Publications

  • Assessing the consistency of public human tissue RNA-seq data sets. Briefings in Bioinformatics, 2015 March 30. Danielsson F, James T, Gomez Cabrero D, Huss M.
    [see pub] 

 

    • Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. Bioinformatics, 2014 Sep 15. Nueda MJ, Tarazona S, Conesa A. 

[see pub] 

 

  • The histone variant H2A. Bbd is enriched at sites of DNA synthesis. Nucleic Acid Res. 2014 Apr 20. Sansoni V, Casas-Delucchi CS, Rajan M, Schmidt A, Bönisch C, Thomae AW, Staege MS, Hake SB, Cardoso MC, Imhof A.

[see pub] 

 

  • Selected articles from the High-Throughput Omics and Data Integrations Workshop.          
    Edited by David Gomez-Cabrero, Ana Conesa, Jesper Tegner, Dieter Maier, Matthias Merkenschlager, Imad Abugessaisa, Andreas Gisel, Erik Bongcam-Rudloff, Esteban Ballestar and Andrew Teschendorff.

 

[see pub] 

BMC_logo

 

 

  • Data integration in the era of omics: current and future challenges
    David Gomez-Cabrero, Imad Abugessaisa, Dieter Maier, Andrew Teschendorff, Matthias Merkenschlager, Andreas Gisel, Esteban Ballestar, Erik Bongcam-Rudloff, Ana Conesa, Jesper Tegnér. BMC Systems Biology 2014, 13 March 2014

 

[see pub] 

 

      • The common ground of genomics and systems biology
        Ana Conesa, Ali Mortazavi. BMC Systems Biology 2014, 13 March 2014 
        [see pub] 

 

      • Use of prior knowledge for the analysis of high-throughput transcriptomics and metabolomics data
        Polina Reshetova, Age K Smilde, Antoine HC van Kampen, Johan A Westerhuis. BMC Systems Biology 2014, 13 March 2014
        [see pub] 

 

      • Bioinformatic analysis of proteomics data
        Andreas Schmidt, Ignasi Forne, Axel Imhof. BMC Systems Biology 2014, 13 March 2014
        [see pub] 

 

    • Integrative omics analysis. A study based on Plasmodium falciparum mRNA and protein data
      Oana A Tomescu, Diethard Mattanovich, Gerhard G Thallinger. BMC Systems Biology 2014, 13 March 2014
      [see pub] 
  • Weighted Interaction SNP Hub (WISH) network method for building genetic networks for complex diseases and traits using whole genome genotype data. Lisette JA Kogelman, Haja N Kadarmideen. BMC Systems Biology 2014, 13 March 2014
    [see pub] 
  • Kernel-PCA data integration with enhanced interpretability
    Ferran Reverter, Esteban Vegas, Josep M Oller. BMC Systems Biology 2014, 13 March 2014
    [see pub] 
  • Pathway network inference from gene expression data
    Ignacio Ponzoni, María Nueda, Sonia Tarazona, Stefan Götz, David Montaner, Julieta Dussaut, Joaquín Dopazo, Ana Conesa. BMC Systems Biology 2014, 13 March 2014
    [see pub] 
  • A diVIsive Shuffling Approach (VIStA) for gene expression analysis to identify subtypes in Chronic Obstructive Pulmonary Disease. Jörg Menche, Amitabh Sharma, Michael H Cho, Ruth J Mayer, Stephen I Rennard, Bartolome Celli, Bruce E Miller, Nick Locantore, Ruth Tal-Singer, Soumitra Ghosh, Chris Larminie, Glyn Bradley, John H Riley, Alvar Agusti, Edwin K Silverman, Albert-László Barabási. BMC Systems Biology 2014, 13 March 2014
    [see pub] 
  • STATegra EMS: an Experiment Management System for complex next-generation omics experiments
    Rafael Hernández-de-Diego, Noemi Boix-Chova, David Gómez-Cabrero, Jesper Tegner, Imad Abugessaisa, Ana Conesa BMC Systems Biology 2014, 13 March 2014
    [see pub] 
  • Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps. Genome Research 2013 Oct 29. Mortazavi A, Pepke S, Jansen C, Marinov GK, Ernst J, Kellis M, Hardison RC, Myers RM, Wold BJ.
  • [see pub]

     

                            • Identification of novel markers in rheumatoid arthritis through integrated analysis of DNA methylation and microRNA expression. Journal of Autoimmunity 2013 Gen 7. de la Rica L, Urquiza JM, Gómez-Cabrero D, Islam AB, López-Bigas N, Tegnér J,Toes RE, Ballestar E.

    [see pub]

     

                                • Scoring and Searching over Bayesian Networks with Informative, Casual and Associative Priors”, Uncertainty in Artificial Intelligence (UAI) 2013. Giorgos Borboudakis, Ioannis Tsamardinos  

    [see pub]

     

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