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2020 – today
- 2023
[i1]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: 499 (2023)- 2022
- [j30]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:
Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches. Briefings Bioinform. 23(4) (2022) - [j29]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): 1062-1068 (2022) - [j28]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:
The Quest for Orthologs orthology benchmark service in 2022. Nucleic Acids Res. 50(W1): 623-632 (2022) - 2021
- [j27]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:
SeqEditor: an application for primer design and sequence analysis with or without GTF/GFF files. Bioinform. 37(11): 1610-1612 (2021) - 2020
- [j26]Hrant Hovhannisyan, Ahmed Ibrahem Hafez, Carlos Lloréns, Toni Gabaldón:
CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies. Bioinform. 36(3): 925-927 (2020) - [j25]Marina Marcet-Houben, Toni Gabaldón:
EvolClust: automated inference of evolutionary conserved gene clusters in eukaryotes. Bioinform. 36(4): 1265-1266 (2020) - [j24]Cinta Pegueroles, Verónica Mixão, Laia Carreté, Manuel Molina, Toni Gabaldón:
HaploTypo: a variant-calling pipeline for phased genomes. Bioinform. 36(8): 2569-2571 (2020) - [j23]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): W553-W557 (2020)
2010 – 2019
- 2018
- [j22]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, 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): 323-329 (2018) - 2016
- [j21]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) - [j20]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): W176-W180 (2016) - 2014
- [j19]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): 2993-2998 (2014) - [j18]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): 231-239 (2014) - [j17]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): 897-902 (2014) - [j16]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:
The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Open. Nat. 505(7484): 546-549 (2014) - 2013
- [j15]Salvador Capella-Gutiérrez, Toni Gabaldón:
Measuring guide-tree dependency of inferred gaps in progressive aligners. Bioinform. 29(8): 1011-1017 (2013) - 2012
- [j14]Christophe Dessimoz, Toni Gabaldón, David S. Roos, Erik L. L. Sonnhammer, Javier Herrero:
Toward community standards in the quest for orthologs. Bioinform. 28(6): 900-904 (2012) - 2011
- [j13]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): 442-448 (2011) - [j12]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) - [j11]Jaime Huerta-Cepas, Toni Gabaldón:
Assigning duplication events to relative temporal scales in genome-wide studies. Bioinform. 27(1): 38-45 (2011) - [j10]Jaime Huerta-Cepas, Salvador Capella-Gutiérrez, Leszek P. Pryszcz, Ivan Andreevich 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): 556-560 (2011) - [j9]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): 470-474 (2011) - 2010
- [j8]Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón:
ETE: a python Environment for Tree Exploration. BMC Bioinform. 11: 24 (2010) - [j7]Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke:
Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinform. 11: 481 (2010) - [j6]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): 800-805 (2010)
2000 – 2009
- 2009
- [j5]Salvador Capella-Gutiérrez, José M. Silla-Martínez, Toni Gabaldón:
trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinform. 25(15): 1972-1973 (2009) - [c2]Mateus Patricio, Jaime Huerta-Cepas, Toni Gabaldón, Rafael Zardoya, David Posada:
Automatic Prediction of the Genetic Code. IWANN (2) 2009: 1125-1129 - 2008
- [j4]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): 491-496 (2008) - 2007
- [j3]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): 815-822 (2007) - [j2]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): 38-42 (2007) - [j1]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) - 2005
- [c1]Toni Gabaldón, Martijn A. Huynen:
Lineage-specific gene loss following mitochondrial endosymbiosis and its potential for function prediction in eukaryotes. ECCB/JBI 2005: 150
Coauthor Index
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