A pluralistic account of homology: adapting the models to the data (Q27024433)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

David A Fitzpatrick

4

1 reference

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8 June 2020

9

Eric Bapteste

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

5

Philippe Lopez

1 reference

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8 June 2020

author name string

Pierre-Alain Jachiet

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

William P Hanage

3

1 reference

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8 June 2020

Mary J O'Connell

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Davide Pisani

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

Mark Wilkinson

8

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

James O McInerney

10

1 reference

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8 June 2020

language of work or name

1 reference

March 2014

1 reference

full work available at URL

1 March 2014

3 references

20 June 2019

19 September 2019

30 October 2020

http://eprints.whiterose.ac.uk/103540/

content deliverer

White Rose Research Online

object has role

published version

0 references

https://doi.org/10.1093/molbev/mst228

object has role

published version

0 references

published in

Molecular Biology and Evolution

5 references

20 June 2019

19 September 2019

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

30 October 2020

31

2 references

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8 June 2020

issue

3

2 references

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8 June 2020

page(s)

501-516

1 reference

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Creative Commons Attribution-NonCommercial 3.0 Unported

8 June 2020

copyright license

3 references

20 June 2019

19 September 2019

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

30 October 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Testing the ortholog conjecture with comparative functional genomic data from mammals

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Fusion and fission of genes define a metric between fungal genomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Cytoscape: a software environment for integrated models of biomolecular interaction networks

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

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

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

A genomic perspective on protein families

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

The COG database: a tool for genome-scale analysis of protein functions and evolution

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

An efficient algorithm for large-scale detection of protein families

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Domain combinations in archaeal, eubacterial and eukaryotic proteomes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Application of phylogenetic networks in evolutionary studies

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Identification of a specific telomere terminal transferase activity in Tetrahymena extracts

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Estimating divergence times in large molecular phylogenies

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Toward community standards in the quest for orthologs

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

FastTree 2--approximately maximum-likelihood trees for large alignments

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Protein interaction maps for complete genomes based on gene fusion events

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

A combined algorithm for genome-wide prediction of protein function

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Homology a personal view on some of the problems

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Reassessing domain architecture evolution of metazoan proteins: major impact of errors caused by confusing paralogs and epaktologs

9 May 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Reassessing domain architecture evolution of metazoan proteins: major impact of gene prediction errors

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

MosaicFinder: identification of fused gene families in sequence similarity networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Metazoan opsin evolution reveals a simple route to animal vision

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Evolutionary analyses of non-genealogical bonds produced by introgressive descent

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

High-quality sequence clustering guided by network topology and multiple alignment likelihood

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

The Public Goods Hypothesis for the evolution of life on Earth

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

28 September 2017

Phylogenomic networks

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Domain recombination: a workhorse for evolutionary innovation.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

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

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Network analyses structure genetic diversity in independent genetic worlds

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Prokaryotic evolution and the tree of life are two different things

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Getting a better picture of microbial evolution en route to a network of genomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Nature of the protein universe

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

A database of domain definitions for proteins with complex interdomain geometry

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Using sequence similarity networks for visualization of relationships across diverse protein superfamilies.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

The role of gene fusions in the evolution of metabolic pathways: the histidine biosynthesis case

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

EVEREST: automatic identification and classification of protein domains in all protein sequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Gene fusion/fission is a major contributor to evolution of multi-domain bacterial proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Identifying remote protein homologs by network propagation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Protein ranking: from local to global structure in the protein similarity network

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Homology in comparative, molecular, and evolutionary developmental biology: the radiation of a concept

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

A review of some fundamental concepts and problems of population genetics

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Protein families and TRIBES in genome sequence space

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

ProtoNet: hierarchical classification of the protein space

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

The structure of the protein universe and genome evolution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Using the COG database to improve gene recognition in complete genomes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

HOBACGEN: database system for comparative genomics in bacteria

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

ProDom and ProDom-CG: tools for protein domain analysis and whole genome comparisons

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

ProtoMap: automatic classification of protein sequences and hierarchy of protein families

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Intermediate sequences increase the detection of homology between sequences

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

HOVERGEN: a database of homologous vertebrate genes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Modular arrangement of proteins as inferred from analysis of homology.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

A survey of combinatorial methods for phylogenetic networks

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Networks of gene sharing among 329 proteobacterial genomes reveal differences in lateral gene transfer frequency at different phylogenetic depths

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

MACHOS: Markov clusters of homologous subsequences

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

"Homology" in proteins and nucleic acids: a terminology muddle and a way out of it.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Increased genome sampling reveals a dynamic relationship between gene duplicability and the structure of the primate protein-protein interaction network.

19 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Relative rates of gene fusion and fission in multi-domain proteins

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

LGL: creating a map of protein function with an algorithm for visualizing very large biological networks.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Exhaustive enumeration of protein domain families

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Scale-free behavior in protein domain networks.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

An insight into domain combinations

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

GeneRAGE: a robust algorithm for sequence clustering and domain detection.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

DIVCLUS: an automatic method in the GEANFAMMER package that finds homologous domains in single- and multi-domain proteins

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3935183

Protein domain prediction

28 November 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/24273322

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

https://pubmed.ncbi.nlm.nih.gov/24273322

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

1 reference

https://pubmed.ncbi.nlm.nih.gov/24273322

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/MOLBEV/MST228

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

8 June 2020

Altmetric DOI

10.1093/MOLBEV/MST228

0 references

CORE ID

87894836

0 references

0 references

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json

8 June 2020

PubMed publication ID

2 references

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:24273322%20AND%20SRC:MED&resulttype=core&format=json