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2020 – today

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2023
[j29]
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  - journals/nar/HernandezPlazaSBCGMKRLJBMH23
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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]
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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]
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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]
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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]
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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]
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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)

2010 – 2019

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2019
[j23]
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  - journals/nar/Huerta-CepasSHH19
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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]
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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]
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  - journals/bioinformatics/ForslundPCSAHMP18
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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]
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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]
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  - journals/biodb/Baa-PuyouletPFH16
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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]
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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]
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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]
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  - journals/nar/SzklarczykFWFHHS0STKBJM15
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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]
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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]
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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]
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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]
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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]
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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]
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Jaime Huerta-Cepas, Toni Gabaldón:
Assigning duplication events to relative temporal scales in genome-wide studies. Bioinform. 27(1): 38-45 (2011)
[j9]
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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]
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  - journals/nar/SanchezSTMCPMCHGDD11
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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]
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Jaime Huerta-Cepas, Joaquín Dopazo, Toni Gabaldón:
ETE: a python Environment for Tree Exploration. BMC Bioinform. 11: 24 (2010)

2000 – 2009

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2009
[c1]
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Mateus Patricio, Jaime Huerta-Cepas, Toni Gabaldón, Rafael Zardoya, David Posada:
Automatic Prediction of the Genetic Code. IWANN (2) 2009: 1125-1129
2008
[j6]
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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]
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  - journals/nar/TarragaMCHMAAVGEGCMD08
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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]
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  - journals/bmcbi/Al-ShahrourADHMMD07
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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]
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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]
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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]
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  - journals/nar/MontanerTHBVCMVMVPAHAD06
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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)

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