Publications

Title
Cited by
Year
Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria
C Sanchis-L�pez, JP Cerna-Vargas, S Santamar�a-Hernando, C Ramos, ...
Msystems 6 (5), e00951-21, 2021
2021
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale
CP Cantalapiedra, A Hern�ndez-Plaza, I Letunic, P Bork, J Huerta-Cepas
bioRxiv, 2021
7 2021
RNA degradation analysis reveals ribosome dynamics in complex microbiome samples
S Huch, L Nersisyan, M Ropat, D Barret, J Wang, J Huerta-Cepas, W Wei, ...
bioRxiv, 2021
1 2021
The Quest for Orthologs benchmark service and consensus calls in 2020
AM Altenhoff, J Garrayo-Ventas, S Cosentino, D Emms, NM Glover, ...
Nucleic acids research 48 (W1), W538-W545, 2020
12 2020
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity
OM Maistrenko, DR Mende, M Luetge, F Hildebrand, TSB Schmidt, SS Li, ...
The ISME journal 14 (5), 1247-1259, 2020
21 2020
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes
DR Mende, I Letunic, OM Maistrenko, TSB Schmidt, A Milanese, L Paoli, ...
Nucleic acids research 48 (D1), D621-D625, 2020
23 2020
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language
LP Coelho, R Alves, P Monteiro, J Huerta-Cepas, AT Freitas, P Bork
Microbiome 7 (1), 1-10, 2019
17 2019
Gene expression changes and community turnover differentially shape the global ocean metatranscriptome
G Salazar, L Paoli, A Alberti, J Huerta-Cepas, HJ Ruscheweyh, M Cuenca, ...
Cell 179 (5), 1068-1083. e21, 2019
97 2019
Advances and Applications in the Quest for Orthologs
N Glover, C Dessimoz, I Ebersberger, SK Forslund, T Gabald�n, ...
Molecular biology and evolution 36 (10), 2157-2164, 2019
45 2019
Antibiotics-induced monodominance of a novel gut bacterial order
F Hildebrand, L Moitinho-Silva, S Blasche, MT Jahn, TI Gossmann, ...
Gut 68 (10), 1781-1790, 2019
42 2019
Microbial abundance, activity and population genomic profiling with mOTUs2
A Milanese, DR Mende, L Paoli, G Salazar, HJ Ruscheweyh, M Cuenca, ...
Nature communications 10 (1), 1-11, 2019
120 2019
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
5495 2019
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 Hern�ndez-Plaza, SK Forslund, ...
Nucleic acids research 47 (D1), D309-D314, 2019
656 2019
Disentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity
OM Maistrenko, DR Mende, M Luetge, F Hildebrand, TSB Schmidt, SS Li, ...
bioRxiv, 735696, 2019
2019
Advances and Applications in the Quest for Orthologs
T Gabald�n, J Huerta-Cepas, MJ Martin, M Muffato, M Patricio, C Pereira, ...
Mol. Biol. Evol, 2019
2019
Profiling cellular diversity in sponges informs animal cell type and nervous system evolution
JM Musser, KJ Schippers, M Nickel, G Mizzon, AB Kohn, C Pape, ...
BioRxiv, 758276, 2019
26 2019
Function, evolution, and structure of J-domain proteins
HH Kampinga, C Andreasson, A Barducci, ME Cheetham, D Cyr, ...
Cell Stress and Chaperones 24 (1), 7-15, 2019
49 2019
Structure and function of the global topsoil microbiome
M Bahram, F Hildebrand, SK Forslund, JL Anderson, NA Soudzilovskaia, ...
Nature 560 (7717), 233-237, 2018
585 2018
Gearing up to handle the mosaic nature of life in the quest for orthologs
K Forslund, C Pereira, S Capella-Gutierrez, AS da Silva, A Altenhoff, ...
Bioinformatics 34 (2), 323-329, 2018
28 2018
Subspecies in the global human gut microbiome
PI Costea, LP Coelho, S Sunagawa, R Munch, J Huerta‐Cepas, ...
Molecular systems biology 13 (12), 960, 2017
75 2017
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
1051 2017
A critical review on the use of support values in tree viewers and bioinformatics toolkits
L Czech, J Huerta-Cepas, A Stamatakis
Molecular biology and evolution 34 (6), 1535-1542, 2017
20 2017
Metabolic anchor reactions for robust biorefining
P Jouhten, J Huerta-Cepas, P Bork, KR Patil
Metabolic engineering 40, 1-4, 2017
11 2017
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes
DR Mende, I Letunic, J Huerta-Cepas, SS Li, K Forslund, S Sunagawa, ...
