(Q35547349)

8 August 2017

title

Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony--a simulation study (English)

1 reference

8 August 2017

2

1 reference

8 August 2017

Ofir Cohen

1

1 reference

8 August 2017

publication date

4 October 2011

1 reference

Genome Biology and Evolution

8 August 2017

published in

1 reference

8 August 2017

volume

3

1 reference

8 August 2017

page(s)

1265-1275

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

8 August 2017

copyright license

start time

3 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

12 July 2018

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12 July 2018

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Inference and characterization of horizontally transferred gene families using stochastic mapping

12 July 2018

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12 July 2018

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12 July 2018

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A likelihood framework to analyse phyletic patterns

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Uncovering rate variation of lateral gene transfer during bacterial genome evolution

12 July 2018

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Microbial diversity and the genetic nature of microbial species

12 July 2018

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Coevolution of gene families in prokaryotes

12 July 2018

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Patterns and implications of gene gain and loss in the evolution of Prochlorococcus

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Three distinct modes of intron dynamics in the evolution of eukaryotes

12 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Systematic overestimation of gene gain through false diagnosis of gene absence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Pathogenicity islands: a molecular toolbox for bacterial virulence

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

On the estimation of intron evolution

12 July 2018

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Bayesian inference of character evolution

12 July 2018

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The fate of laterally transferred genes: life in the fast lane to adaptation or death

12 July 2018

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Toward Automatic Reconstruction of a Highly Resolved Tree of Life

12 July 2018

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Horizontal gene transfer, genome innovation and evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Computing prokaryotic gene ubiquity: rescuing the core from extinction

12 July 2018

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Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance

12 July 2018

1 reference

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Computational inference of scenarios for alpha-proteobacterial genome evolution

12 July 2018

1 reference

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Trends between gene content and genome size in prokaryotic species with larger genomes

12 July 2018

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Language-tree divergence times support the Anatolian theory of Indo-European origin

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Tracing the evolution of gene loss in obligate bacterial symbionts

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

The COG database: an updated version includes eukaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

The source of laterally transferred genes in bacterial genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Stochastic Mapping of Morphological Characters

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Gaps as characters in sequence-based phylogenetic analyses

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

A phylogenomic approach to microbial evolution

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Assessing the accuracy of prediction algorithms for classification: an overview

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Gene transfer, speciation, and the evolution of bacterial genomes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Molecular archaeology of the Escherichia coli genome

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Phylogenetic analysis using parsimony and likelihood methods

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Comparison of the predicted and observed secondary structure of T4 phage lysozyme

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

PHYLOGENIES FROM RESTRICTION SITES: A MAXIMUM-LIKELIHOOD APPROACH.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

GLOOME: gain loss mapping engine

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

A phylogenetic mixture model for gene family loss in parasitic bacteria

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

The dynamics and time scale of ongoing genomic erosion in symbiotic bacteria

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

High rates of lateral gene transfer are not due to false diagnosis of gene absence

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Integration of horizontally transferred genes into regulatory interaction networks takes many million years

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Counting labeled transitions in continuous-time Markov models of evolution.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Limitations of compositional approach to identifying horizontally transferred genes

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Codon bias and base composition are poor indicators of horizontally transferred genes.

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content

26 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3215202

Mapping mutations on phylogenies

7 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21971516

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Microbiology. Researchers trade insights about gene swapping

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21971516

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Phylogenetic Inference from Restriction Endonuclease Cleavage Site Maps with Particular Reference to the Evolution of Humans and the Apes

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21971516

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/GBE/EVR101

1 reference

8 August 2017

1 reference

8 August 2017

1 reference