Toni Gabaldón

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 12

Top Topics

Experimental Designs

Sequence Analysis

Top Venues

Nucleic Acids Res.

Briefings Bioinform.

Database J. Biol. Databases Curation

Publications

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, Niels Raes, Josephine Burgin, Toni Gabaldón
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity. F1000Research 12 (2023)
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, Mark Hickman, Emma Persson, Ivana Pilizota, Cristina Guijarro-Clarke, Adrian M. Altenhoff, Elspeth A. Bruford, Christophe Dessimoz, Ingo Ebersberger, David M. Emms, Toni Gabaldón, Natasha Glover, Yanhui Hu, Wataru Iwasaki, Odile Lecompte, Benjamin Linard, María J. Martín, David S. Roos, Erik Sonhammer, Paul D. Thomas, David Thybert, Klaas Vandepoele, Salvador Capella-Gutiérrez, Asier Gonzalez-Uriarte, Javier Garrayo-Ventas, Dmitry Repchevsky, Vicky Sundesha, Erik L. L. Sonnhammer
The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 50 (W1) (2022)
Diego Fuentes, Manuel Molina, Uciel Chorostecki, Salvador Capella-Gutiérrez, Marina Marcet-Houben, Toni Gabaldón
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Res. 50 (D1) (2022)
Leandro A Bugnon, Alejandro A. Edera, S. Prochetto, Matias Gerard, Jonathan Raad, E. Fenoy, Mariano Rubiolo, Uciel Chorostecki, Toni Gabaldón, Federico Ariel, Leandro E. Di Persia, Diego H. Milone, Georgina Stegmayer
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches. Briefings Bioinform. 23 (4) (2022)
Ahmed Hafez, Ricardo Futami, Amir Arastehfar, Farnaz Daneshnia, Ana Miguel, Francisco J. Roig, Beatriz Soriano, Jaume Pérez-Sánchez, Teun Boekhout, Toni Gabaldón, Carlos Lloréns
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. Bioinform. 37 (11) (2021)
Marina Marcet-Houben, Toni Gabaldón
EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes. Bioinform. 36 (4) (2020)
Hrant Hovhannisyan, Ahmed Hafez, Carlos Lloréns, Toni Gabaldón
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. Bioinform. 36 (3) (2020)
Uciel Chorostecki, Manuel Molina, Leszek P. Pryszcz, Toni Gabaldón
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life. Nucleic Acids Res. 48 (Webserver-Issue) (2020)
Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manuel Molina, Toni Gabaldón
HaploTypo: a variant-calling pipeline for phased genomes. Bioinform. 36 (8) (2020)
Kristoffer Forslund, Cecile 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, The Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis
Gearing up to handle the mosaic nature of life in the quest for orthologs. Bioinform. 34 (2) (2018)
Pedro Furió-Tarí, Sonia Tarazona, Toni Gabaldón, Anton J. Enright, Ana Conesa
spongeScan: A web for detecting microRNA binding elements in lncRNA sequences. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Patrice Baa-Puyoulet, Nicolas Parisot, Gérard Febvay, Jaime Huerta-Cepas, Augusto F. Vellozo, Toni Gabaldón, Federica Calevro, Hubert Charles, Stefano Colella
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. Database J. Biol. Databases Curation 2016 (2016)
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, Britta Schulz, Peter F. Stadler, Thomas Schmidt, Toni Gabaldón, Hans Lehrach, Bernd Weisshaar, Heinz Himmelbauer
) Open. Nat. 505 (7484) (2014)
Erik L. L. Sonnhammer, Toni Gabaldón, Alan W. Sousa da Silva, Maria Jesus Martin, Marc Robinson-Rechavi, Brigitte Boeckmann, Paul D. Thomas, Christophe Dessimoz, The Quest for Orthologs Consortium
Big data and other challenges in the quest for orthologs. Bioinform. 30 (21) (2014)
Sean Powell, Kristoffer Forslund, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Jaime Huerta-Cepas, Toni Gabaldón, Thomas Rattei, Christopher J. Creevey, Michael Kuhn, Lars Juhl Jensen, Christian von Mering, Peer Bork
eggNOG v4.0: nested orthology inference across 3686 organisms. Nucleic Acids Res. 42 (Database-Issue) (2014)
Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Marina Marcet-Houben, Toni Gabaldón
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. Nucleic Acids Res. 42 (Database-Issue) (2014)
Salvador Capella-Gutiérrez, Toni Gabaldón
Measuring guide-tree dependency of inferred gaps in progressive aligners. Bioinform. 29 (8) (2013)
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero
Toward community standards in the quest for orthologs. Bioinform. 28 (6) (2012)
Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Ivan Denisov, Diego Kormes, Marina Marcet-Houben, Toni Gabaldón
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. Nucleic Acids Res. 39 (Database-Issue) (2011)
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, Stefano Colella
CycADS: an annotation database system to ease the development and update of BioCyc databases. Database J. Biol. Databases Curation 2011 (2011)
Rubén Sánchez, 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
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. Nucleic Acids Res. 39 (Web-Server-Issue) (2011)
Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication. Briefings Bioinform. 12 (5) (2011)
Jaime Huerta-Cepas, Toni Gabaldón
Assigning duplication events to relative temporal scales in genome-wide studies. Bioinform. 27 (1) (2011)
Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke
Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinform. 11 (2010)
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón
ETE: a python Environment for Tree Exploration. BMC Bioinform. 11 (2010)
Agatha Schlüter, Alejandro Real-Chicharro, Toni Gabaldón, Francisca Sánchez-Jiménez, Aurora Pujol
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome. Nucleic Acids Res. 38 (Database-Issue) (2010)
Mateus Patricio, Jaime Huerta-Cepas, Toni Gabaldón, Rafael Zardoya, David Posada
Automatic Prediction of the Genetic Code. IWANN (2) (2009)
Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinform. 25 (15) (2009)
Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón
PhylomeDB: a database for genome-wide collections of gene phylogenies. Nucleic Acids Res. 36 (Database-Issue) (2008)
Toni Gabaldón, Martijn A. Huynen
From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism. PLoS Comput. Biol. 3 (11) (2007)
Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics. Nucleic Acids Res. 35 (Web-Server-Issue) (2007)
Agatha Schlüter, Stéphane Fourcade, Enric Domènech-Estévez, Toni Gabaldón, Jaime Huerta-Cepas, Guillaume Berthommier, Raymond Ripp, Ronald J. A. Wanders, Olivier Poch, Aurora Pujol
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease. Nucleic Acids Res. 35 (Database-Issue) (2007)
Toni Gabaldón, Martijn A. Huynen
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. ECCB/JBI (2005)