Predicting effective drug combinations via network propagation. - Balázs Ligeti; Roberto Vera; Gergely Lukács; Balazs Györffy; Sándor Pongor (BioCAS, 2013)

JBioWH: an open-source Java framework for bioinformatics data integration. - Roberto Vera; Yasset Pérez-Riverol; Sonia Pérez; Balázs Ligeti; Attila Kertész-Farkas; Sándor Pongor (Database J. Biol. Databases Curation, 2013)

A UML-based Approach to Design Parallel and Distributed Applications. - Yasset Pérez-Riverol; Roberto Vera Alvarez (CoRR, 2013)

PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. - Attila Kertész-Farkas; Beáta Reiz; Roberto Vera; Michael P. Myers; Sándor Pongor (Bioinform., 2014)

Large scale annotation of biological data using integrated database managament tools - Roberto Vera (2014)

Workflow and web application for annotating NCBI BioProject transcriptome data. - Roberto Vera Alvarez; Newton Medeiros Vidal; Gina A. Garzón-Martínez; Luz S. Barrero; David Landsman; Leonardo Mariño-Ramírez (Database J. Biol. Databases Curation, 2017)

BioContainers: an open-source and community-driven framework for software standardization. - Felipe da Veiga Leprevost; Björn A. Grüning; Saulo Aflitos; Hannes L. Röst; Julian Uszkoreit; Harald Barsnes; Marc Vaudel; Pablo A. Moreno; Laurent Gatto; Jonas Weber; Mingze Bai; Rafael C. Jiménez; et al. (Bioinform., 2017)

SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. - Roberto Vera Alvarez; Shan Li; David Landsman; Ivan Ovcharenko (Bioinform., 2018)

TPMCalculator: one-step software to quantify mRNA abundance of genomic features. - Roberto Vera Alvarez; Lorinc Sándor Pongor; Leonardo Mariño-Ramírez; David Landsman (Bioinform., 2019)

LitSense: making sense of biomedical literature at sentence level. - Alexis Allot; Qingyu Chen 001; Sun Kim; Roberto Vera Alvarez; Donald C. Comeau; W. John Wilbur; Zhiyong Lu (Nucleic Acids Res., 2019)

COG database update: focus on microbial diversity, model organisms, and widespread pathogens. - Michael Y. Galperin; Yuri I. Wolf; Kira S. Makarova; Roberto Vera Alvarez; David Landsman; Eugene V. Koonin (Nucleic Acids Res., 2021)

ElasticBLAST: accelerating sequence search via cloud computing. - Christiam Camacho; Grzegorz M. Boratyn; Victor Joukov; Roberto Vera Alvarez; Thomas L. Madden (BMC Bioinform., 2023)