Jaime Huerta-Cepas

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Peer BorkDirector of EMBL HeidelbergVerified email at embl.de
Sofia K. ForslundJunior Group Leader, ECRC (joint Max Delbrück Center and Charité University Hospital unit), BerlinVerified email at embl.de
Toni GabaldonGroup Leader, Institute for Research in Biomedicine (IRB) and Barcelona Supercomputing Centre (BSC)Verified email at crg.es
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Christian von MeringProfessor of Computational Biology, University of Zurich and Swiss Institute of BioinformaticsVerified email at imls.uzh.ch
Lars Juhl JensenUniversity of CopenhagenVerified email at cpr.ku.dk
Shinichi SunagawaETH Zurich; Swiss Institute of BioinformaticsVerified email at ethz.ch
Luis Pedro CoelhoISTBI, Fudan UniversityVerified email at fudan.edu.cn
Joaquin DopazoHead of the Clinical Bioinformatics Area, FPS, Hospital Virgen del Rocio, Sevilla, SpainVerified email at juntadeandalucia.es
Daniel R. MendeAsst. Professor, Amsterdam University Medical Center, University of AmsterdamVerified email at amsterdamumc.nl
Michael Kuhnstaff scientist in the lab of Peer Bork, EMBLVerified email at embl.de
Falk HildebrandQuadram & Earlham Institute, Norwich, UKVerified email at quadram.ac.uk
Ivica Letunićbiobyte solutions GmbHVerified email at biobyte.de
Georg ZellerEMBL, HeidelbergVerified email at embl.de
Marina Marcet-HoubenBarcelona Supercomputing Center - BSCVerified email at bsc.es
Salvador Capella-GutiérrezBarcelona Supercomputing Centre (BSC)Verified email at bsc.es
françois serra3D Chromatin Organization - IJCVerified email at carrerasresearch.org
Paul Igor CosteaBASFVerified email at basf.com
Simone S LiNHMRC Australia Early Career Fellow, Novo Nordisk Foundation Center for Biosustainability (Denmark)Verified email at biosustain.dtu.dk
Pablo MinguezResearcher & Head of Bioinformatics Unit - IIS Fundación Jiménez Díaz (Madrid, Spain)Verified email at quironsalud.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	8701	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	8486	2015
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	1644	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	1587	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	1480	2017
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	1267	2019
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	1256	2016
Genome Sequence of the Pea Aphid Acyrthosiphon pisum International Aphid Genomics Consortium PLoS biology 8 (2), e1000313, 2010	911	2010
Structure and function of the global topsoil microbiome M Bahram, F Hildebrand, SK Forslund, JL Anderson, NA Soudzilovskaia, ... Nature 560 (7717), 233-237, 2018	890	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	490	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	426	2016
ETE: a python Environment for Tree Exploration J Huerta-Cepas, J Dopazo, T Gabaldón BMC bioinformatics 11 (1), 1-7, 2010	419	2010
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	234	2014
The human phylome J Huerta-Cepas, H Dopazo, J Dopazo, T Gabaldón Genome biology 8 (6), 1-16, 2007	210	2007
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	208	2019
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	194	2016
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	193	2011
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	188	2021
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	179	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	159	2007

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