(Q34135992)

31 July 2017

title

HGTector: an automated method facilitating genome-wide discovery of putative horizontal gene transfers (English)

1 reference

31 July 2017

0 references

Qiyun Zhu

1

1 reference

31 July 2017

Michael Kosoy

series ordinal

2

1 reference

31 July 2017

Katharina Dittmar

series ordinal

3

1 reference

31 July 2017

language of work or name

English

0 references

publication date

26 August 2014

1 reference

31 July 2017

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31 July 2017

volume

15

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31 July 2017

page(s)

717

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Gene Transfer from Bacteria and Archaea Facilitated Evolution of an Extremophilic Eukaryote

31 July 2017

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An automated approach for the identification of horizontal gene transfers from complete genomes reveals the rhizome of Rickettsiales

5 July 2018

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Lateral gene transfer as a support for the tree of life

5 July 2018

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5 July 2018

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Taxonomizing, sizing, and overcoming the incidentalome

5 July 2018

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

5 July 2018

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Trends and barriers to lateral gene transfer in prokaryotes

5 July 2018

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Resolving difficult phylogenetic questions: why more sequences are not enough

5 July 2018

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High frequency of horizontal gene transfer in the oceans

5 July 2018

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5 July 2018

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More than 1,001 problems with protein domain databases: transmembrane regions, signal peptides and the issue of sequence homology

5 July 2018

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5 July 2018

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Prokaryotic evolution and the tree of life are two different things

5 July 2018

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The fundamental units, processes and patterns of evolution, and the tree of life conundrum

5 July 2018

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IslandViewer: an integrated interface for computational identification and visualization of genomic islands

5 July 2018

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A database of phylogenetically atypical genes in archaeal and bacterial genomes, identified using the DarkHorse algorithm

5 July 2018

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Evaluation of genomic island predictors using a comparative genomics approach

5 July 2018

1 reference

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

5 July 2018

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Lateral gene transfer between obligate intracellular bacteria: evidence from the Rickettsia massiliae genome

5 July 2018

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Systematic overestimation of gene gain through false diagnosis of gene absence

5 July 2018

1 reference

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

5 July 2018

1 reference

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Rickettsiae phylogeny: a multigenic approach.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

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5 July 2018

1 reference

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Do different surrogate methods detect lateral genetic transfer events of different relative ages?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

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5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

The genome sequence of Rickettsia felis identifies the first putative conjugative plasmid in an obligate intracellular parasite

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Phylogenomics and the reconstruction of the tree of life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Decoding the genomic tree of life

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Computing prokaryotic gene ubiquity: rescuing the core from extinction

5 July 2018

1 reference

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PhyloGenie: automated phylome generation and analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

The origin of new genes: glimpses from the young and old

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Characterization of species-specific genes using a flexible, web-based querying system

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

How big is the iceberg of which organellar genes in nuclear genomes are but the tip?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

NEXUS: an extensible file format for systematic information

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Horizontal gene transfer in prokaryotes: quantification and classification

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

A phylogenomic approach to microbial evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Assessing evolutionary relationships among microbes from whole-genome analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Pathogenicity islands and the evolution of microbes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Lateral gene transfer and the nature of bacterial innovation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Finding families for genomic ORFans

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Phylogenetic classification and the universal tree

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Rickettsiae and Chlamydiae: evidence of horizontal gene transfer and gene exchange

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

The use of gene clusters to infer functional coupling

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

A genomic perspective on protein families

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

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

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Amelioration of bacterial genomes: rates of change and exchange

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Ecology drives a global network of gene exchange connecting the human microbiome.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

INDeGenIUS, a new method for high-throughput identification of specialized functional islands in completely sequenced organisms.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Horizontal gene transfer in evolution: facts and challenges.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Conjugation genes are common throughout the genus Rickettsia and are transmitted horizontally

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Detection and quantitative assessment of horizontal gene transfer

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Choosing BLAST options for better detection of orthologs as reciprocal best hits.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

IslandPath: aiding detection of genomic islands in prokaryotes.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Contamination in the draft of the human genome masquerades as lateral gene transfer.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Reconciling the many faces of lateral gene transfer.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

The closest BLAST hit is often not the nearest neighbor.

28 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4155097

Errors in genome annotation

28 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25159222

12 December 2020

inferred from PubMed ID database lookup

Detecting pathogenicity islands and anomalous gene clusters by iterative discriminant analysis

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25159222

12 December 2020

inferred from PubMed ID database lookup

Phylogenetic analyses do not support horizontal gene transfers from bacteria to vertebrates

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25159222

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1186/1471-2164-15-717

1 reference

release_v3uu2yg7b5hyrccsojfpde5w4i

31 July 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/v3uu2yg7b5hyrccsojfpde5w4i

24 November 2022

mapped directly with Wikidata item

PMC publication ID

4155097

1 reference

31 July 2017

1 reference