Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. - Toni Gabaldón; Martijn A. Huynen (ECCB/JBI, 2005)

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)

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism. - Toni Gabaldón; Martijn A. Huynen (PLoS Comput. Biol., 2007)

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

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. - Salvador Capella-Gutiérrez; José M. Silla-Martínez; Toni Gabaldón (Bioinform., 2009)

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

Predicting phenotypic traits of prokaryotes from protein domain frequencies. - Thomas Lingner; Stefanie Mühlhausen; Toni Gabaldón; Cédric Notredame; Peter Meinicke (BMC Bioinform., 2010)

PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. - Agatha Schlüter; Alejandro Real-Chicharro; Toni Gabaldón; Francisca Sánchez-Jiménez; Aurora Pujol (Nucleic Acids Res., 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)

Toward community standards in the quest for orthologs. - Christophe Dessimoz; Toni Gabaldón; David S. Roos; Erik L. L. Sonnhammer; Javier Herrero (Bioinform., 2012)

Measuring guide-tree dependency of inferred gaps in progressive aligners. - Salvador Capella-Gutiérrez; Toni Gabaldón (Bioinform., 2013)

Big data and other challenges in the quest for orthologs. - Erik L. L. Sonnhammer; Toni Gabaldón; Alan W. Sousa da Silva; Maria Jesus Martin; Marc Robinson-Rechavi; Brigitte Boeckmann; Paul D. Thomas; Christophe Dessimoz; Quest for Orthologs Consortium (Bioinform., 2014)

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)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Open. - Juliane C. Dohm; André E. Minoche; Daniela Holtgräwe; Salvador Capella-Gutiérrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sörensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; et al. (Nat., 2014)

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)

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)

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)

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. - Hrant Hovhannisyan; Ahmed Ibrahem Hafez; Carlos Lloréns; Toni Gabaldón (Bioinform., 2020)

EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes. - Marina Marcet-Houben; Toni Gabaldón (Bioinform., 2020)

HaploTypo: a variant-calling pipeline for phased genomes. - Cinta Pegueroles; Verónica Mixão; Laia Carreté; Manuel Molina; Toni Gabaldón (Bioinform., 2020)

MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. - Uciel Chorostecki; Manuel Molina; Leszek P. Pryszcz; Toni Gabaldón (Nucleic Acids Res., 2020)

SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. - Ahmed Ibrahem Hafez; Ricardo Futami; Amir Arastehfar; Farnaz Daneshnia; Ana Miguel; Francisco J. Roig; Beatriz Soriano; Jaume Pérez-Sánchez; Teun Boekhout; Toni Gabaldón; Carlos Lloréns (Bioinform., 2021)

Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches. - Leandro A Bugnon; Alejandro A. Edera; Santiago Prochetto; Matias Gerard; Jonathan Raad; Emilio Fenoy; Mariano Rubiolo; Uciel Chorostecki; Toni Gabaldón; Federico Ariel; Leandro E. Di Persia; Diego H. Milone; et al. (Briefings Bioinform., 2022)

PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. - Diego Fuentes; Manuel Molina; Uciel Chorostecki; Salvador Capella-Gutiérrez; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2022)

The Quest for Orthologs orthology benchmark service in 2022. - Yannis Nevers; Tamsin E. M. Jones; Dushyanth Jyothi; Bethan Yates; Meritxell Ferret; Laura Portell-Silva; Laia Codó; Salvatore Cosentino; Marina Marcet-Houben; Anna Vlasova; Laetitia Poidevin; Arnaud Kress; et al. (Nucleic Acids Res., 2022)

The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. - Robert M. Waterhouse; Anne-Françoise Adam-Blondon; Bachir Balech; Endre Barta; Katharina F. Heil; Graham M. Hughes; Lars S. Jermiin; Matús Kalas; Jerry Lanfear; Evangelos Pafilis; Aristotelis C. Papageorgiou; Fotis E. Psomopoulos; et al. (F1000Research, 2023)