Jaime Huerta-Cepas

Orcid: 0000-0003-4195-5025

According to our database1, Jaime Huerta-Cepas authored at least 30 papers between 2006 and 2023.

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Bibliography

2023
eggNOG 6.0: enabling comparative genomics across 12 535 organisms.
Nucleic Acids Res., January, 2023

proGenomes3: approaching one million accurately and consistently annotated high-quality prokaryotic genomes.
Nucleic Acids Res., January, 2023

2022
PhyloCloud: an online platform for making sense of phylogenomic data.
Nucleic Acids Res., 2022

GeCoViz: genomic context visualisation of prokaryotic genes from a functional and evolutionary perspective.
Nucleic Acids Res., 2022

2020
proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes.
Nucleic Acids Res., 2020

The Quest for Orthologs benchmark service and consensus calls in 2020.
Nucleic Acids Res., 2020

2019
STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets.
Nucleic Acids Res., 2019

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses.
Nucleic Acids Res., 2019

2018
Gearing up to handle the mosaic nature of life in the quest for orthologs.
Bioinform., 2018

2017
proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes.
Nucleic Acids Res., 2017

2016
eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences.
Nucleic Acids Res., 2016

MOCAT2: a metagenomic assembly, annotation and profiling framework.
Bioinform., 2016

ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods.
Database J. Biol. Databases Curation, 2016

2015
STRING v10: protein-protein interaction networks, integrated over the tree of life.
Nucleic Acids Res., 2015

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins.
Nucleic Acids Res., 2015

2014
eggNOG v4.0: nested orthology inference across 3686 organisms.
Nucleic Acids Res., 2014

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome.
Nucleic Acids Res., 2014

2011
Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing.
Nucleic Acids Res., 2011

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions.
Nucleic Acids Res., 2011

Assigning duplication events to relative temporal scales in genome-wide studies.
Bioinform., 2011

CycADS: an annotation database system to ease the development and update of BioCyc databases.
Database J. Biol. Databases Curation, 2011

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication.
Briefings Bioinform., 2011

2010
ETE: a python Environment for Tree Exploration.
BMC Bioinform., 2010

2009
Automatic Prediction of the Genetic Code.
Proceedings of the Distributed Computing, 2009

2008
GEPAS, a web-based tool for microarray data analysis and interpretation.
Nucleic Acids Res., 2008

PhylomeDB: a database for genome-wide collections of gene phylogenies.
Nucleic Acids Res., 2008

2007
Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics.
Nucleic Acids Res., 2007

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease.
Nucleic Acids Res., 2007

From genes to functional classes in the study of biological systems.
BMC Bioinform., 2007

2006
Next station in microarray data analysis: GEPAS.
Nucleic Acids Res., 2006


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