Nucleic acids research, gkw989, 2016
70 2016
MOCAT2: a metagenomic assembly, annotation and profiling framework
JR Kultima, LP Coelho, K Forslund, J Huerta-Cepas, SS Li, M Driessen, ...
Bioinformatics 32 (16), 2520-2523, 2016
116 2016
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
172 2016
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
364 2016
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
1005 2016
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
1414 2016
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods
P Baa-Puyoulet, N Parisot, G Febvay, J Huerta-Cepas, AF Vellozo, ...
Database 2016, 2016
11 2016
Quest for orthologs entails quest for tree of life: in search of the gene stream
B Boeckmann, M Marcet-Houben, JA Rees, K Forslund, J Huerta-Cepas, ...
Genome biology and evolution 7 (7), 1988-1999, 2015
22 2015
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
7488 2015
PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins
P Minguez, I Letunic, L Parca, L Garcia-Alonso, J Dopazo, ...
Nucleic acids research 43 (D1), D494-D502, 2015
66 2015
Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites
CF Djuika, J Huerta-Cepas, JM Przyborski, S Deil, CP Sanchez, T Doerks, ...
Microbial Cell 2 (1), 5, 2015
8 2015
An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum
T Bock, WH Chen, A Ori, N Malik, N Silva-Martin, J Huerta-Cepas, ...
Nucleic acids research 42 (22), 13525-13533, 2014
44 2014
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
1486 2014
Annotating arthropods genome to study and compare their metabolism: the ArthropodaCyc collection of Cyc databases powered by CycADS
P Baa-Puyoulet, A Vellozo, J Huerta-Cepas, G Febvay, F Calevro, ...
13. European Conference on Computational Biology (ECCB), 1 p., 2014
2014
Neuroprotection elicited by P2Y13 receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery
V Morente, R P�rez-Sen, F Ortega, J Huerta-Cepas, EG Delicado, ...
Biochimica et Biophysica Acta (BBA)-Molecular Cell Research 1843 (9), 1886-1898, 2014
33 2014
A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life
J Huerta-Cepas, M Marcet-Houben, T Gabald�n
PeerJ PrePrints, 2014
4 2014
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
455 2014
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
216 2014
Comparative transcriptomics of early dipteran development
E Jim�nez-Guri, J Huerta-Cepas, L Cozzuto, KR Wotton, H Kang, ...
BMC genomics 14 (1), 1-17, 2013
50 2013
The CycADS annotation database system to support the development and update of enriched BioCyc databases. Development of ad hoc BioCyc DB: AcypiCyc, ArthopodaCyc
P Baa-Puyoulet, A Vellozo, J Huerta-Cepas, G Febvay, T Gabaldon, ...
5. R�union R�seau BAPOA, 2012
2012
Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication
J Huerta-Cepas, J Dopazo, MA Huynen, T Gabald�n
Briefings in bioinformatics 12 (5), 442-448, 2011
53 2011
“ArthropodaCyc”: a BioCyc database powered by CycADS to study and compare the metabolism of arthropods
P Baa-Puyoulet, A Vellozo, J Huerta-Cepas, G Febvay, T Gabaldon, ...
5. Annual Arthropod Genomics Symposium “Arthropod Genomics 2011: Exploring�…, 2011
2011
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing
R S�nchez, F Serra, J T�rraga, I Medina, J Carbonell, L Pulido, ...
Nucleic acids research 39 (suppl_2), W470-W474, 2011
175 2011
Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”
P Baa-Puyoulet, A Vellozo, J Huerta-Cepas, G Febvay, T Gabaldon, ...
Rencontres bioinformaticiens et statisticiens de l’INRA, 1 p., 2011
2011
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
146 2011
From Genomics to Microevolution and Ecology: The Case of Salinibacter ruber
A Pena, H Teeling, J Huerta-Cepas, F Santos, I Meseguer, M Lucio, ...
Halophiles and hypersaline environments, 109-122, 2011
6 2011
CycADS: an annotation database system to ease the development and update of BioCyc databases
AF Vellozo, AS Veron, P Baa-Puyoulet, J Huerta-Cepas, L Cottret, ...
Database 2011, 2011
20 2011
Assigning duplication events to relative temporal scales in genome-wide studies
J Huerta-Cepas, T Gabald�n
Bioinformatics 27 (1), 38-45, 2011
59 2011
ETE: a python Environment for Tree Exploration
J Huerta-Cepas, J Dopazo, T Gabald�n
BMC bioinformatics 11 (1), 1-7, 2010
399 2010
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
172 2010
A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources
F Legeai, S Colella, J Huerta-Cepas, JP Gauthier, A Vellozo, ...
