(Q37335459)

19 August 2017

Bacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes (English)

1 reference

19 August 2017

1 reference

Evgeni Bolotin

1

1 reference

19 August 2017

Ruth Hershberg

series ordinal

2

1 reference

19 August 2017

language of work or name

English

0 references

publication date

13 October 2016

1 reference

19 August 2017

1 reference

19 August 2017

6

1 reference

19 August 2017

35168

1 reference

Creative Commons Attribution 4.0 International

19 August 2017

start time

13 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/srep35168

0 references

cites work

Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis

1 reference

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The bacterial pangenome as a new tool for analysing pathogenic bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Long-term social dynamics drive loss of function in pathogenic bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Gene Loss Dominates As a Source of Genetic Variation within Clonal Pathogenic Bacterial Species

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Co-evolution of Mycobacterium tuberculosis and Homo sapiens

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

POGO-DB--a database of pairwise-comparisons of genomes and conserved orthologous genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Genome reduction as the dominant mode of evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Gene frequency distributions reject a neutral model of genome evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Selection-driven gene loss in bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Synonymous but not the same: the causes and consequences of codon bias

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Ecosystem-specific selection pressures revealed through comparative population genomics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Deletional bias across the three domains of life.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Comparative genomics reveals mechanism for short-term and long-term clonal transitions in pandemic Vibrio cholerae.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Genome sequencing and comparative analysis of Klebsiella pneumoniae NTUH-K2044, a strain causing liver abscess and meningitis

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Estimating the size of the bacterial pan-genome

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

6 September 2017

Selection on Codon Bias

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Molecular pathogenesis of Shigella spp.: controlling host cell signaling, invasion, and death by type III secretion.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Reduced selection leads to accelerated gene loss in Shigella

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

PAML 4: phylogenetic analysis by maximum likelihood

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Gene loss rate: a probabilistic measure for the conservation of eukaryotic genes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Synonymous codon usage in Escherichia coli: selection for translational accuracy.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Comparative genomics of the lactic acid bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Molecular interactions between bacterial symbionts and their hosts

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Genome dynamics and diversity of Shigella species, the etiologic agents of bacillary dysentery

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Evolution and molecular phylogeny of Listeria monocytogenes isolated from human and animal listeriosis cases and foods

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Comparative genomics of insect-symbiotic bacteria: influence of host environment on microbial genome composition

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

The balance of driving forces during genome evolution in prokaryotes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Microbial minimalism: genome reduction in bacterial pathogens

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Pathoadaptive mutations that enhance virulence: genetic organization of the cadA regions of Shigella spp.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Deletional bias and the evolution of bacterial genomes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Insights into the evolutionary process of genome degradation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

PAML: a program package for phylogenetic analysis by maximum likelihood

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Accelerated evolution and Muller's rachet in endosymbiotic bacteria

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Improved tools for biological sequence comparison

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Evolution of pan-genomes of Escherichia coli, Shigella spp., and Salmonella enterica

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

Accounting for background nucleotide composition when measuring codon usage bias.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5062063

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

2 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP35168

Database resources of the National Center for Biotechnology Information

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FSREP35168

The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/27734920

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/SREP35168

1 reference

Dimensions Publication ID

19 August 2017

0 references

1 reference

19 August 2017

1 reference