Jaime Huerta-Cepas
Jaime Huerta-Cepas
Group Leader at CBGP (UPM-INIA), Madrid, Spain
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STRING v10: protein–protein interaction networks, integrated over the tree of life
D Szklarczyk, A Franceschini, S Wyder, K Forslund, D Heller, ...
Nucleic acids research 43 (D1), D447-D452, 2015
69032015
STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
D Szklarczyk, AL Gable, D Lyon, A Junge, S Wyder, J Huerta-Cepas, ...
Nucleic acids research 47 (D1), D607-D613, 2019
36512019
Whole-genome analyses resolve early branches in the tree of life of modern birds
ED Jarvis, S Mirarab, AJ Aberer, B Li, P Houde, C Li, SYW Ho, ...
Science 346 (6215), 1320-1331, 2014
13802014
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences
J Huerta-Cepas, D Szklarczyk, K Forslund, H Cook, D Heller, MC Walter, ...
Nucleic acids research 44 (D1), D286-D293, 2016
12862016
ETE 3: reconstruction, analysis, and visualization of phylogenomic data
J Huerta-Cepas, F Serra, P Bork
Molecular biology and evolution 33 (6), 1635-1638, 2016
8542016
Genome sequence of the pea aphid Acyrthosiphon pisum
International Aphid Genomics Consortium
PLOS biol 8 (2), e1000313, 2010
8062010
Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper
J Huerta-Cepas, K Forslund, LP Coelho, D Szklarczyk, LJ Jensen, ...
Molecular biology and evolution 34 (8), 2115-2122, 2017
8052017
Structure and function of the global topsoil microbiome
M Bahram, F Hildebrand, SK Forslund, JL Anderson, NA Soudzilovskaia, ...
Nature 560 (7717), 233-237, 2018
4562018
eggNOG v4. 0: nested orthology inference across 3686 organisms
S Powell, K Forslund, D Szklarczyk, K Trachana, A Roth, J Huerta-Cepas, ...
Nucleic acids research 42 (D1), D231-D239, 2014
4242014
eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
J Huerta-Cepas, D Szklarczyk, D Heller, A Hernández-Plaza, SK Forslund, ...
Nucleic acids research 47 (D1), D309-D314, 2019
3962019
ETE: a python Environment for Tree Exploration
J Huerta-Cepas, J Dopazo, T Gabaldón
BMC bioinformatics 11 (1), 1-7, 2010
3942010
Durable coexistence of donor and recipient strains after fecal microbiota transplantation
SS Li, A Zhu, V Benes, PI Costea, R Hercog, F Hildebrand, ...
Science 352 (6285), 586-589, 2016
3162016
PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
J Huerta-Cepas, S Capella-Gutierrez, LP Pryszcz, M Marcet-Houben, ...
Nucleic acids research 42 (D1), D897-D902, 2014
2032014
The human phylome
J Huerta-Cepas, H Dopazo, J Dopazo, T Gabaldón
Genome biology 8 (6), 1-16, 2007
1982007
PhylomeDB v3. 0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions
J Huerta-Cepas, S Capella-Gutierrez, LP Pryszcz, I Denisov, D Kormes, ...
Nucleic acids research 39 (suppl_1), D556-D560, 2010
1702010
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
R Sánchez, F Serra, J Tárraga, I Medina, J Carbonell, L Pulido, ...
Nucleic acids research 39 (suppl_2), W470-W474, 2011
1692011
Standardized benchmarking in the quest for orthologs
AM Altenhoff, B Boeckmann, S Capella-Gutierrez, DA Dalquen, T DeLuca, ...
Nature methods 13 (5), 425-430, 2016
1562016
From genes to functional classes in the study of biological systems
F Al-Shahrour, L Arbiza, H Dopazo, J Huerta-Cepas, P Mínguez, ...
BMC bioinformatics 8 (1), 1-17, 2007
1562007
Next station in microarray data analysis: GEPAS
D Montaner, J Tárraga, J Huerta-Cepas, J Burguet, JM Vaquerizas, ...
Nucleic Acids Research 34 (suppl_2), W486-W491, 2006
1482006
MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
LP Pryszcz, J Huerta-Cepas, T Gabaldon
Nucleic acids research 39 (5), e32-e32, 2011
1432011
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