Search for a 'Tree of Life' in the thicket of the phylogenetic forest
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* Corresponding author: Eugene V Koonin koonin@ncbi.nlm.nih.gov
Journal of Biology 2009, 8:59 doi:10.1186/jbiol159
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Review
David Williams, Gregory P Fournier, Pascal Lapierre, Kristen S Swithers, Anna G Green, Cheryl P Andam, J Peter Gogarten Biology Direct 2011, 6:45 (21 September 2011) |
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Hypothesis
The public goods hypothesis for the evolution of life on Earth James O McInerney, Davide Pisani, Eric Bapteste, Mary J O'Connell Biology Direct 2011, 6:41 (23 August 2011) |
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Research
Julie Beauregard-Racine, Cédric Bicep, Klaus Schliep, Philippe Lopez, François-Joseph Lapointe, Eric Bapteste Biology Direct 2011, 6:39 (20 July 2011) |
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Methodology article
Split-based computation of majority-rule supertrees Anne Kupczok BMC Evolutionary Biology 2011, 11:205 (13 July 2011) |
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Research
Telling the whole story in a 10,000-genome world Robert G Beiko Biology Direct 2011, 6:34 (30 June 2011) |
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Review
How stands the Tree of Life a century and a half after The Origin? Maureen A O'Malley, Eugene V Koonin Biology Direct 2011, 6:32 (30 June 2011) |
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Research article
Assembling networks of microbial genomes using linear programming Catherine Holloway, Robert G Beiko BMC Evolutionary Biology 2010, 10:360 (20 November 2010) An approach that uses linear programming and BLAST scores to capture ‘between-genome’ relationships can uncover vertical and lateral relationships among genomes and serve as an effective inference tool in its own right.
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Editorial
Top ten in Journal of Biology in 2009: stem cells, influenza, pit bulls, Darwin, and more Miranda Robertson Journal of Biology 2009, 8:102 (31 December 2009) |
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Research
Natalya Yutin, Yuri I Wolf, Didier Raoult, Eugene V Koonin Virology Journal 2009, 6:223 (17 December 2009) |
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Research article
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer Talima Pearson, Philip Giffard, Stephen Beckstrom-Sternberg, Raymond Auerbach, Heidie Hornstra, Apichai Tuanyok, Erin P Price, Mindy B Glass, Benjamin Leadem, James S Beckstrom-Sternberg, Gerard J Allan, Jeffrey T Foster, David M Wagner, Richard T Okinaka, Siew Sim, Ofori Pearson, Zaining Wu, Jean Chang, Rajinder Kaul, Alex R Hoffmaster, Thomas S Brettin, Richard A Robison, Mark Mayo, Jay E Gee, Patrick Tan, Bart J Currie, Paul Keim BMC Biology 2009, 7:78 (18 November 2009) Despite a high level of lateral gene transfer, the phylogeny of Burkholderia pseudomallei is resolved by SNPs in orthologous shared regions, enabling a wider gene-based analysis to define two populations, ancestral Australian, and South East Asian, separated by the Wallace Line.
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Opinion
The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum Eugene V Koonin, Yuri I Wolf Biology Direct 2009, 4:33 (29 September 2009) A tree is a natural representation of evolution owing to the inherent tree-like character of the replication process but the fundamental units of evolution amenable to tree analysis seem to be individual genetic elements rather than complete genomes.
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Research
Structural analysis of polarizing indels: an emerging consensus on the root of the tree of life Ruben E Valas, Philip E Bourne Biology Direct 2009, 4:30 (25 August 2009) The disparate rootings of the tree of life by Cavalier-Smith and Lake et al. converge on a single root when polarizable indels are analyzed using protein structure.
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Editorial
Of primordial genomes and cooperative kittens Miranda Robertson Journal of Biology 2009, 8:52 (20 July 2009) |
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Minireview
Kristen S Swithers, J Peter Gogarten, Gregory P Fournier Journal of Biology 2009, 8:54 (13 July 2009) Gogarten and colleagues review new research by Koonin and colleagues in Journal of Biology and explain how the obstacle of horizontal gene transfer can be circumvented to reconstruct the prokaryotic Tree of Life.
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