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Comparative genomics of archaea: how much have we learned in six years, and what's next?
Kira S Makarova, Eugene V Koonin
Genome Biol. 2003; 4(8): 115. Published online 2003 July 16.
PMCID:
PMC193635
Abstract Full Text PDF–186K Supplementary Material

Is Cited by the Following 22 Articles in this Archive:

Crenarchaeal CdvA Forms Double-Helical Filaments Containing DNA and Interacts with ESCRT-III-Like CdvB
Christine Moriscot, Simonetta Gribaldo, Jean-Michel Jault, Mart Krupovic, Julie Arnaud, Marc Jamin, Guy Schoehn, Patrick Forterre, Winfried Weissenhorn, Patricia Renesto
PLoS One. 2011; 6(7): e21921. Published online 2011 July 8. doi: 10.1371/journal.pone.0021921
PMCID:
PMC3132758
Abstract Full Text PDF–1.0M Supplementary Material
Evolution of diverse cell division and vesicle formation systems in Archaea
Kira S. Makarova, Natalya Yutin, Stephen D. Bell, Eugene V. Koonin
Nat Rev Microbiol. Author manuscript; available in PMC 2012 March 5.
Published in final edited form as: Nat Rev Microbiol. 2010 October; 8(10): 731–741. Published online 2010 September 6. doi: 10.1038/nrmicro2406
PMCID:
PMC3293450
Abstract Full Text PDF–1.5M 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
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
Crystal structure of the human GINS complex
Jung Min Choi, Hye Seong Lim, Jeong Joo Kim, Ok-Kyu Song, Yunje Cho
Genes Dev. 2007 June 1; 21(11): 1316–1321. doi: 10.1101/gad.1548107
PMCID:
PMC1877744
Abstract Full Text PDF–459K
Genome and proteome of long-chain alkane degrading Geobacillus thermodenitrificans NG80-2 isolated from a deep-subsurface oil reservoir
Lu Feng, Wei Wang, Jiansong Cheng, Yi Ren, Guang Zhao, Chunxu Gao, Yun Tang, Xueqian Liu, Weiqing Han, Xia Peng, Rulin Liu, Lei Wang
Proc Natl Acad Sci U S A. 2007 March 27; 104(13): 5602–5607. Published online 2007 March 19. doi: 10.1073/pnas.0609650104
PMCID:
PMC1838512
Abstract Full Text PDF–1.0M Supplementary Material
Identification of Genes Encoding tRNA Modification Enzymes by Comparative Genomics
Valérie de Crécy-Lagard
Methods Enzymol. Author manuscript; available in PMC 2011 February 7.
Published in final edited form as: Methods Enzymol. 2007; 425: 153–183. doi: 10.1016/S0076-6879(07)25007-4
PMCID:
PMC3034448
Abstract Full Text PDF–209K
High precision multi-genome scale reannotation of enzyme function by EFICAz
Adrian K Arakaki, Weidong Tian, Jeffrey Skolnick
BMC Genomics. 2006; 7: 315. Published online 2006 December 13. doi: 10.1186/1471-2164-7-315
PMCID:
PMC1764738
Abstract Full Text PDF–464K Supplementary Material
The cbiS Gene of the Archaeon Methanopyrus kandleri AV19 Encodes a Bifunctional Enzyme with Adenosylcobinamide Amidohydrolase and α-Ribazole-Phosphate Phosphatase Activities
Jesse D. Woodson, Jorge C. Escalante-Semerena
J Bacteriol. 2006 June; 188(12): 4227–4235. doi: 10.1128/JB.00227-06
PMCID:
PMC1482944
Abstract Full Text PDF–398K
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
Characterization of a Thermophilic ATP-Dependent DNA Ligase from the Euryarchaeon Pyrococcus horikoshii
Niroshika Keppetipola, Stewart Shuman
J Bacteriol. 2005 October; 187(20): 6902–6908. doi: 10.1128/JB.187.20.6902-6908.2005
