HXMS: a standardized file format for HX-MS data.

Roberto Vera Roberto Vera Alvarez https://orcid.org/0000-0002-4108-5982

Kyle C. Weber Chenlin Lu Roberto Vera Alvarez Bruce D. Pascal Anum Glasgow HXMS: a standardized file format for HX-MS data. 2026 42 Bioinform. 4 https://doi.org/10.1093/bioinformatics/btag113 db/journals/bioinformatics/bioinformatics42.html#WeberLAPG26 streams/journals/bioinformatics

Christiam Camacho Grzegorz M. Boratyn Victor Joukov Roberto Vera Alvarez Thomas L. Madden ElasticBLAST: accelerating sequence search via cloud computing. 117 2023 December 24 BMC Bioinform. 1 https://doi.org/10.1186/s12859-023-05245-9 https://www.wikidata.org/entity/Q117886139 db/journals/bmcbi/bmcbi24.html#CamachoBJAM23

Michael Y. Galperin Yuri I. Wolf Kira S. Makarova Roberto Vera Alvarez David Landsman Eugene V. Koonin COG database update: focus on microbial diversity, model organisms, and widespread pathogens. D274-D281 2021 49 Nucleic Acids Res. Database-Issue https://doi.org/10.1093/nar/gkaa1018 https://www.wikidata.org/entity/Q101470934 db/journals/nar/nar49.html#GalperinWMALK21

Roberto Vera Alvarez Lorinc Sándor Pongor Leonardo Mariño-Ramírez David Landsman TPMCalculator: one-step software to quantify mRNA abundance of genomic features. 1960-1962 2019 35 Bioinform. 11 https://doi.org/10.1093/bioinformatics/bty896 https://www.wikidata.org/entity/Q58086626 db/journals/bioinformatics/bioinformatics35.html#AlvarezPML19

Alexis Allot Qingyu Chen 0001 Sun Kim Roberto Vera Alvarez Donald C. Comeau W. John Wilbur Zhiyong Lu LitSense: making sense of biomedical literature at sentence level. W594-W599 2019 47 Nucleic Acids Res. Webserver-Issue https://doi.org/10.1093/nar/gkz289 https://www.wikidata.org/entity/Q90290716 db/journals/nar/nar47.html#Allot0KACWL19

Roberto Vera Alvarez Shan Li David Landsman Ivan Ovcharenko SNPDelScore: combining multiple methods to score deleterious effects of noncoding mutations in the human genome. 289-291 2018 34 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btx583 https://www.wikidata.org/entity/Q47884066 db/journals/bioinformatics/bioinformatics34.html#AlvarezLLO18

Roberto Vera Alvarez Newton Medeiros Vidal Gina A. Garzón-Martínez Luz S. Barrero David Landsman Leonardo Mariño-Ramírez Workflow and web application for annotating NCBI BioProject transcriptome data. bax008 2017 2017 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bax008 https://www.wikidata.org/entity/Q33787541 db/journals/biodb/biodb2017.html#AlvarezVGBLM17

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 Timo Sachsenberg Julianus Pfeuffer Roberto Vera Alvarez Johannes Griss Alexey I. Nesvizhskii Yasset Pérez-Riverol BioContainers: an open-source and community-driven framework for software standardization. 2580-2582 2017 33 Bioinform. 16 https://doi.org/10.1093/bioinformatics/btx192 https://www.wikidata.org/entity/Q36335520 db/journals/bioinformatics/bioinformatics33.html#LeprevostGARUBV17

Roberto Vera Large scale annotation of biological data using integrated database managament tools Pázmány Péter Catholic University, Hungary 2014 https://doktori.hu/index.php?menuid=193&lang=HU&vid=13702

Attila Kertész-Farkas Beáta Reiz Roberto Vera Michael P. Myers Sándor Pongor PTMTreeSearch: a novel two-stage tree-search algorithm with pruning rules for the identification of post-translational modification of proteins in MS/MS spectra. 234-241 2014 30 Bioinform. 2 https://doi.org/10.1093/bioinformatics/btt642 https://www.wikidata.org/entity/Q43923015 db/journals/bioinformatics/bioinformatics30.html#Kertesz-FarkasRVMP14

Roberto Vera Yasset Pérez-Riverol Sonia Pérez Balázs Ligeti Attila Kertész-Farkas Sándor Pongor <i>JBioWH</i>: an open-source Java framework for bioinformatics data integration. 2013 2013 Database J. Biol. Databases Curation https://doi.org/10.1093/database/bat051 http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3708619/ https://www.wikidata.org/entity/Q28679153 db/journals/biodb/biodb2013.html#VeraPPLKP13

Balázs Ligeti Roberto Vera Gergely Lukács Balazs Györffy Sándor Pongor Predicting effective drug combinations via network propagation. 378-381 2013 BioCAS https://doi.org/10.1109/BioCAS.2013.6679718 conf/biocas/2013 db/conf/biocas/biocas2013.html#LigetiVLGP13

Yasset Pérez-Riverol Roberto Vera Alvarez A UML-based Approach to Design Parallel and Distributed Applications. 2013 CoRR http://arxiv.org/abs/1311.7011 abs/1311.7011 db/journals/corr/corr1311.html#Perez-RiverolA13

Saulo Aflitos Alexis Allot Mingze Bai Luz S. Barrero Harald Barsnes Grzegorz M. Boratyn Christiam Camacho Qingyu Chen 0001 Donald C. Comeau Michael Y. Galperin Gina A. Garzón-Martínez Laurent Gatto Anum Glasgow Johannes Griss Björn A. Grüning Balazs Györffy Rafael C. Jiménez Victor Joukov Attila Kertész-Farkas Sun Kim Eugene V. Koonin David Landsman Felipe da Veiga Leprevost Shan Li Balázs Ligeti Chenlin Lu Zhiyong Lu Gergely Lukács Thomas L. Madden Kira S. Makarova Leonardo Mariño-Ramírez Pablo A. Moreno Michael P. Myers Alexey I. Nesvizhskii Ivan Ovcharenko Bruce D. Pascal Sonia Pérez Yasset Pérez-Riverol Julianus Pfeuffer Sándor PongorLorinc Sándor Pongor Beáta Reiz Hannes L. Röst Timo Sachsenberg Julian Uszkoreit Marc Vaudel Newton Medeiros Vidal Jonas Weber Kyle C. Weber W. John Wilbur Yuri I. Wolf