Jaime Huerta Cepas
Profile
| Institution | CBGP |
| Position | Group Leader |
| Home page | https://www.linkedin.com/in/jaime-huerta-cepas/ |
| Contact email | j.huerta@csic.es |
| ORCID | 0000-0003-4195-5025 |
BCB Hub
| BCB Committee | Not a member |
| BCB Tools | ETE Toolkit, eggNOG/eggNOG-mapper, GeCoViz, PhyloCloud, TreeProfiler, deluxpore, FESNov catalog |
| BCB Services |
Research
Research topics
None
Research lines
Publications 67 entries
- Coupled enzyme discovery, evolution and synthetic yeast chassis adaptation for microbial biopolymer valorisation Preprint · 29 Sep 2026
- deluxpore: a Nextflow pipeline for demultiplexing Illumina dual-indexed Nanopore libraries Preprint · 30 Mar 2026
- TreeProfiler: large-scale metadata profiling along gene and species trees Software · Feb 2026
- eggNOG v7: phylogeny-based orthology predictions and functional annotations Article · 8 Dec 2025
- Quest for Orthologs in the Era of Biodiversity Genomics Article · Oct 2024
View all (62 more)
- Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments Article · 22 Mar 2024
- Functional and evolutionary significance of unknown genes from uncultivated taxa Software · 18 Dec 2023
- Atlas of mRNA translation and decay for bacteria Article · 22 May 2023
- New globally distributed bacterial phyla within the FCB superphylum Article · 6 Dec 2022
- Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity Article · 28 Nov 2022
- proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes Article · 21 Nov 2022
- eggNOG 6.0: enabling comparative genomics across 12 535 organisms Article · 18 Nov 2022
- Comparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses Preprint · 27 Sep 2022
- GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective Software · 26 May 2022
- New globally distributed bacteria with high proportions of novel protein families involved in sulfur and nitrogen cycling Preprint · 11 May 2022
- PhyloCloud: an online platform for making sense of phylogenomic data Software · 11 May 2022
- Functional and evolutionary significance of unknown genes from uncultivated taxa Preprint · 27 Jan 2022
- Towards the biogeography of prokaryotic genes Article · 15 Dec 2021
- Profiling cellular diversity in sponges informs animal cell type and nervous system evolution Article · 5 Nov 2021
- Prevalence and Specificity of Chemoreceptor Profiles in Plant-Associated Bacteria Article · 26 Oct 2021
- eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale Software · 1 Oct 2021
- RNA degradation analysis reveals ribosome dynamics in complex microbiome samples Preprint · 10 Apr 2021
- Ten Years of Collaborative Progress in the Quest for Orthologs Article · 2 Apr 2021
- The Quest for Orthologs benchmark service and consensus calls in 2020 Article · 6 May 2020
- Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity Article · 11 Feb 2020
- proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes Article · 24 Oct 2019
- Advances and Applications in the Quest for Orthologs Article · 27 Jun 2019
- NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language Article · 3 Jun 2019
- Antibiotics-induced monodominance of a novel gut bacterial order Article · 18 Jan 2019
- Function, evolution, and structure of J-domain proteins Article · Jan 2019
- STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets Article · 22 Nov 2018
- eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses Software · 12 Nov 2018
- Structure and function of the global topsoil microbiome Article · Aug 2018
- Subspecies in the global human gut microbiome Article · 1 Dec 2017
- Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper Article · 29 Apr 2017
- A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits Article · 22 Mar 2017
- Metabolic anchor reactions for robust biorefining Article · Mar 2017
- proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes Article · 24 Oct 2016
- Durable coexistence of donor and recipient strains after fecal microbiota transplantation Article · 29 Apr 2016
- MOCAT2: a metagenomic assembly, annotation and profiling framework Article · 8 Apr 2016
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data Software · 26 Feb 2016
- ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods Article · 2016
- eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences Article · 17 Nov 2015
- Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream Article · Jul 2015
- Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites Article · 5 Jan 2015
- An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum Article · 14 Nov 2014
- PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins Article · 31 Oct 2014
- STRING v10: protein–protein interaction networks, integrated over the tree of life Article · 28 Oct 2014
- Neuroprotection elicited by P2Y13 receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery Article · Sep 2014
- A nested phylogenetic reconstruction approach provides scalable resolution in the eukaryotic Tree Of Life Preprint · 28 Jan 2014
- eggNOG v4.0: nested orthology inference across 3686 organisms Article · 1 Dec 2013
- Comparative transcriptomics of early dipteran development Article · 24 Feb 2013
- Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication Article · 22 Apr 2011
- CycADS: an annotation database system to ease the development and update of BioCyc databases Article · 7 Apr 2011
- MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score Article · 11 Dec 2010
- Assigning duplication events to relative temporal scales in genome-wide studies Article · 11 Nov 2010
- Genome Sequence of the Pea Aphid Acyrthosiphon pisum Article · 23 Feb 2010
- The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes Article · 23 Feb 2010
- Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains Article · 18 Feb 2010
- ETE: a python Environment for Tree Exploration Article · 13 Jan 2010
- PhylomeDB: a database for genome-wide collections of gene phylogenies Article · 23 Dec 2007
- Evidence for systems-level molecular mechanisms of tumorigenesis Article · 20 Jun 2007
- The human phylome Article · 13 Jun 2007
- Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics Article · 8 May 2007
- From genes to functional classes in the study of biological systems Article · 3 Apr 2007
- PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease Article · 3 Jan 2007
- Next station in microarray data analysis: GEPAS Article · 1 Jul 2006