| 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 | 15421 | 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 | 10652 | 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 | 3271 | 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 | 2368 | 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 | 2187 | 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 | 2016 | 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 | 1991 | 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 | 1907 | 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 | 1824 | 2018 |
| Genome Sequence of the Pea Aphid Acyrthosiphon pisum International Aphid Genomics Consortium PLoS biology 8 (2), e1000313, 2010 | 1004 | 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 | 626 | 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 | 571 | 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 | 420 | 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 | 328 | 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 | 252 | 2011 |
| The human phylome J Huerta-Cepas, H Dopazo, J Dopazo, T Gabaldón Genome biology 8, 1-16, 2007 | 238 | 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 |
| 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, ... Science 374 (6568), 717-723, 2021 | 188 | 2021 |
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