Standardized benchmarking in the quest for orthologs (Q30002371)

Salvador Capella-Gutierrez

Kimmen Sjölander

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Cécile Pereira

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Leszek P Pryszcz

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Salvador Capella-Gutierrez

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Adrian M Altenhoff

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Paul D Thomas

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Ioannis Xenarios

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Suzanna Lewis

Suzanna E Lewis

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Maria-Jesus Martin

Maria J Martin

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Odile Lecompte

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Daniel A Dalquen

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Todd DeLuca

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Benjamin Linard

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Fabian Schreiber

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Alan Sousa da Silva

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Clément-Marie Train

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Kimmen Sjölander

Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported

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publication date

4 April 2016

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number of pages

1 reference

based on heuristic

inferred from page(s)

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425-430

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start time

4 April 2016

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April 2022 Public Data File from Crossref

copyrighted

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cites work

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Big data and other challenges in the quest for orthologs

22 May 2017

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eggNOG v4.0: nested orthology inference across 3686 organisms

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PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

22 May 2017

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Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs

22 May 2017

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Toward community standards in the quest for orthologs

22 May 2017

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Reorganizing the protein space at the Universal Protein Resource (UniProt)

22 May 2017

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Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

22 May 2017

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Orthology prediction methods: a quality assessment using curated protein families

22 May 2017

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Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

22 May 2017

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Testing the Ortholog Conjecture with Comparative Functional Genomic Data from Mammals

22 May 2017

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New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

22 May 2017

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ETE: a python Environment for Tree Exploration

22 May 2017

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Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

22 May 2017

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

22 May 2017

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Recent developments in the MAFFT multiple sequence alignment program

22 May 2017

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eggNOG: automated construction and annotation of orthologous groups of genes

22 May 2017

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M-Coffee: combining multiple sequence alignment methods with T-Coffee

22 May 2017

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Orthologs, paralogs, and evolutionary genomics

22 May 2017

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MUSCLE: multiple sequence alignment with high accuracy and high throughput

22 May 2017

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The ENZYME database in 2000

22 May 2017

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The use of gene clusters to infer functional coupling

22 May 2017

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Distinguishing Homologous from Analogous Proteins

22 May 2017

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

22 May 2017

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The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

3 June 2018

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OrthoInspector 2.0: Software and database updates

3 June 2018

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

3 June 2018

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Evolution of the ferric reductase domain (FRD) superfamily: modularity, functional diversification, and signature motifs

3 June 2018

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Hieranoid: hierarchical orthology inference

3 June 2018

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The impact of gene duplication, insertion, deletion, lateral gene transfer and sequencing error on orthology inference: a simulation study

3 June 2018

1 reference

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Inferring hierarchical orthologous groups from orthologous gene pairs

3 June 2018

1 reference

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The ortholog conjecture is untestable by the current gene ontology but is supported by RNA sequencing data

3 June 2018

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A tight link between orthologs and bidirectional best hits in bacterial and archaeal genomes

3 June 2018

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On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report

3 June 2018

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Roundup 2.0: enabling comparative genomics for over 1800 genomes

3 June 2018

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The UniProt-GO Annotation database in 2011.

3 June 2018

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Evaluating ortholog prediction algorithms in a yeast model clade

3 June 2018

1 reference

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OrthoInspector: comprehensive orthology analysis and visual exploration

3 June 2018

1 reference

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

GIGA: a simple, efficient algorithm for gene tree inference in the genomic age.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

Parallelization of the MAFFT multiple sequence alignment program

3 June 2018

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Phylogenetic and functional assessment of orthologs inference projects and methods

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

Assessing performance of orthology detection strategies applied to eukaryotic genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

A new measure for functional similarity of gene products based on Gene Ontology

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

Benchmarking ortholog identification methods using functional genomics data

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4827703

Darwin v. 2.0: an interpreted computer language for the biosciences

3 June 2018

1 reference

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Functional and evolutionary implications of gene orthology.

3 June 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

Editorial: Orthology and applications

21 January 2018

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https://api.crossref.org/works/10.1038%2FNMETH.3830

Joining forces in the quest for orthologs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

Letter to the editor: SeqXML and OrthoXML: standards for sequence and orthology information

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

Detecting putative orthologs

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

Bidirectional best hits miss many orthologs in duplication-rich clades such as plants and animals

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

Probabilistic orthology analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

My worries are no longer behind me.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNMETH.3830

21 January 2018

Identifiers

DOI

10.1038/NMETH.3830

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Dimensions Publication ID

1009914770

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1 reference

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PubMed publication ID

27043882

1 reference