Toni Gabaldón

33 papers Journal 31Unranked 2
YearRankTypeTitle / Venue / Authors
2023 J jnl
The ELIXIR Biodiversity Community: Understanding short- and long-term changes in biodiversity.
F1000Research
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
2022 J jnl
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.
Nucleic Acids Res.
Diego Fuentes, Manuel Molina, Uciel Chorostecki, Salvador Capella-Gutiérrez, Marina Marcet-Houben, Toni Gabaldón
2022 J jnl
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches.
Briefings Bioinform.
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, Georgina Stegmayer
2022 J jnl
The Quest for Orthologs orthology benchmark service in 2022.
Nucleic Acids Res.
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 M. 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
2021 J jnl
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files.
Bioinform.
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
2020 J jnl
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies.
Bioinform.
Hrant Hovhannisyan, Ahmed Ibrahem Hafez, Carlos Lloréns, Toni Gabaldón
2020 J jnl
EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes.
Bioinform.
Marina Marcet-Houben, Toni Gabaldón
2020 J jnl
HaploTypo: a variant-calling pipeline for phased genomes.
Bioinform.
Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manuel Molina, Toni Gabaldón
2020 J jnl
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.
Nucleic Acids Res.
Uciel Chorostecki, Manuel Molina, Leszek P. Pryszcz, Toni Gabaldón
2018 J jnl
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Bioinform.
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, Quest for Orthologs Consortium, Brigitte Boeckmann, Toni Gabaldón, Erik L. L. Sonnhammer, Christophe Dessimoz, Suzanna Lewis
2016 J jnl
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.
Database J. Biol. Databases Curation
Patrice Baa-Puyoulet, Nicolas Parisot, Gérard Febvay, Jaime Huerta-Cepas, Augusto F. Vellozo, Toni Gabaldón, Federica Calevro, Hubert Charles, Stefano Colella
2016 J jnl
spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.
Nucleic Acids Res.
Pedro Furió-Tarí, Sonia Tarazona, Toni Gabaldón, Anton J. Enright, Ana Conesa
2014 J jnl
Big data and other challenges in the quest for orthologs.
Bioinform.
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
2014 J jnl
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
Nucleic Acids Res.
Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Marina Marcet-Houben, Toni Gabaldón
2014 J jnl
The genome of the recently domesticated crop plant sugar beet (
Nat.
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
2014 J jnl
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res.
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
2013 J jnl
Measuring guide-tree dependency of inferred gaps in progressive aligners.
Bioinform.
Salvador Capella-Gutiérrez, Toni Gabaldón
2012 J jnl
Toward community standards in the quest for orthologs.
Bioinform.
Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero
2011 J jnl
Assigning duplication events to relative temporal scales in genome-wide studies.
Bioinform.
Jaime Huerta-Cepas, Toni Gabaldón
2011 J jnl
CycADS: an annotation database system to ease the development and update of BioCyc databases.
Database J. Biol. Databases Curation
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
2011 J jnl
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings Bioinform.
Jaime Huerta-Cepas, Joaquín Dopazo, Martijn A. Huynen, Toni Gabaldón
2011 J jnl
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Res.
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
2011 J jnl
PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
Nucleic Acids Res.
Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Ivan Andreevich Denisov, Diego Kormes, Marina Marcet-Houben, Toni Gabaldón
2010 J jnl
ETE: a python Environment for Tree Exploration.
BMC Bioinform.
Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón
2010 J jnl
PeroxisomeDB 2.0: an integrative view of the global peroxisomal metabolome.
Nucleic Acids Res.
Agatha Schlüter, Alejandro Real-Chicharro, Toni Gabaldón, Francisca Sánchez-Jiménez, Aurora Pujol
2010 J jnl
Predicting phenotypic traits of prokaryotes from protein domain frequencies.
BMC Bioinform.
Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke
2009 — conf
Automatic Prediction of the Genetic Code.
IWANN (2)
Mateus Patricio, Jaime Huerta-Cepas, Toni Gabaldón, Rafael Zardoya, David Posada
2009 J jnl
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses.
Bioinform.
Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón
2008 J jnl
PhylomeDB: a database for genome-wide collections of gene phylogenies.
Nucleic Acids Res.
Jaime Huerta-Cepas, Anibal Bueno, Joaquín Dopazo, Toni Gabaldón
2007 J jnl
From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism.
PLoS Comput. Biol.
Toni Gabaldón, Martijn A. Huynen
2007 J jnl
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
Nucleic Acids Res.
Agatha Schlüter, Stéphane Fourcade, Enric Domènech-Estévez, Toni Gabaldón, Jaime Huerta-Cepas, Guillaume Berthommier, Raymond Ripp, Ronald J. A. Wanders, Olivier Poch, Aurora Pujol
2007 J jnl
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic Acids Res.
Joaquín Tárraga, Ignacio Medina, Leonardo Arbiza, Jaime Huerta-Cepas, Toni Gabaldón, Joaquín Dopazo, Hernán Dopazo
2005 — conf
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes.
ECCB/JBI
Toni Gabaldón, Martijn A. Huynen