Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

Raquel Bromberg; Nick V. Grishin; Zbyszek Otwinowski

doi:10.1371/journal.pcbi.1004985

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer

PLoS Computational Biology ◽

10.1371/journal.pcbi.1004985 ◽

2016 ◽

Vol 12 (6) ◽

pp. e1004985 ◽

Cited By ~ 21

Author(s):

Raquel Bromberg ◽

Nick V. Grishin ◽

Zbyszek Otwinowski

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogeny Reconstruction ◽

Alignment Free

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Background Adjusted Alignment-Free Dissimilarity Measures Improve the Detection of Horizontal Gene Transfer

Frontiers in Microbiology ◽

10.3389/fmicb.2018.00711 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 6

Author(s):

Kujin Tang ◽

Yang Young Lu ◽

Fengzhu Sun

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Dissimilarity Measures ◽

Alignment Free

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The statistical power of k-mer based aggregative statistics for alignment-free detection of horizontal gene transfer

Synthetic and Systems Biotechnology ◽

10.1016/j.synbio.2019.08.001 ◽

2019 ◽

Vol 4 (3) ◽

pp. 150-156

Author(s):

Guan-Da Huang ◽

Xue-Mei Liu ◽

Tian-Lai Huang ◽

Li- C. Xia

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Statistical Power ◽

Alignment Free

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Alignment-free detection of horizontal gene transfer between closely related bacterial genomes

Mobile Genetic Elements ◽

10.4161/mge.1.3.18065 ◽

2011 ◽

Vol 1 (3) ◽

pp. 230-235 ◽

Cited By ~ 12

Author(s):

Mirjana Domazet-Lošo ◽

Bernhard Haubold

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Bacterial Genomes ◽

Alignment Free

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Molecular epidemiological analysis of the first outbreaks of OXA-48-producing Enterobacteriaceae in the Czech Republic with an evidence of horizontal gene transfer

10.26226/morressier.56d5ba27d462b80296c95fa0 ◽

2016 ◽

Author(s):

Anna Skalova

Keyword(s):

Czech Republic ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

The Czech Republic ◽

Epidemiological Analysis

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Ecological overlap and horizontal gene transfer in clinical Staphylococcus aureus and Staphylococcus epidermidis

10.26226/morressier.56d6be80d462b80296c95ccf ◽

2016 ◽

Author(s):

Guillaume Meric

Keyword(s):

Staphylococcus Aureus ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Staphylococcus Epidermidis

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Faculty Opinions recommendation of Deriving the genomic tree of life in the presence of horizontal gene transfer: conditioned reconstruction.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1017190.202386 ◽

2004 ◽

Author(s):

William Martin

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Tree Of Life

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Faculty Opinions recommendation of Stochastic models for horizontal gene transfer: taking a random walk through tree space.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1026516.323363 ◽

2005 ◽

Author(s):

Jeffrey Thorne

Keyword(s):

Random Walk ◽

Gene Transfer ◽

Horizontal Gene Transfer ◽

Stochastic Models ◽

Tree Space

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Faculty Opinions recommendation of Ancient horizontal gene transfer can benefit phylogenetic reconstruction.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1046784.496796 ◽

2006 ◽

Author(s):

Nicolas Galtier

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Phylogenetic Reconstruction

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Faculty Opinions recommendation of Global extent of horizontal gene transfer.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1071748.524662 ◽

2007 ◽

Author(s):

John Jaenike

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer

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Faculty Opinions recommendation of Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1089714.544996 ◽

2007 ◽

Author(s):

Mohan Balasubramanian

Keyword(s):

Gene Transfer ◽

Horizontal Gene Transfer ◽

Cytoskeletal Elements

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