Functional assessment of time course microarray data. - María José Nueda; Patricia Sebastián; Sonia Tarazona; Francisco García-García 002; Joaquín Dopazo; Alberto Ferrer 001; Ana Conesa (BMC Bioinform., 2009)

Qualimap: evaluating next-generation sequencing alignment data. - Fernando García-Alcalde; Konstantin Okonechnikov; José Carbonell; Luis M. Cruz; Stefan Götz 003; Sonia Tarazona; Joaquín Dopazo; Thomas F. Meyer; Ana Conesa (Bioinform., 2012)

Next maSigPro: updating maSigPro bioconductor package for RNA-seq time series. - María José Nueda; Sonia Tarazona; Ana Conesa (Bioinform., 2014)

Pathway network inference from gene expression data. - Ignacio Ponzoni; María José Nueda; Sonia Tarazona; Stefan Götz 003; David Montaner; Julieta Sol Dussaut; Joaquín Dopazo; Ana Conesa (BMC Syst. Biol., 2014)

Understanding disease mechanisms with models of signaling pathway activities. - Patricia Sebastián-León; Enrique Vidal 002; Pablo Minguez; Ana Conesa; Sonia Tarazona; Alicia Amadoz; Carmen Armero; Francisco Salavert; Antonio Vidal-Puig; David Montaner; Joaquín Dopazo (BMC Syst. Biol., 2014)

RGmatch: matching genomic regions to proximal genes in omics data integration. - Pedro Furió-Tarí; Ana Conesa; Sonia Tarazona (BMC Bioinform., 2016)

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. - Pedro Furió-Tarí; Sonia Tarazona; Toni Gabaldón; Anton J. Enright; Ana Conesa (Nucleic Acids Res., 2016)

Identification and visualization of differential isoform expression in RNA-seq time series. - María José Nueda; Jordi Martorell-Marugan; Cristina Martí; Sonia Tarazona; Ana Conesa (Bioinform., 2018)

PaintOmics 3: a web resource for the pathway analysis and visualization of multi-omics data. - Rafael Hernández-de-Diego; Sonia Tarazona; Carlos Martínez-Mira; Leandro Balzano-Nogueira; Pedro Furió-Tarí; Georgios Joannis Pappas Jr.; Ana Conesa (Nucleic Acids Res., 2018)

Undisclosed, unmet and neglected challenges in multi-omics studies. - Sonia Tarazona; Angeles Arzalluz-Luque; Ana Conesa (Nat. Comput. Sci., 2021)

MultiBaC: an R package to remove batch effects in multi-omic experiments. - Manuel Ugidos; María José Nueda; José Manuel Prats-Montalbán; Alberto Ferrer 001; Ana Conesa; Sonia Tarazona (Bioinform., 2022)

PaintOmics 4: new tools for the integrative analysis of multi-omics datasets supported by multiple pathway databases. - Tianyuan Liu; Pedro Salguero; Marko Petek; Carlos Martínez-Mira; Leandro Balzano-Nogueira; Ziva Ramsak; Lauren McIntyre; Kristina Gruden; Sonia Tarazona; Ana Conesa (Nucleic Acids Res., 2022)

MORE interpretable multi-omic regulatory networks to characterise phenotypes. - Maider Aguerralde-Martin; Mónica Clemente-Císcar; Ana Conesa; Sonia Tarazona (Briefings Bioinform., 2025)

MOSim: bulk and single-cell multilayer regulatory network simulator. - Carolina Monzó; Maider Aguerralde-Martin; Carlos Martínez-Mira; Angeles Arzalluz-Luque; Ana Conesa; Sonia Tarazona (Briefings Bioinform., 2025)