Genome Biology

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Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox

Céline Brochier*, Patrick Forterre and Simonetta Gribaldo

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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Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation

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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Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea

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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Genetic and transcriptomic analysis of transcription factor genes in the model halophilic Archaeon: coordinate action of TbpD and TfbA

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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Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis

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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Assessment of methods for amino acid matrix selection and their use on empirical data shows that ad hoc assumptions for choice of matrix are not justified

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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RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits

Hanno Teeling, Frank Gloeckner BMC Bioinformatics 2006, 7:66 (13 February 2006)

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Asymmetry in the burial of hydrophobic residues along the histone chains of Eukarya, Archaea and a transcription factor

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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An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences

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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Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales?

Celine Brochier, Simonetta Gribaldo, Yvan Zivanovic, Fabrice Confalonieri, Patrick Forterre Genome Biology 2005, 6:R42 (14 April 2005)

An analysis of the position of Nanoarcheum equitans in the archaeal phylogeny using a large dataset of concatenated ribosomal proteins from 25 archaeal genomes suggests that N. equitans is likely to be the representative of a fast-evolving euryarchaeal lineage.

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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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A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

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.