PMCID:
PMC1251619
Abstract Full Text PDF–222K
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
Kira S. Makarova, Yuri I. Wolf, Sergey L. Mekhedov, Boris G. Mirkin, Eugene V. Koonin
Nucleic Acids Res. 2005; 33(14): 4626–4638. Published online 2005 August 16. doi: 10.1093/nar/gki775
PMCID:
PMC1187821
Abstract Full Text PDF–211K Supplementary Material
Evolution of a microbial nitrilase gene family: a comparative and environmental genomics study
Mircea Podar, Jonathan R Eads, Toby H Richardson
BMC Evol Biol. 2005; 5: 42. Published online 2005 August 6. doi: 10.1186/1471-2148-5-42
PMCID:
PMC1199592
Abstract Full Text PDF–645K Supplementary Material
Predicted highly expressed genes in archaeal genomes
Samuel Karlin, Jan Mrázek, Jiong Ma, Luciano Brocchieri
Proc Natl Acad Sci U S A. 2005 May 17; 102(20): 7303–7308. Published online 2005 May 9. doi: 10.1073/pnas.0502313102
PMCID:
PMC1129124
Abstract Full Text PDF–248K Supplementary Material
Genomic and proteomic comparisons between bacterial and archaeal genomes and related comparisons with the yeast and fly genomes
Samuel Karlin, Luciano Brocchieri, Allan Campbell, Martha Cyert, Jan Mrázek
Proc Natl Acad Sci U S A. 2005 May 17; 102(20): 7309–7314. Published online 2005 May 9. doi: 10.1073/pnas.0502314102
PMCID:
PMC1129125
Abstract Full Text PDF–248K
Deciphering structure and topology of conserved COG2042 orphan proteins
Jean Armengaud, Alain Dedieu, Olivier Solques, Jean-Luc Pellequer, Eric Quemeneur
BMC Struct Biol. 2005; 5: 3. Published online 2005 February 8. doi: 10.1186/1472-6807-5-3
PMCID:
PMC549553
Abstract Full Text PDF–962K
Computing prokaryotic gene ubiquity: Rescuing the core from extinction
Robert L. Charlebois, W. Ford Doolittle
Genome Res. 2004 December; 14(12): 2469–2477. doi: 10.1101/gr.3024704
PMCID:
PMC534671
Abstract Full Text PDF–295K
Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes
Tobias Doerks, Christian von Mering, Peer Bork
Nucleic Acids Res. 2004; 32(21): 6321–6326. Published online 2004 December 1. doi: 10.1093/nar/gkh973
PMCID:
PMC535681
Abstract Full Text PDF–397K Supplementary Material
Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central Carbohydrate Metabolism
Thijs J. G. Ettema, Kira S. Makarova, Gera L. Jellema, Hinco J. Gierman, Eugene V. Koonin, Martijn A. Huynen, Willem M. de Vos, John van der Oost
J Bacteriol. 2004 November; 186(22): 7754–7762. doi: 10.1128/JB.186.22.7754-7762.2004
PMCID:
PMC524890
Abstract Full Text PDF–955K
Detection of evolutionarily stable fragments of cellular pathways by hierarchical clustering of phyletic patterns
Galina V Glazko, Arcady R Mushegian
Genome Biol. 2004; 5(5): R32. Published online 2004 April 27.
PMCID:
PMC416468
Abstract Full Text PDF–609K Supplementary Material
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
Cysteinyl-tRNACys Formation in Methanocaldococcus jannaschii: the Mechanism Is Still Unknown
Benfang Ruan, Hiroaki Nakano, Masashi Tanaka, Jonathan A. Mills, Joseph A. DeVito, Bokkee Min, K. Brooks Low, John R. Battista, Dieter Söll
J Bacteriol. 2004 January; 186(1): 8–14. doi: 10.1128/JB.186.1.8-14.2004
PMCID:
PMC303452
Abstract Full Text PDF–381K
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