(Q33886663)

29 July 2017

Evaluating ortholog prediction algorithms in a yeast model clade (English)

1 reference

29 July 2017

0 references

Antonis Rokas

2

0 references

author name string

Leonidas Salichos

series ordinal

1

1 reference

PubMed ID

21533202

29 July 2017

language of work or name

English

0 references

publication date

13 April 2011

1 reference

29 July 2017

1 reference

29 July 2017

6

1 reference

29 July 2017

e18755

1 reference

29 July 2017

4

1 reference

Complete bacteriophage transfer in a bacterial endosymbiont (Wolbachia) determined by targeted genome capture

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

FUNGIpath: a tool to assess fungal metabolic pathways predicted by orthology.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Database resources of the National Center for Biotechnology Information

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Phylogenetic and functional assessment of orthologs inference projects and methods

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

The quest for orthologs: finding the corresponding gene across genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Natural history and evolutionary principles of gene duplication in fungi.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Assessing performance of orthology detection strategies applied to eukaryotic genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Detecting non-orthology in the COGs database and other approaches grouping orthologs using genome-specific best hits

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Roundup: a multi-genome repository of orthologs and evolutionary distances

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Benchmarking ortholog identification methods using functional genomics data

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

OrthologID: automation of genome-scale ortholog identification within a parsimony framework

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Orthologs, paralogs, and evolutionary genomics

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Functional genomic analysis of the rates of protein evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Inparanoid: a comprehensive database of eukaryotic orthologs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Genome evolution in yeasts

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Structure, function and evolution of multidomain proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

The Ashbya gossypii Genome as a Tool for Mapping the Ancient Saccharomyces cerevisiae Genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Comprehensive analysis of orthologous protein domains using the HOPS database

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Automated ortholog inference from phylogenetic trees and calculation of orthology reliability

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Automatic clustering of orthologs and in-paralogs from pairwise species comparisons

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

28 July 2018

Computational genomics

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

The use of gene clusters to infer functional coupling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Predicting function: from genes to genomes and back

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

A genomic perspective on protein families

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Synteny conservation and chromosome rearrangements during mammalian evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Molecular evidence for an ancient duplication of the entire yeast genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Metabolism and evolution of Haemophilus influenzae deduced from a whole-genome comparison with Escherichia coli

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Exploring the Mycoplasma capricolum genome: a minimal cell reveals its physiology

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Sampling properties of DNA sequence data in phylogenetic analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Distinguishing Homologous from Analogous Proteins

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

Basic local alignment search tool

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3076445

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Automatic clustering of orthologs and inparalogs shared by multiple proteomes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Detecting putative orthologs.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Automatic genome-wide reconstruction of phylogenetic gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Predicting gene function by conserved co-expression

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Genome-scale approaches to resolving incongruence in molecular phylogenies

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Simultaneous Bayesian gene tree reconstruction and reconciliation analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

The diversity and evolution of circadian clock proteins in fungi

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

The closest BLAST hit is often not the nearest neighbor.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0018755

Using orthologous and paralogous proteins to identify specificity determining residues

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21533202

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0018755

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference

PubMed ID

21533202