(Q35751642)

10 August 2017

title

DarkHorse: a method for genome-wide prediction of horizontal gene transfer (English)

1 reference

10 August 2017

main subject

horizontal gene transfer

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2

Terry Gaasterland

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author name string

Sheila Podell

series ordinal

1

1 reference

10 August 2017

publication date

1 January 2007

1 reference

10 August 2017

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10 August 2017

volume

8

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10 August 2017

issue

2

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10 August 2017

page(s)

R16

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describes a project that uses

10 August 2017

SQL

1 reference

26 June 2022

https://europepmc.org/article/PMC/PMC1852411

based on heuristic

inferred from PubMed Central ID database lookup

cites work

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2 October 2017

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2 October 2017

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2 October 2017

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Horizontal gene transfer, genome innovation and evolution

2 October 2017

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The cobweb of life revealed by genome-scale estimates of horizontal gene transfer

2 October 2017

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2 October 2017

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2 October 2017

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Examining bacterial species under the specter of gene transfer and exchange

2 October 2017

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Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement

2 October 2017

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2 October 2017

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2 October 2017

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A new computational method for the detection of horizontal gene transfer events

2 October 2017

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Inter-species horizontal transfer resulting in core-genome and niche-adaptive variation within Helicobacter pylori

2 October 2017

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2 October 2017

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2 October 2017

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A first glimpse into the pattern and scale of gene transfer in Apicomplexa

2 October 2017

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Speciation in Chlamydia: genomewide phylogenetic analyses identified a reliable set of acquired genes.

2 October 2017

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An improved probability mapping approach to assess genome mosaicism

2 October 2017

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Quartet mapping and the extent of lateral transfer in bacterial genomes

2 October 2017

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2 October 2017

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Lateral gene transfer (LGT) between Archaea and Escherichia coli is a contributor to the emergence of novel infectious disease

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Methods of horizontal gene transfer determination using phylogenetic data.

2 October 2017

1 reference

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HGT-DB: a database of putative horizontally transferred genes in prokaryotic complete genomes

2 October 2017

1 reference

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Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Horizontal gene transfer in prokaryotes: quantification and classification

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Phylogenetic analyses of two "archaeal" genes in thermotoga maritima reveal multiple transfers between archaea and bacteria

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

A phylogenomic approach to microbial evolution

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Horizontal gene transfer among microbial genomes: new insights from complete genome analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

The genome sequence of the thermoacidophilic scavenger Thermoplasma acidophilum

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Cloning, expression, and sequencing of a cell surface antigen containing a leucine-rich repeat motif from Bacteroides forsythus ATCC 43037.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Amelioration of bacterial genomes: rates of change and exchange

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Gene transfer and genome plasticity in Thermotoga maritima, a model hyperthermophilic species

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Bayesian classifiers for detecting HGT using fixed and variable order markov models of genomic signatures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Identification and phylogenetic sorting of bacterial lineages with universally conserved genes and proteins

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Reconciling the many faces of lateral gene transfer.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Limitations of compositional approach to identifying horizontally transferred genes

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

Intragenomic base content variation is a potential source of biases when searching for horizontally transferred genes.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

The closest BLAST hit is often not the nearest neighbor.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

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

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1852411

25 September 2018

Identifiers

DOI

10.1186/GB-2007-8-2-R16

1 reference

Dimensions Publication ID

10 August 2017

0 references

1 reference

10 August 2017

1 reference