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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
Biol Direct. 2007; 2: 33. Published online 2007 November 27. doi: 10.1186/1745-6150-2-33
PMCID:
PMC2222616
Abstract Full Text PDF–593K

Is Cited by the Following 47 Articles in this Archive:

Assigning a function to a conserved archaeal metallo-β-lactamase from Haloferax volcanii
Susan Fischer, Simona John von Freyend, Anice Sabag-Daigle, Charles J. Daniels, Thorsten Allers, Anita Marchfelder
Extremophiles. 2012 March; 16(2): 333–343. Published online 2012 February 18. doi: 10.1007/s00792-012-0433-4
PMCID:
PMC3296008
Abstract Full Text PDF–736K Supplementary Material
The CMG (CDC45/RecJ, MCM, GINS) complex is a conserved component of the DNA replication system in all archaea and eukaryotes
Kira S Makarova, Eugene V Koonin, Zvi Kelman
Biol Direct. 2012; 7: 7. Published online 2012 February 13. doi: 10.1186/1745-6150-7-7
PMCID:
PMC3307487
Abstract Full Text PDF–546K Supplementary Material
The core and unique proteins of haloarchaea
Melinda D Capes, Priya DasSarma, Shiladitya DasSarma
BMC Genomics. 2012; 13: 39. Published online 2012 January 24. doi: 10.1186/1471-2164-13-39
PMCID:
PMC3287961
Abstract Full Text PDF–2.4M Supplementary Material
Purine biosynthesis in archaea: variations on a theme
Anne M Brown, Samantha L Hoopes, Robert H White, Catherine A Sarisky
Biol Direct. 2011; 6: 63. Published online 2011 December 14. doi: 10.1186/1745-6150-6-63
PMCID:
PMC3261824
Abstract Full Text PDF–3.8M Supplementary Material
Calculating Orthologs in Bacteria and Archaea: A Divide and Conquer Approach
Mihail R. Halachev, Nicholas J. Loman, Mark J. Pallen
PLoS One. 2011; 6(12): e28388. Published online 2011 December 12. doi: 10.1371/journal.pone.0028388
PMCID:
PMC3236195
Abstract Full Text PDF–1.3M Supplementary Material
Displacement of the canonical single-stranded DNA-binding protein in the Thermoproteales
Sonia Paytubi, Stephen A. McMahon, Shirley Graham, Huanting Liu, Catherine H. Botting, Kira S. Makarova, Eugene V. Koonin, James H. Naismith, Malcolm F. White
Proc Natl Acad Sci U S A. 2012 February 14; 109(7): E398–E405. Published online 2011 November 21. doi: 10.1073/pnas.1113277108
Includes additional comments & authors
PMCID:
PMC3289382
Free in PMC on 2012/08/14
eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges
Sean Powell, Damian Szklarczyk, Kalliopi Trachana, Alexander Roth, Michael Kuhn, Jean Muller, Roland Arnold, Thomas Rattei, Ivica Letunic, Tobias Doerks, Lars J. Jensen, Christian von Mering, Peer Bork
Nucleic Acids Res. 2012 January; 40(D1): D284–D289. Published online 2011 November 16. doi: 10.1093/nar/gkr1060
PMCID:
PMC3245133
Abstract Full Text PDF–5.0M
The UCSC Archaeal Genome Browser: 2012 update
Patricia P. Chan, Andrew D. Holmes, Andrew M. Smith, Danny Tran, Todd M. Lowe
Nucleic Acids Res. 2012 January; 40(D1): D646–D652. Published online 2011 November 12. doi: 10.1093/nar/gkr990
PMCID:
PMC3245099
Abstract Full Text PDF–7.9M
The Complete Genome Sequence of Thermoproteus tenax: A Physiologically Versatile Member of the Crenarchaeota
Bettina Siebers, Melanie Zaparty, Guenter Raddatz, Britta Tjaden, Sonja-Verena Albers, Steve D. Bell, Fabian Blombach, Arnulf Kletzin, Nikos Kyrpides, Christa Lanz, André Plagens, Markus Rampp, Andrea Rosinus, Mathias von Jan, Kira S. Makarova, Hans-Peter Klenk, Stephan C. Schuster, Reinhard Hensel
