(Q30503641)

1 September 2017

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli (English)

1 reference

1 September 2017

0 references

Klaus Schliep

3

1 reference

ORCID Public Data File 2021

Eric Bapteste

6

object named as

Eric Bapteste

1 reference

1 September 2017

Julie Beauregard-Racine

1

1 reference

1 September 2017

Cédric Bicep

2

1 reference

1 September 2017

Philippe Lopez

4

1 reference

1 September 2017

François-Joseph Lapointe

5

1 reference

1 September 2017

language of work or name

1 reference

20 July 2011

1 reference

1 September 2017

1 reference

1 September 2017

6

1 reference

1 September 2017

39; discussion 39

1 reference

describes a project that uses

1 September 2017

Cytoscape

object named as

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/1745-6150-6-39

0 references

cites work

The rhizome of life: the sympatric Rickettsia felis paradigm demonstrates the random transfer of DNA sequences

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

14 July 2018

A rooted net of life.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

How stands the Tree of Life a century and a half after The Origin?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Defining pathogenic bacterial species in the genomic era.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Harvesting evolutionary signals in a forest of prokaryotic gene trees.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Rapid evolutionary innovation during an Archaean genetic expansion.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The tree and net components of prokaryote evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Some considerations for analyzing biodiversity using integrative metagenomics and gene networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Viruses in the faecal microbiota of monozygotic twins and their mothers

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Comparison of 61 sequenced Escherichia coli genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Intertwined evolutionary histories of marine Synechococcus and Prochlorococcus marinus

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Thinking laterally about genomes.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Genome analysis of microorganisms living in amoebae reveals a melting pot of evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Network analyses structure genetic diversity in independent genetic worlds

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Trees and networks before and after Darwin

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Horizontal gene transfer of the secretome drives the evolution of bacterial cooperation and virulence.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Prokaryotic evolution and the tree of life are two different things

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Search for a 'Tree of Life' in the thicket of the phylogenetic forest

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Lateral genetic transfer: open issues

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The network of life: genome beginnings and evolution. Introduction

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Estimating maximum likelihood phylogenies with PhyML.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Molecular phylogeny: reconstructing the forest

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The modern concept of the procaryote

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The Genome of Thermosipho africanus TCF52B: Lateral Genetic Connections to the Firmicutes and Archaea

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Analysis of plasmid genes by phylogenetic profiling and visualization of homology relationships using Blast2Network

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Dealing with incongruence in phylogenomic analyses

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

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

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The prokaryotic tree of life: past, present... and future?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Genome evolution in cyanobacteria: the stable core and the variable shell

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Consistency of the neighbor-net algorithm

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Pattern pluralism and the Tree of Life hypothesis

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

14 July 2018

The tree of one percent.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Visualizing and assessing phylogenetic congruence of core gene sets: a case study of the gamma-proteobacteria

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The genome of Salinibacter ruber: convergence and gene exchange among hyperhalophilic bacteria and archaea

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Application of phylogenetic networks in evolutionary studies

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Highways of gene sharing in prokaryotes

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Here a virus, there a virus, everywhere the same virus?

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

CDD: a Conserved Domain Database for protein classification

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Phylogenetic reconstruction and lateral gene transfer.

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

MUSCLE: multiple sequence alignment with high accuracy and high throughput

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Neighbor-net: an agglomerative method for the construction of phylogenetic networks

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Evolutionary relationships among diverse bacteriophages and prophages: all the world's a phage

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

SplitsTree: analyzing and visualizing evolutionary data

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Split decomposition: a technique to analyze viral evolution

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The detection of disease clustering and a generalized regression approach

14 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

The post-Darwinist rhizome of life

14 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Reticulate representation of evolutionary and functional relationships between phage genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Untangling hybrid phylogenetic signals: horizontal gene transfer and artifacts of phylogenetic reconstruction

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Clanistics: a multi-level perspective for harvesting unrooted gene trees.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Type I restriction-modification loci reveal high allelic diversity in clinical Helicobacter pylori isolates

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Human and mouse oligonucleotide-based array CGH.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Quantifying nonvertical inheritance in the evolution of Legionella pneumophila.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1745-6150-6-39

Extracellular vesicles derived from Acholeplasma laidlawii PG8.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3160433

Of clades and clans: terms for phylogenetic relationships in unrooted trees

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21774799

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Cytoscape: a community-based framework for network modeling

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21774799

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1745-6150-6-39

1 reference

Dimensions Publication ID

1 September 2017

0 references

1 reference

1 September 2017

PubMed publication ID

21774799

1 reference