Jaime Huerta-Cepas

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Peer BorkDirector of EMBL HeidelbergVerified 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
Toni GabaldonGroup Leader, Institute for Research in Biomedicine (IRB), Barcelona Supercomputing Centre (BSC)Verified email at crg.es
Lars Juhl JensenUniversity of CopenhagenVerified email at cpr.ku.dk
Shinichi SunagawaETH Zurich; Swiss Institute of BioinformaticsVerified email at ethz.ch
Luis Pedro CoelhoCentre for Microbiome Research, Queensland University of TechnologyVerified email at qut.edu.au
Michael Kuhnresearch staff scientist & research coordinator 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
Ivica Letunićbiobyte solutions GmbHVerified email at biobyte.de
Joaquin DopazoComputational Medicine Platform, FPS, Hospital Virgen del Rocio, Sevilla, SpainVerified email at juntadeandalucia.es
Falk HildebrandGroup Leader, Quadram & Earlham Institute, Norwich, UKVerified email at quadram.ac.uk
Carlos P CantalapiedraCentro de Biotecnología y Genómica de Plantas - UPM-INIAVerified email at inia.csic.es
Georg ZellerEMBL, HeidelbergVerified email at embl.de
Marina Marcet-HoubenBarcelona Supercomputing Center - BSCVerified email at bsc.es
françois serra3D Chromatin Organization - IJCVerified email at carrerasresearch.org
Paul Igor CosteaBASFVerified email at basf.com
Salvador Capella-GutiérrezBarcelona Supercomputing Centre (BSC)Verified email at bsc.es
Simone S LiNHMRC Early Career Fellow, Biomedicine Discovery Institute (Monash University, Australia)Verified email at monash.edu
Alvaro Rodriguez del RioFU BerlinVerified email at alumnos.upm.es

Jaime Huerta-Cepas

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

Verified email at embl.de - Homepage

Phylogenomics Phylogenetics Evolution Computational Biology Metagenomics


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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	15060	2019
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	10530	2015
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	3136	2019
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	2315	2017
eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale CP Cantalapiedra, A Hernández-Plaza, I Letunic, P Bork, J Huerta-Cepas Molecular Biology and Evolution 38 (12), 2021	2017	2021
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	1995	2016
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	1963	2014
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	1865	2016
Structure and function of the global topsoil microbiome M Bahram, F Hildebrand, SK Forslund, JL Anderson, NA Soudzilovskaia, ... Nature 560 (7717), 233-237, 2018	1761	2018
Genome Sequence of the Pea Aphid Acyrthosiphon pisum International Aphid Genomics Consortium PLoS biology 8 (2), e1000313, 2010	1002	2010
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	618	2014
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	561	2016
ETE: a python Environment for Tree Exploration J Huerta-Cepas, J Dopazo, T Gabaldón BMC bioinformatics 11, 1-7, 2010	450	2010
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), 1014, 2019	398	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	314	2019
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	255	2014
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	247	2011
The human phylome J Huerta-Cepas, H Dopazo, J Dopazo, T Gabaldón Genome biology 8, 1-16, 2007	235	2007
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	232	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	185	2010

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