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Archaeal phylogeny based on proteins of the transcription and translation machineries: tackling the Methanopyrus kandleri paradox
Céline Brochier, Patrick Forterre, Simonetta Gribaldo
Genome Biol. 2004; 5(3): R17. Published online 2004 February 26.
PMCID:
PMC395767
Abstract Full Text PDF–294K
 Is Cited by the Following 27 Articles in this Archive:
Assembling networks of microbial genomes using linear programming
Catherine Holloway, Robert G Beiko
BMC Evol Biol. 2010; 10: 360. Published online 2010 November 20. doi: 10.1186/1471-2148-10-360
PMCID:
PMC3224671
Abstract Full Text PDF–2.7M Supplementary Material
Complete genome sequence of Archaeoglobus profundus type strain (AV18T)
Mathias von Jan, Alla Lapidus, Tijana Glavina Del Rio, Alex Copeland, Hope Tice, Jan-Fang Cheng, Susan Lucas, Feng Chen, Matt Nolan, Lynne Goodwin, Cliff Han, Sam Pitluck, Konstantinos Liolios, Natalia Ivanova, Konstantinos Mavromatis, Galina Ovchinnikova, Olga Chertkov, Amrita Pati, Amy Chen, Krishna Palaniappan, Miriam Land, Loren Hauser, Yun-Juan Chang, Cynthia D. Jeffries, Elizabeth Saunders, Thomas Brettin, John C. Detter, Patrick Chain, Konrad Eichinger, Harald Huber, Stefan Spring, Manfred Rohde, Markus Göker, Reinhard Wirth, Tanja Woyke, Jim Bristow, Jonathan A. Eisen, Victor Markowitz, Philip Hugenholtz, Nikos C Kyrpides, Hans-Peter Klenk
Stand Genomic Sci. 2010 June 30; 2(3): 327–346. Published online 2010 June 15. doi: 10.4056/sigs.942153
PMCID:
PMC3035285
Abstract Full Text PDF–3.9M
Streamlining and Large Ancestral Genomes in Archaea Inferred with a Phylogenetic Birth-and-Death Model
Miklós Csűrös, István Miklós
Mol Biol Evol. 2009 September; 26(9): 2087–2095. Published online 2009 June 30. doi: 10.1093/molbev/msp123
PMCID:
PMC2726834
Abstract Full Text PDF–745K Supplementary Material
Genomic context analysis in Archaea suggests previously unrecognized links between DNA replication and translation
Jonathan Berthon, Diego Cortez, Patrick Forterre
Genome Biol. 2008; 9(4): R71. Published online 2008 April 9. doi: 10.1186/gb-2008-9-4-r71
PMCID:
PMC2643942
Abstract Full Text PDF–526K Supplementary Material
Divergence of selenocysteine tRNA recognition by archaeal and eukaryotic O-phosphoseryl-tRNASec kinase
R. Lynn Sherrer, Joanne M. L. Ho, Dieter Söll
Nucleic Acids Res. 2008 April; 36(6): 1871–1880. Published online 2008 April. doi: 10.1093/nar/gkn036
PMCID:
PMC2330242
Abstract Full Text PDF–2.3M
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
Biol Direct. 2007; 2: 33. Published online 2007 November 27. doi: 10.1186/1745-6150-2-33
PMCID:
PMC2222616
Abstract Full Text PDF–593K
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 Genet. 2007; 8: 61. Published online 2007 September 24. doi: 10.1186/1471-2156-8-61
PMCID:
PMC2121645
Abstract Full Text PDF–761K Supplementary Material
The Biological Big Bang model for the major transitions in evolution
Eugene V Koonin
Biol Direct. 2007; 2: 21. Published online 2007 August 20. doi: 10.1186/1745-6150-2-21
PMCID:
PMC1973067
Abstract Full Text PDF–467K
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. Published online 2007 March 29. doi: 10.1186/1471-2164-8-86
PMCID:
PMC1852104
Abstract Full Text PDF–533K Supplementary Material
Lineage-specific partitions in archaeal transcription
Richard M.R. Coulson, Nathalie Touboul, Christos A. Ouzounis
Archaea. 2007 May; 2(2): 117–125. Published online 2006 November 20.
