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

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

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

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

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

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

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

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

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

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

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

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