Next station in microarray data analysis: GEPAS. - David Montaner; Joaquín Tárraga; Jaime Huerta-Cepas; Jordi Burguet-Castell; Juan M. Vaquerizas; Lucía Conde; Pablo Minguez; Javier Vera; Sach Mukherjee; Joan Valls; Miguel A. G. Pujana; Eva Alloza; et al. (Nucleic Acids Res., 2006)

From genes to functional classes in the study of biological systems. - Fátima Al-Shahrour; Leonardo Arbiza; Hernán Dopazo; Jaime Huerta-Cepas; Pablo Minguez; David Montaner; Joaquín Dopazo (BMC Bioinform., 2007)

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. - Agatha Schlüter; Stéphane Fourcade; Enric Domènech-Estévez; Toni Gabaldón; Jaime Huerta-Cepas; Guillaume Berthommier; Raymond Ripp; Ronald J. A. Wanders; Olivier Poch; Aurora Pujol (Nucleic Acids Res., 2007)

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. - Joaquín Tárraga; Ignacio Medina; Leonardo Arbiza; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2007)

PhylomeDB: a database for genome-wide collections of gene phylogenies. - Jaime Huerta-Cepas; Anibal Bueno; Joaquín Dopazo; Toni Gabaldón (Nucleic Acids Res., 2008)

GEPAS, a web-based tool for microarray data analysis and interpretation. - Joaquín Tárraga; Ignacio Medina; José Carbonell; Jaime Huerta-Cepas; Pablo Minguez; Eva Alloza; Fátima Al-Shahrour; Susana Vegas-Azcárate; Stefan Götz 003; Pablo Escobar; Francisco García-García 002; Ana Conesa; et al. (Nucleic Acids Res., 2008)

Automatic Prediction of the Genetic Code. - Mateus Patricio; Jaime Huerta-Cepas; Toni Gabaldón; Rafael Zardoya; David Posada (IWANN (2), 2009)

ETE: a python Environment for Tree Exploration. - Jaime Huerta-Cepas; Joaquín Dopazo; Toni Gabaldón (BMC Bioinform., 2010)

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. - Jaime Huerta-Cepas; Joaquín Dopazo; Martijn A. Huynen; Toni Gabaldón (Briefings Bioinform., 2011)

CycADS: an annotation database system to ease the development and update of BioCyc databases. - Augusto F. Vellozo; Amélie S. Véron; Patrice Baa-Puyoulet; Jaime Huerta-Cepas; Ludovic Cottret; Gérard Febvay; Federica Calevro; Yvan Rahbé; Angela E. Douglas; Toni Gabaldón; Marie-France Sagot; Hubert Charles; et al. (Database J. Biol. Databases Curation, 2011)

Assigning duplication events to relative temporal scales in genome-wide studies. - Jaime Huerta-Cepas; Toni Gabaldón (Bioinform., 2011)

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. - Jaime Huerta-Cepas; Salvador Capella-Gutiérrez; Leszek P. Pryszcz; Ivan Andreevich Denisov; Diego Kormes; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2011)

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. - Rubén Sánchez 002; François Serra; Joaquín Tárraga; Ignacio Medina; José Carbonell; Luis Pulido; Alejandro de María; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2011)

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. - Jaime Huerta-Cepas; Salvador Capella-Gutiérrez; Leszek P. Pryszcz; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2014)

eggNOG v4.0: nested orthology inference across 3686 organisms. - Sean Powell; Kristoffer Forslund; Damian Szklarczyk; Kalliopi Trachana; Alexander Roth 001; Jaime Huerta-Cepas; Toni Gabaldón; Thomas Rattei; Christopher J. Creevey; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2014)

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. - Pablo Minguez; Ivica Letunic; Luca Parca; Luz Garcia-Alonso; Joaquín Dopazo; Jaime Huerta-Cepas; Peer Bork (Nucleic Acids Res., 2015)

STRING v10: protein-protein interaction networks, integrated over the tree of life. - Damian Szklarczyk; Andrea Franceschini; Stefan Wyder; Kristoffer Forslund; Davide Heller; Jaime Huerta-Cepas; Milan Simonovic; Alexander Roth 001; Alberto Santos; Kalliopi Tsafou; Michael Kuhn 004; Peer Bork; et al. (Nucleic Acids Res., 2015)

ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. - Patrice Baa-Puyoulet; Nicolas Parisot; Gérard Febvay; Jaime Huerta-Cepas; Augusto F. Vellozo; Toni Gabaldón; Federica Calevro; Hubert Charles; Stefano Colella (Database J. Biol. Databases Curation, 2016)

MOCAT2: a metagenomic assembly, annotation and profiling framework. - Jens Roat Kultima; Luís Pedro Coelho; Kristoffer Forslund; Jaime Huerta-Cepas; Simone S. Li; Marja Driessen; Anita Yvonne Voigt; Georg Zeller; Shinichi Sunagawa; Peer Bork (Bioinform., 2016)

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. - Jaime Huerta-Cepas; Damian Szklarczyk; Kristoffer Forslund; Helen Cook; Davide Heller; Mathias C. Walter; Thomas Rattei; Daniel R. Mende; Shinichi Sunagawa; Michael Kuhn 004; Lars Juhl Jensen; Christian von Mering; et al. (Nucleic Acids Res., 2016)

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. - Daniel R. Mende; Ivica Letunic; Jaime Huerta-Cepas; Simone S. Li; Kristoffer Forslund; Shinichi Sunagawa; Peer Bork (Nucleic Acids Res., 2017)

Gearing up to handle the mosaic nature of life in the quest for orthologs. - Kristoffer Forslund; Cécile Pereira; Salvador Capella-Gutiérrez; Alan W. Sousa da Silva; Adrian M. Altenhoff; Jaime Huerta-Cepas; Matthieu Muffato; Mateus Patricio; Klaas Vandepoele; Ingo Ebersberger; Judith A. Blake; Jesualdo Tomás Fernández-Breis; et al. (Bioinform., 2018)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. - Jaime Huerta-Cepas; Damian Szklarczyk; Davide Heller; Ana Hernández-Plaza; Sofia K. Forslund; Helen Cook; Daniel R. Mende; Ivica Letunic; Thomas Rattei; Lars Juhl Jensen; Christian von Mering; Peer Bork (Nucleic Acids Res., 2019)

STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. - Damian Szklarczyk; Annika L. Gable; David Lyon; Alexander Junge; Stefan Wyder; Jaime Huerta-Cepas; Milan Simonovic; Nadezhda T. Doncheva; John H. Morris; Peer Bork; Lars Juhl Jensen; Christian von Mering (Nucleic Acids Res., 2019)

The Quest for Orthologs benchmark service and consensus calls in 2020. - Adrian M. Altenhoff; Javier Garrayo-Ventas; Salvatore Cosentino; David Emms; Natasha M. Glover; Ana Hernández-Plaza; Yannis Nevers; Vicky Sundesha; Damian Szklarczyk; José María Fernández 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. - Daniel R. Mende; Ivica Letunic; Oleksandr M. Maistrenko; Thomas S. B. Schmidt; Alessio Milanese; Lucas Paoli; Ana Hernández-Plaza; Askarbek N. Orakov; Sofia K. Forslund; Shinichi Sunagawa; Georg Zeller; Jaime Huerta-Cepas; et al. (Nucleic Acids Res., 2020)

GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. - Jorge Botas; Álvaro Rodríguez del Río; Joaquín Giner-Lamia; Jaime Huerta-Cepas (Nucleic Acids Res., 2022)

PhyloCloud: an online platform for making sense of phylogenomic data. - Ziqi Deng; Jorge Botas; Carlos P. Cantalapiedra; Ana Hernández-Plaza; Jordi Burguet-Castell; Jaime Huerta-Cepas (Nucleic Acids Res., 2022)

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. - Anthony Fullam; Ivica Letunic; Thomas S. B. Schmidt; Quinten R. Ducarmon; Nicolai Karcher; Supriya Khedkar; Michael Kuhn 004; Martin Larralde; Oleksandr M. Maistrenko; Lukas Malfertheiner; Alessio Milanese; João F. Matias Rodrigues; et al. (Nucleic Acids Res., 2023)

eggNOG 6.0: enabling comparative genomics across 12 535 organisms. - Ana Hernández-Plaza; Damian Szklarczyk; Jorge Botas; Carlos P. Cantalapiedra; Joaquín Giner-Lamia; Daniel R. Mende; Rebecca Kirsch; Thomas Rattei; Ivica Letunic; Lars Juhl Jensen; Peer Bork; Christian von Mering; et al. (Nucleic Acids Res., 2023)