PMCID:
PMC2686387
Abstract Full Text PDF–2.4M Supplementary Material
Refuting phylogenetic relationships
James Bucknam, Yan Boucher, Eric Bapteste
Biol Direct. 2006; 1: 26. Published online 2006 September 6. doi: 10.1186/1745-6150-1-26
PMCID:
PMC1574289
Abstract Full Text PDF–375K Supplementary Material
The origin and evolution of Archaea: a state of the art
Simonetta Gribaldo, Celine Brochier-Armanet
Philos Trans R Soc Lond B Biol Sci. 2006 June 29; 361(1470): 1007–1022. Published online 2006 May 9. doi: 10.1098/rstb.2006.1841
PMCID:
PMC1578729
Abstract Full Text PDF–325K
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 Evol Biol. 2006; 6: 29. Published online 2006 March 24. doi: 10.1186/1471-2148-6-29
PMCID:
PMC1435933
Abstract Full Text PDF–379K
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. Published online 2006 March 16. doi: 10.1186/1746-1448-2-3
PMCID:
PMC1447603
Abstract Full Text PDF–1.0M
RibAlign: a software tool and database for eubacterial phylogeny based on concatenated ribosomal protein subunits
Hanno Teeling, Frank Oliver Gloeckner
BMC Bioinformatics. 2006; 7: 66. Published online 2006 February 13. doi: 10.1186/1471-2105-7-66
PMCID:
PMC1421441
Abstract Full Text PDF–283K
Distribution, structure and diversity of “bacterial” genes encoding two-component proteins in the Euryarchaeota
Mark K. Ashby
Archaea. 2006 August; 2(1): 11–30. Published online 2006 January 23.
PMCID:
PMC2685588
Abstract Full Text PDF–1.4M
The evolutionary history of Cys-tRNACys formation
Patrick O'Donoghue, Anurag Sethi, Carl R. Woese, Zaida A. Luthey-Schulten
Proc Natl Acad Sci U S A. 2005 December 27; 102(52): 19003–19008. doi: 10.1073/pnas.0509617102
PMCID:
PMC1323144
Abstract Full Text PDF–1.7M
Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands
William W. L Hsiao, Korine Ung, Dana Aeschliman, Jenny Bryan, B. Brett Finlay, Fiona S. L Brinkman
PLoS Genet. 2005 November; 1(5): e62. Prepublished online 2005 October 13. Published online 2005 November 18. doi: 10.1371/journal.pgen.0010062
PMCID:
PMC1285063
Abstract Full Text PDF–482K Supplementary Material
Asymmetry in the burial of hydrophobic residues along the histone chains of Eukarya, Archaea and a transcription factor
B David Silverman
BMC Struct Biol. 2005; 5: 20. Published online 2005 October 21. doi: 10.1186/1472-6807-5-20
PMCID:
PMC1283977
Abstract Full Text PDF–573K
The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer
Fan Ge, Li-San Wang, Junhyong Kim
PLoS Biol. 2005 October; 3(10): e316. Published online 2005 August 30. doi: 10.1371/journal.pbio.0030316
PMCID:
PMC1233574
Abstract Full Text PDF–396K
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 Evol Biol. 2005; 5: 36. Published online 2005 June 2. doi: 10.1186/1471-2148-5-36
PMCID:
PMC1177939
Abstract Full Text PDF–287K
Do orthologous gene phylogenies really support tree-thinking?
E Bapteste, E Susko, J Leigh, D MacLeod, RL Charlebois, WF Doolittle
BMC Evol Biol. 2005; 5: 33. Published online 2005 May 24. doi: 10.1186/1471-2148-5-33
PMCID:
PMC1156881
Abstract Full Text PDF–724K Supplementary Material
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 Biol. 2005; 6(5): R42. Published online 2005 April 14. doi: 10.1186/gb-2005-6-5-r42
PMCID:
PMC1175954
Abstract Full Text PDF–243K Supplementary Material
Higher-level classification of the Archaea: evolution of methanogenesis and methanogens
Éric Bapteste, Céline Brochier, Yan Boucher
Archaea. 2005 May; 1(5): 353–363. Published online 2005 April 13.
PMCID:
PMC2685549
Abstract Full Text PDF–235K
Evolutionary sequence analysis of complete eukaryote genomes
Jaime E Blair, Prachi Shah, S Blair Hedges
BMC Bioinformatics. 2005; 6: 53. Published online 2005 March 11. doi: 10.1186/1471-2105-6-53
PMCID:
PMC1274250
Abstract Full Text PDF–367K Supplementary Material
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 Evol Biol. 2004; 4: 44. Published online 2004 November 9. doi: 10.1186/1471-2148-4-44
PMCID:
PMC533871
Abstract Full Text PDF–593K Supplementary Material
Identification of replication origins in archaeal genomes based on the Z-curve method
Ren Zhang, Chun-Ting Zhang
Archaea. 2005 May; 1(5): 335–346. Published online 2004 November 9.
PMCID:
PMC2685548
Abstract Full Text PDF–228K
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