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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] (http://www.ncbi.nlm.nih.gov/pubmed/17138587) 23(3):390-1
  • Cancer/OncodriveFM: Functional impact bias reveals cancer drivers. (2012) Gonzalez-Perez A, Lopez-Bigas N. [Nucleic Acids Res.] (http://www.ncbi.nlm.nih.gov/pubmed/22904074) 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] (http://www.ncbi.nlm.nih.gov/pubmed/23884480) 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] (http://www.ncbi.nlm.nih.gov/pubmed/14990455) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/17407596) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/19454602) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/22844098) 40(20):e158
  • For the rest of the analyses, please refer to the original publications of the corresponding method. More details in the [Tutorial] (https://github.com/babelomics/babelomics/wiki) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/25897133) (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.] (http://www.ncbi.nlm.nih.gov/pubmed/20478823) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/18515841) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/16845052) 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.] (http://www.ncbi.nlm.nih.gov/pubmed/15980512) 33(Web Server issue):W460-4.