How to cite babelomics

Ralonso edited this page Jun 5, 2015 · 15 revisions
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Please, use the following convention to cite Babelomics and the corresponding tools:

... the ANALYSIS analysis (Tool_reference) has been carried out using the Babelomics (Babelomics_reference) tool.

Or something with a similar meaning that acknowledges both the method and Babelomics.

The references for the different analyses are:

  • Expression/Clustering with the SOTA method: Herrero J, Valencia A, Dopazo J (2001) A hierarchical unsupervised growing neural network for clustering gene expression patterns. Bioinformatics. 17(2):126-36
  • Expression/Class Prediction: Medina I, Montaner D, Tárraga J, Dopazo J. (2007) Prophet, a web-based tool for class prediction using microarray data. Bioinformatics 23(3):390-1
  • Cancer/OncodriveFM: Functional impact bias reveals cancer drivers. (2012) Gonzalez-Perez A, Lopez-Bigas N. Nucleic Acids Res. 40(21):e169.
  • Cancer/OncodriveClust: Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. (2013) OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics 29(18):2238-44.
  • Functional/Single enrichment: Al-Shahrour F, Díaz-Uriarte R, Dopazo J. (2004) FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes. Bioinformatics 20(4):578-80.
  • Functional/Gene set Enrichment: Al-Shahrour F, Arbiza L, Dopazo H, Huerta-Cepas J, Mínguez P, Montaner D, Dopazo J. (2007) From genes to functional classes in the study of biological systems. BMC Bioinformatics. 8:114.
  • Functional/Network Enrichment: Minguez P, Götz S, Montaner D, Al-Shahrour F, Dopazo J.(2009) SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks. Nucleic Acids Res. 37(Web Server issue):W109-14
  • Functional/Gene set Network Enrichment: García-Alonso L, Alonso R, Vidal E, Amadoz A, de María A, Minguez P, Medina I, Dopazo J. (2012) Discovering the hidden sub-network component in a ranked list of genes or proteins derived from genomic experiments. Nucleic Acids Res. 40(20):e158
  • For the rest of the analyses, please refer to the original publications of the corresponding method. More details in the Tutorial pages.

References for Babelomics

Use one of these, preferentially most recent one:

  • Alonso R, Salavert F, Garcia-Garcia F, Carbonell-Caballero J, Bleda M, Garcia-Alonso L, Sanchis-Juan A, Perez-Gil D, Marin-Garcia P, Sanchez R, Cubuk C, Hidalgo MR, Amadoz A, Hernansaiz-Ballesteros RD, Alemán A, Tarraga J, Montaner D, Medina I, Dopazo J. (2015) Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic Acids Res. (2015 Apr 20. pii: gkv384.)

  • Medina, I., Carbonell, J., Pulido, L., Madeira, S.C., Goetz, S., Conesa, A., Tarraga, J., Pascual-Montano, A., Nogales-Cadenas, R., Santoyo, J., García F, Marbà M, Montaner D, Dopazo J. (2010) Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Res. 38(Web Server issue):W210-213

  • Al-Shahrour F, Carbonell J, Minguez P, Goetz S, Conesa A, Tárraga J, Medina I, Alloza E, Montaner D, Dopazo J. (2008) Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments. Nucleic Acids Res. 36(Web Server issue):W341-6

  • Al-Shahrour F, Minguez P, Tárraga J, Montaner D, Alloza E, Vaquerizas JM, Conde L, Blaschke C, Vera J, Dopazo J. (2006) BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments. Nucleic Acids Res. 34(Web Server issue):W472-6

  • Al-Shahrour F, Minguez P, Vaquerizas JM, Conde L, Dopazo J. (2005) BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments. Nucleic Acids Res. 33(Web Server issue):W460-4.