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A
Tárraga J, Arnau V, Martinez H, et al. Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. Bioinformatics (Oxford, England). 2014;30:3396-3398. doi:10.1093/bioinformatics/btu553.
B
Alonso R, Salavert F, Garcia-Garcia F, et al. Babelomics 5.0: functional interpretation for new generations of genomic data. Nucleic acids research. 2015;43:W117-W121. doi:10.1093/nar/gkv384.
Medina I, Carbonell J, Pulido L, et al. Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling. Nucleic Acids Research. 2010;38:W210-W213. Featured in NAR. Available at: http://nar.oxfordjournals.org/content/38/suppl_2/W210.full.
C
Bleda M, Tárraga J, De Maria A, et al. CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic acids research. 2012;40:W609-14. doi:10.1093/nar/gks575.
Martinez H, Tárraga J, Medina I, et al. Concurrent and Accurate Short Read Mapping on Multicore Processors. IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM. 2015;12:995-1007. doi:10.1109/TCBB.2015.2392077.
F
Salavert J, Tomás A, Tárraga J, Medina I, Dopazo J, Blanquer I. Fast inexact mapping using advanced tree exploration on backward search methods. BMC Bioinformatics. 2015;16:18. doi:10.1186/s12859-014-0438-3.
Al-Shahrour F, Minguez P, Tárraga J, et al. FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res. 2007;35(Web Server issue):W91-6. doi:10.1093/nar/gkm260.
Conde L, Montaner D, Burguet-Castell J, Tárraga J, Al-Shahrour F, Dopazo J. Functional profiling and gene expression analysis of chromosomal copy number alterations. Bioinformation. 2007;1(10):432-5. doi:10.6026/97320630001432.
G
Medina I, Montaner D, Bonifaci N, et al. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucl. Acids Res. 2009;37:W340-344. doi:10.1093/nar/gkp481.
Medina I, Montaner D, Bonifaci N, et al. Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies. Nucleic Acids Res. 2009;37(Web Server issue):W340-4. doi:10.1093/nar/gkp481.
Tárraga J, Medina I, Carbonell J, et al. GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 2008;36(Web Server issue):W308-14. doi:10.1093/nar/gkn303.
H
Lopez J, Coll J, Haimel M, et al. HGVA: the Human Genome Variation Archive. Nucleic Acids Res. 2017;45(W1):W189-W194. doi:10.1093/nar/gkx445.
Tárraga J, Gallego A, Arnau V, Medina I, Dopazo J. HPG pore: an efficient and scalable framework for nanopore sequencing data. BMC bioinformatics. 2016;17:107. doi:10.1186/s12859-016-0966-0.
Tárraga J, Gallego A, Arnau V, Medina I, Dopazo J. HPG pore: an efficient and scalable framework for nanopore sequencing data. BMC Bioinformatics. 2016;17(1). doi:10.1186/s12859-016-0966-0.
I
Wilkinson MD, Senger M, Kawas E, et al. Interoperability with Moby 1.0--it's better than sharing your toothbrush!. Brief Bioinform. 2008;9(3):220-31. doi:10.1093/bib/bbn003.
Conde L, Montaner D, Burguet-Castell J, et al. ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling. Nucleic Acids Res. 2007;35(Web Server issue):W81-5. doi:10.1093/nar/gkm257.
N
Olanda R, Pérez M, Orduña JM, Tárraga J, Dopazo J. A new parallel pipeline for DNA methylation analysis of long reads datasets. BMC bioinformatics. 2017;18:161. doi:10.1186/s12859-017-1574-3.
P
Tárraga J, Pérez M, Orduña JM, Duato J, Medina I, Dopazo J. A Parallel and Sensitive Software Tool for Methylation Analysis on Multicore Platforms. Bioinformatics (Oxford, England). 2015;31:3130-3138. doi:10.1093/bioinformatics/btv357.
Sánchez R, Serra F, Tárraga J, et al. Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res. 2011;39(Web Server issue):W470-4. doi:10.1093/nar/gkr408.
V
Juanes JM, Gallego A, Tárraga J, et al. VISMapper: ultra-fast exhaustive cartography of viral insertion sites for gene therapy. BMC Bioinformatics. 2017;18(1):421. doi:10.1186/s12859-017-1837-z.