration in the protein predicted as pathogenic in at least 2 of the in silico tools used to predict pathogenicity (SIFT, Po […]

library_books

Using genome wide association studies to identify common QTL regions in three different genetic backgrounds based on Iberian pig breed

2018
PLoS One
PMCID: 5844516
PMID: 29522525
DOI: 10.1371/journal.pone.0190184

[…] m the Porcine Ensembl database, Sscrofa11.1. In order to identify potential candidate genes the function of genes within each of the selected regions (±1Mb) were examined using VarElect [], STRING [] Babelomics [] and ncbi databases (growth, muscle development and fat metabolism related genes). Moreover, additional information of gene expression data from a previous study in BC_LD [] and a paralle […]

library_books

Strong phenotypic plasticity limits potential for evolutionary responses to climate change

2018
Nat Commun
PMCID: 5843647
PMID: 29520061
DOI: 10.1038/s41467-018-03384-9

[…] We performed gene ontology (GO) gene set enrichment (GSE) analyses in Babelomics v. 5, using the FatiScan module. As input, we used lists of genes (and their fold change) that were significantly season-biased in thorax, abdomen or both body parts, and the Argot2 GO anno […]

library_books

Genome wide scan for commons SNPs affecting bovine leukemia virus infection level in dairy cattle

2018
BMC Genomics
PMCID: 5812220
PMID: 29439661
DOI: 10.1186/s12864-018-4523-2

[…] cess” (14%), “cellular process” (12%) and “localization” (11%). The search for GO terms and/or KEGG pathways overrepresented on the gene set identified vs those present in whole bovine gene set using FatiGO method [] did not produce significant results (data not shown).Fig. 5 […]

library_books

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo and autopolyploidization events

2018
BMC Biol
PMCID: 5785856
PMID: 29370802
DOI: 10.1186/s12915-018-0482-y

[…] red to the olive proteome using one-to-one and one-to-many orthologs. GO term enrichment of proteins duplicated at the different species-specific expansions and duplication peaks was calculated using FatiGO []. […]


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Babelomics institution(s)
Computational Genomics Department, Centro de Investigacio n Principe Felipe (CIPF), Valencia, Spain; Computational Genomics Chair, Bull-CIPF, Valencia, , Spain; Bioinformatics of Rare Diseases (BIER), CIBER de Enfermedades Raras (CIBERER), Valencia, Spain; Department of Medicine, University of Cambridge, School of Clinical Medicine, Addenbrooke’s Hospital, Cambridge, UK; Fundacion Investigacion Clinico de Valencia - INCLIVA, Valencia, Spain; Functional Genomics Node, (INB) at CIPF, Valencia, Spain; HPC Services, University of Cambridge, Cambridge, UK
Babelomics funding source(s)
Supported by Spanish Ministry of Economy and Competitiveness [BIO2011-27069], Conselleria d’Educacio of the Valencian Community [PROMETEOII/2014/025]; EU FP7-PEOPLE Project MLPM [316861]; Fundacio la Marato TV3 [151/C/2013].

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