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Jaime Huerta-Cepas
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Journal Articles
- 2023
- [j29]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
, Jaime Huerta-Cepas
:
eggNOG 6.0: enabling comparative genomics across 12 535 organisms. Nucleic Acids Res. 51(D1): 389-394 (2023) - [j28]Anthony Fullam
, Ivica Letunic
, Thomas S. B. Schmidt
, Quinten R. Ducarmon
, Nicolai Karcher
, Supriya Khedkar
, Michael Kuhn
, Martin Larralde
, Oleksandr M. Maistrenko
, Lukas Malfertheiner
, Alessio Milanese
, João F. Matias Rodrigues, Claudia Sanchis-López
, Christian Schudoma
, Damian Szklarczyk
, Shinichi Sunagawa
, Georg Zeller
, Jaime Huerta-Cepas
, Christian von Mering
, Peer Bork
, Daniel R. Mende
:
proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes. Nucleic Acids Res. 51(D1): 760-766 (2023) - 2022
- [j27]Jorge Botas
, Álvaro Rodríguez del Río
, Joaquín Giner-Lamia
, Jaime Huerta-Cepas
:
GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective. Nucleic Acids Res. 50(W1): 352-357 (2022) - [j26]Ziqi Deng
, Jorge Botas
, Carlos P. Cantalapiedra
, Ana Hernández-Plaza
, Jordi Burguet-Castell
, Jaime Huerta-Cepas
:
PhyloCloud: an online platform for making sense of phylogenomic data. Nucleic Acids Res. 50(W1): 577-582 (2022) - 2020
- [j25]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
, Luís Pedro Coelho
, Peer Bork:
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes. Nucleic Acids Res. 48(Database-Issue): D621-D625 (2020) - [j24]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
, Laia Codó
, The Quest for Orthologs Consortium, Josep Lluis Gelpí
, Jaime Huerta-Cepas
, Wataru Iwasaki
, Steven Kelly
, Odile Lecompte
, Matthieu Muffato
, Maria Jesus Martin
, Salvador Capella-Gutiérrez
, Paul D. Thomas
, Erik L. L. Sonnhammer
, Christophe Dessimoz
:
The Quest for Orthologs benchmark service and consensus calls in 2020. Nucleic Acids Res. 48(Webserver-Issue): W538-W545 (2020) - 2019
- [j23]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:
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 47(Database-Issue): D309-D314 (2019) - [j22]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
:
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47(Database-Issue): D607-D613 (2019) - 2018
- [j21]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) - 2017
- [j20]Daniel R. Mende
, Ivica Letunic
, Jaime Huerta-Cepas
, Simone S. Li
, Kristoffer Forslund
, Shinichi Sunagawa
, Peer Bork:
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes. Nucleic Acids Res. 45(Database-Issue): D529-D534 (2017) - 2016
- [j19]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) - [j18]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:
MOCAT2: a metagenomic assembly, annotation and profiling framework. Bioinform. 32(16): 2520-2523 (2016) - [j17]Jaime Huerta-Cepas
, Damian Szklarczyk, Kristoffer Forslund
, Helen Cook
, Davide Heller, Mathias C. Walter
, Thomas Rattei
, Daniel R. Mende
, Shinichi Sunagawa
, Michael Kuhn
, Lars Juhl Jensen
, Christian von Mering
, Peer Bork
:
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences. Nucleic Acids Res. 44(Database-Issue): 286-293 (2016) - 2015
- [j16]Damian Szklarczyk, Andrea Franceschini
, Stefan Wyder
, Kristoffer Forslund
, Davide Heller, Jaime Huerta-Cepas
, Milan Simonovic, Alexander Roth, Alberto Santos
, Kalliopi Tsafou, Michael Kuhn
, Peer Bork
, Lars Juhl Jensen
, Christian von Mering
:
STRING v10: protein-protein interaction networks, integrated over the tree of life. Nucleic Acids Res. 43(Database-Issue): 447-452 (2015) - [j15]Pablo Minguez
, Ivica Letunic
, Luca Parca
, Luz Garcia-Alonso
, Joaquín Dopazo, Jaime Huerta-Cepas
, Peer Bork
:
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins. Nucleic Acids Res. 43(Database-Issue): 494-502 (2015) - 2014
- [j14]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) - [j13]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) - 2011
- [j12]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) - [j11]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) - [j10]Jaime Huerta-Cepas
, Toni Gabaldón
:
Assigning duplication events to relative temporal scales in genome-wide studies. Bioinform. 27(1): 38-45 (2011) - [j9]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) - [j8]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
- [j7]Jaime Huerta-Cepas
, Joaquín Dopazo
, Toni Gabaldón
:
ETE: a python Environment for Tree Exploration. BMC Bioinform. 11: 24 (2010) - 2008
- [j6]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) - [j5]Joaquín Tárraga, Ignacio Medina
, José Carbonell
, Jaime Huerta-Cepas
, Pablo Minguez
, Eva Alloza
, Fátima Al-Shahrour, Susana Vegas-Azcárate, Stefan Götz
, Pablo Escobar, Francisco García-García
, Ana Conesa
, David Montaner
, Joaquín Dopazo
:
GEPAS, a web-based tool for microarray data analysis and interpretation. Nucleic Acids Res. 36(Web-Server-Issue): 308-314 (2008) - 2007
- [j4]Fátima Al-Shahrour, Leonardo Arbiza, Hernán Dopazo
, Jaime Huerta-Cepas
, Pablo Minguez
, David Montaner
, Joaquín Dopazo
:
From genes to functional classes in the study of biological systems. BMC Bioinform. 8 (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) - 2006
- [j1]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
, Javier Herrero
, Fátima Al-Shahrour, Joaquín Dopazo
:
Next station in microarray data analysis: GEPAS. Nucleic Acids Res. 34(Web-Server-Issue): 486-491 (2006)
Conference and Workshop Papers
- 2009
- [c1]Mateus Patricio, Jaime Huerta-Cepas, Toni Gabaldón, Rafael Zardoya
, David Posada
:
Automatic Prediction of the Genetic Code. IWANN (2) 2009: 1125-1129
Coauthor Index
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