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List of works by Jaime Huerta-Cepas

A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits.

scientific article published on 22 March 2017

Advances and Applications in the Quest for Orthologs

scientific article published on 01 October 2019

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

scientific article published on 14 November 2014

Antibiotics-induced monodominance of a novel gut bacterial order

scientific article published on 18 January 2019

ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods

scientific article published on 30 May 2016

Assigning duplication events to relative temporal scales in genome-wide studies

scientific article published on 11 November 2010

Automatic Prediction of the Genetic Code

Comparative transcriptomics of early dipteran development

scientific article

CycADS: an annotation database system to ease the development and update of BioCyc databases

scientific article

Disentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity

scientific article published on 11 February 2020

Durable coexistence of donor and recipient strains after fecal microbiota transplantation.

scientific article

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data.

scientific article

ETE: a python Environment for Tree Exploration

scientific article published in 2010

Evidence for short-time divergence and long-time conservation of tissue-specific expression after gene duplication

scientific article published on 22 April 2011

Evidence for systems-level molecular mechanisms of tumorigenesis

scientific article

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

scientific article published on 29 April 2017

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

article

Fine-scale evolution: genomic, phenotypic and ecological differentiation in two coexisting Salinibacter ruber strains

scientific article

From genes to functional classes in the study of biological systems

scientific article

Function, evolution, and structure of J-domain proteins

scientific article published on 26 November 2018

GEPAS, a web-based tool for microarray data analysis and interpretation

scientific article

Gearing up to handle the mosaic nature of life in the quest for orthologs

scientific article published on 30 August 2017

Gene Expression Changes and Community Turnover Differentially Shape the Global Ocean Metatranscriptome

scientific article published on 01 November 2019

Interoperability with Moby 1.0--it's better than sharing your toothbrush!

scientific article

MOCAT2: a metagenomic assembly, annotation and profiling framework

scientific article

MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score.

scientific article published on 11 December 2010

Metabolic anchor reactions for robust biorefining

scientific article

Microbial abundance, activity and population genomic profiling with mOTUs2

scientific article published on 4 March 2019

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language

NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language.

scientific article

Neuroprotection elicited by P2Y13 receptors against genotoxic stress by inducing DUSP2 expression and MAPK signaling recovery.

scientific article published on 20 May 2014

Next station in microarray data analysis: GEPAS.

scientific article

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

scientific article published on 31 October 2014

PeroxisomeDB: a database for the peroxisomal proteome, functional genomics and disease

scientific article published on 28 November 2006

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing

scientific article

Phylemon: a suite of web tools for molecular evolution, phylogenetics and phylogenomics

scientific article published on 22 April 2007

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

scientific article

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

scientific article

PhylomeDB: a database for genome-wide collections of gene phylogenies

scientific article

Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites

scientific article (publication date: 5 January 2015)

Quest for Orthologs Entails Quest for Tree of Life: In Search of the Gene Stream

scientific article published in July 2015

STRING v10: protein-protein interaction networks, integrated over the tree of life

scientific article (publication date: 2015)

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

scientific article published on 22 November 2018

Standardized benchmarking in the quest for orthologs

scientific article (publication date: 4 April 2016)

Structure and function of the global topsoil microbiome

scientific article published in Nature

Subspecies in the global human gut microbiome.

scientific article published on 14 December 2017

The Quest for Orthologs benchmark service and consensus calls in 2020

scientific article published on 06 May 2020

The human phylome

scientific article published on January 2007

Whole-genome analyses resolve early branches in the tree of life of modern birds

scientific article

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

scientific article (publication date: 17 November 2015)

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

scientific article published on 01 January 2019

eggNOG v4.0: nested orthology inference across 3686 organisms

scientific article (publication date: December 2013)

proGenomes2: an improved database for accurate and consistent habitat, taxonomic and functional annotations of prokaryotic genomes

scientific article published on 01 January 2020

proGenomes: a resource for consistent functional and taxonomic annotations of prokaryotic genomes

scientific article

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