10. Cold Spring Harbor Laboratory/Wellcome Trust conference on Genome�…, 2010
2010
Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains
A Pena, H Teeling, J Huerta-Cepas, F Santos, P Yarza, J Brito-Echeverr�a, ...
The ISME Journal 4 (7), 882-895, 2010
80 2010
Using the “CycADS” annotation management system to develop a BioCyc metabolic network database for sequenced arthropods genomes: first steps towards “ArthropodsCyc”
A Vellozo, P Baa-Puyoulet, J Huerta-Cepas, G Febvay, F Calevro, ...
4. Annual Arthropod Genomics Symposium on “Arthropod Genomics: New�…, 2010
2010
The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes
J Huerta‐Cepas, M Marcet‐Houben, M Pignatelli, A Moya, T Gabald�n
Insect molecular biology 19, 13-21, 2010
51 2010
Genome Sequence of the Pea Aphid Acyrthosiphon pisum
International Aphid Genomics Consortium
PLoS biology 8 (2), e1000313, 2010
835 2010
Automatic Prediction of the Genetic Code
M Patricio, J Huerta-Cepas, T Gabald�n, R Zardoya, D Posada
International Work-Conference on Artificial Neural Networks, 1125-1129, 2009
1 2009
CycADS: an annotation management system for the development and update of BioCyc metabolic network databases
A Vellozo, P Baa-Puyoulet, A Veron, J Huerta-Cepas, L Cottret, G Febvay, ...
1st International Workshop on Information Systems for Insect Pests, Rennes�…, 2009
2009
GEPAS, a web-based tool for microarray data analysis and interpretation
J T�rraga, I Medina, J Carbonell, J Huerta-Cepas, P Minguez, E Alloza, ...
Nucleic acids research 36 (suppl_2), W308-W314, 2008
87 2008
Interoperability with Moby 1.0—It's better than sharing your toothbrush
BioMoby Consortium
Briefings in Bioinformatics 9 (3), 220-231, 2008
115* 2008
The human phylome: a large scale phylogenetic study on the human genome evolution
J Huerta Cepas
2008
Reconstruction and analysis of large-scale phylogenetic data, challenges and opportunities
T Gabaldon, M Marcet-Houben, J Huerta-Cepas, A Russe
Computational Biology: New Research, 129-146, 2008
5 2008
Evidence for systems-level molecular mechanisms of tumorigenesis
P Hern�ndez, J Huerta-Cepas, D Montaner, F Al-Shahrour, J Valls, ...
BMC genomics 8 (1), 1-12, 2007
45 2007
From genes to functional classes in the study of biological systems
F Al-Shahrour, L Arbiza, H Dopazo, J Huerta-Cepas, P M�nguez, ...
BMC bioinformatics 8 (1), 1-17, 2007
157 2007
PhylomeDB: a database for genome-wide collections of gene phylogenies
J Huerta-Cepas, A Bueno, J Dopazo, T Gabald�n
Nucleic acids research 36 (suppl_1), D491-D496, 2007
130 2007
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics
J T�rraga, I Medina, L Arbiza, J Huerta-Cepas, T Gabald�n, J Dopazo, ...
Nucleic acids research 35 (suppl_2), W38-W42, 2007
54 2007
The human phylome
J Huerta-Cepas, H Dopazo, J Dopazo, T Gabald�n
Genome biology 8 (6), 1-16, 2007
202 2007
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
A Schl�ter, S Fourcade, E Dom�nech-Est�vez, T Gabald�n, ...
Nucleic acids research 35 (suppl_1), D815-D822, 2007
77 2007
Next station in microarray data analysis: GEPAS
D Montaner, J T�rraga, J Huerta-Cepas, J Burguet, JM Vaquerizas, ...
Nucleic Acids Research 34 (suppl_2), W486-W491, 2006
146 2006
PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease
J Huerta-Cepas, G Berthommier, R Ripp, RJA Wanders, O Poch, A Pujol
2006
New steps on phylomeDB
J Huerta-Cepas, S Capella-Gutierrez, L Pryszcz, M Marcet-Houben, ...
SUPPLEMENTARY MATERIAL FOR THE PAPER A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life
J Huerta-Cepas, M Marcet-Houben, T Gabald�n
The GEPAS: a web-based suite for microarray data analysis
D Montaner, J T�rraga, I Medina, J Huerta-Cepas, P Minguez, E Alloza, ...