Jaime Huerta-Cepas

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Peer BorkEMBLVerified email at embl.de
Toni GabaldonGroup Leader, Institute for Research in Biomedicine (IRB) and Barcelona Supercomputing Centre (BSC)Verified email at crg.es
Sofia K. ForslundJunior Group Leader, ECRC (joint Max Delbrück Center and Charité University Hospital unit), BerlinVerified email at embl.de
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Lars Juhl JensenUniversity of CopenhagenVerified email at cpr.ku.dk
Shinichi SunagawaETH Zurich; Swiss Institute of Bioinformatics; ETH AI CenterVerified email at ethz.ch
Joaquin DopazoHead of the Clinical Bioinformatics Area, FPS, Hospital Virgen del Rocio, Sevilla, SpainVerified email at juntadeandalucia.es
Luis Pedro CoelhoISTBI, Fudan UniversityVerified email at fudan.edu.cn
Michael Kuhnstaff scientist in the lab of Peer Bork, EMBLVerified email at embl.de
Daniel R. MendeAsst. Professor, Amsterdam University Medical Center, University of AmsterdamVerified email at amsterdamumc.nl
Falk HildebrandQuadram & Earlham Institute, Norwich, UKVerified email at quadram.ac.uk
Ivica Letunićbiobyte solutions GmbHVerified email at biobyte.de
Marina Marcet-HoubenBSCVerified email at bsc.es
Georg ZellerEMBL, HeidelbergVerified email at embl.de
Salvador Capella-GutiérrezBarcelona Supercomputing Centre (BSC)Verified email at bsc.es
françois serraComputational Biology Group - BSCVerified email at bsc.es
Paul Igor CosteaBASFVerified email at basf.com
Hernan DopazoProfessor of evolutionary and population genomicsVerified email at ege.fcen.uba.ar
Simone S LiEMBO Research Fellow, Novo Nordisk Center for Biosustainability (Technical University of Denmark)Verified email at biosustain.dtu.dk

Jaime Huerta-Cepas

Group Leader at CBGP (UPM-INIA), Madrid, Spain

Verified email at embl.de - Homepage

Phylogenomics Phylogenetics Evolution Computational Biology Metagenomics


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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	7513	2015
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	5619	2019
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	1494	2014
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	1430	2016
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	1067	2017
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	1023	2016
Genome Sequence of the Pea Aphid Acyrthosiphon pisum International Aphid Genomics Consortium PLoS biology 8 (2), e1000313, 2010	840	2010
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	677	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	597	2018
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	459	2014
ETE: a python Environment for Tree Exploration J Huerta-Cepas, J Dopazo, T Gabaldón BMC bioinformatics 11 (1), 1-7, 2010	400	2010
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	368	2016
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	218	2014
The human phylome J Huerta-Cepas, H Dopazo, J Dopazo, T Gabaldón Genome biology 8 (6), 1-16, 2007	202	2007
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	175	2011
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	173	2016
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
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	157	2007
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
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	146	2006

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