Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox
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* Corresponding author: Céline Brochier celine.brochier@up.univ-mrs.fr
Genome Biology 2004, 5:R17 doi:
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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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Jonathan Berthon, Diego Cortez, Patrick Forterre Genome Biology 2008, 9:R71 (9 April 2008) Specific functional interactions of proteins involved in DNA replication and/or DNA repair or transcription might occur in Archaea, suggesting a previously unrecognized regulatory network coupling DNA replication and translation, which might also exist in Eukarya. |
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Kira S Makarova, Alexander V Sorokin, Pavel S Novichkov, Yuri I Wolf, Eugene V Koonin Biology Direct 2007, 2:33 (27 November 2007) |
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James A Coker, Shiladitya DasSarma BMC Genetics 2007, 8:61 (24 September 2007) |
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The Biological Big Bang model for the major transitions in evolution Eugene V Koonin Biology Direct 2007, 2:21 (20 August 2007) |
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Beile Gao, Radhey S Gupta BMC Genomics 2007, 8:86 (29 March 2007) |
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Refuting phylogenetic relationships James Bucknam, Yan Boucher, Eric Bapteste Biology Direct 2006, 1:26 (6 September 2006) |
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Thomas M Keane, Christopher J Creevey, Melissa M Pentony, Thomas J Naughton, James O Mclnerney BMC Evolutionary Biology 2006, 6:29 (24 March 2006) |
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Post-genomics of the model haloarchaeon Halobacterium sp. NRC-1 Shiladitya DasSarma, Brian R Berquist, James A Coker, Priya DasSarma, Jochen A Müller Saline Systems 2006, 2:3 (16 March 2006) |
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Hanno Teeling, Frank Gloeckner BMC Bioinformatics 2006, 7:66 (13 February 2006) |
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B David Silverman BMC Structural Biology 2005, 5:20 (21 October 2005) Comparison of atomic resolution structures of eukaryotic and archaeal histones and the structurally homologous segment of a fruit fly transcription factor suggests that reduced burial of hydrophobic residues in the region corresponding to the histone 3 carboxy-terminus gives raise to the relative instability of the dimer composed of histone 3 and histone 4.
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Céline Brochier, Patrick Forterre, Simonetta Gribaldo BMC Evolutionary Biology 2005, 5:36 (2 June 2005) |
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Do orthologous gene phylogenies really support tree-thinking? E Bapteste, E Susko, J Leigh, D MacLeod, RL Charlebois, WF Doolittle BMC Evolutionary Biology 2005, 5:33 (24 May 2005) |
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Celine Brochier, Simonetta Gribaldo, Yvan Zivanovic, Fabrice Confalonieri, Patrick Forterre Genome Biology 2005, 6:R42 (14 April 2005) An analysis of the position of |
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Evolutionary sequence analysis of complete eukaryote genomes Jaime E Blair, Prachi Shah, S Blair Hedges BMC Bioinformatics 2005, 6:53 (11 March 2005) An evolutionary analysis based only on 'panorthologs' - genes that are found as a single copy among divergent species - matches up well to slower methods in indicating a divergence of deuterostomes and arthropods 400 million years before the Cambrian explosion of fossils.
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Fabia U Battistuzzi, Andreia Feijao, S Blair Hedges BMC Evolutionary Biology 2004, 4:44 (9 November 2004) Phylogenetic analysis of 72 prokaryote species suggests a timescale for the origin of life, the divergence of major bacterial groups, the origin of methanogenesis and phototrophy, and the colonisation of land.
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