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
Damian SzklarczykSIB Swiss Institute of Bioinformatics / University of ZurichVerified email at isb-sib.ch
Toni GabaldonGroup Leader, Institute for Research in Biomedicine (IRB) and Barcelona Supercomputing Centre (BSC)Verified email at crg.es
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
Daniel R. MendeAsst. Professor, Amsterdam University Medical Center, University of AmsterdamVerified email at amsterdamumc.nl
Joaquin DopazoComputational Medicine Platform, FPS, Hospital Virgen del Rocio, Sevilla, SpainVerified email at juntadeandalucia.es
Michael Kuhnresearch staff scientist & research coordinator in the lab of Peer Bork, EMBLVerified email at embl.de
Ivica Letunićbiobyte solutions GmbHVerified email at biobyte.de
Falk HildebrandQuadram & Earlham Institute, Norwich, UKVerified email at quadram.ac.uk
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
Salvador Capella-GutiérrezBarcelona Supercomputing Centre (BSC)Verified email at bsc.es
Carlos P CantalapiedraCentro de Biotecnología y Genómica de Plantas - UPM-INIAVerified email at inia.csic.es
Paul Igor CosteaBASFVerified email at basf.com
Simone S LiNHMRC Australia Early Career Fellow, Novo Nordisk Center for Biosustainability (Denmark)Verified email at biosustain.dtu.dk

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	11310	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	9185	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	1878	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	1810	2017
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	1764	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	1730	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	1447	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	1171	2018
Genome Sequence of the Pea Aphid Acyrthosiphon pisum International Aphid Genomics Consortium PLoS biology 8 (2), e1000313, 2010	937	2010
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	600	2021
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	529	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	490	2016
ETE: a python Environment for Tree Exploration J Huerta-Cepas, J Dopazo, T Gabaldón BMC bioinformatics 11, 1-7, 2010	429	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	266	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	240	2014
The human phylome J Huerta-Cepas, H Dopazo, J Dopazo, T Gabaldón Genome biology 8 (6), 1-16, 2007	215	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	212	2011
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	211	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	205	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	178	2010

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