PLoS One. 2011; 6(10): e24222. Published online 2011 October 7. doi: 10.1371/journal.pone.0024222
PMCID:
PMC3189178
Abstract Full Text PDF–469K Supplementary Material
The evolution of the cytoskeleton
Bill Wickstead, Keith Gull
J Cell Biol. 2011 August 22; 194(4): 513–525. doi: 10.1083/jcb.201102065
PMCID:
PMC3160578
Abstract Full Text PDF–2.4M
Proteomic Characterization of Cellular and Molecular Processes that Enable the Nanoarchaeum equitans-Ignicoccus hospitalis Relationship
Richard J. Giannone, Harald Huber, Tatiana Karpinets, Thomas Heimerl, Ulf Küper, Reinhard Rachel, Martin Keller, Robert L. Hettich, Mircea Podar
PLoS One. 2011; 6(8): e22942. Published online 2011 August 3. doi: 10.1371/journal.pone.0022942
PMCID:
PMC3149612
Abstract Full Text PDF–1.1M Supplementary Material
Unification of Cas protein families and a simple scenario for the origin and evolution of CRISPR-Cas systems
Kira S Makarova, L Aravind, Yuri I Wolf, Eugene V Koonin
Biol Direct. 2011; 6: 38. Published online 2011 July 14. doi: 10.1186/1745-6150-6-38
PMCID:
PMC3150331
Abstract Full Text PDF–2.9M Supplementary Material
Formation of m2G6 in Methanocaldococcus jannaschii tRNA catalyzed by the novel methyltransferase Trm14
Sheena Menezes, Kirk W. Gaston, Kady L. Krivos, Ethel E. Apolinario, Norbert O. Reich, Kevin R. Sowers, Patrick A. Limbach, John J. Perona
Nucleic Acids Res. 2011 September; 39(17): 7641–7655. Published online 2011 June 21. doi: 10.1093/nar/gkr475
PMCID:
PMC3177210
Abstract Full Text PDF–11M Supplementary Material
Computational methods for Gene Orthology inference
David M. Kristensen, Yuri I. Wolf, Arcady R. Mushegian, Eugene V. Koonin
Brief Bioinform. 2011 September; 12(5): 379–391. Published online 2011 June 17. doi: 10.1093/bib/bbr030
PMCID:
PMC3178053
Free in PMC on 2012/09/01
Characterization of a Zinc-Containing Alcohol Dehydrogenase with Stereoselectivity from the Hyperthermophilic Archaeon Thermococcus guaymasensis
Xiangxian Ying, Kesen Ma
J Bacteriol. 2011 June; 193(12): 3009–3019. doi: 10.1128/JB.01433-10
PMCID:
PMC3133181
Abstract Full Text PDF–833K
Structure and Activity of a Novel Archaeal β-CASP Protein with N-Terminal KH Domains
Ana P.G. Silva, Maria Chechik, Robert T. Byrne, David G. Waterman, C. Leong Ng, Eleanor J. Dodson, Eugene V. Koonin, Alfred A. Antson, Callum Smits
Structure. 2011 May 11; 19(5): 622–632. doi: 10.1016/j.str.2011.03.002
PMCID:
PMC3095777
Abstract Full Text Supplementary Material
The GreenCut2 Resource, a Phylogenomically Derived Inventory of Proteins Specific to the Plant Lineage
Steven J. Karpowicz, Simon E. Prochnik, Arthur R. Grossman, Sabeeha S. Merchant
J Biol Chem. 2011 June 17; 286(24): 21427–21439. Published online 2011 April 22. doi: 10.1074/jbc.M111.233734
PMCID:
PMC3122202
Free in PMC on 2012/06/17
The Human Postsynaptic Density Shares Conserved Elements with Proteomes of Unicellular Eukaryotes and Prokaryotes
Richard David Emes, Seth G. N. Grant
Front Neurosci. 2011; 5: 44. Published online 2011 March 31. doi: 10.3389/fnins.2011.00044
PMCID:
PMC3071500
Abstract Full Text PDF–1.3M
Insights into the evolution of Archaea and eukaryotic protein modifier systems revealed by the genome of a novel archaeal group
Takuro Nunoura, Yoshihiro Takaki, Jungo Kakuta, Shinro Nishi, Junichi Sugahara, Hiromi Kazama, Gab-Joo Chee, Masahira Hattori, Akio Kanai, Haruyuki Atomi, Ken Takai, Hideto Takami
Nucleic Acids Res. 2011 April; 39(8): 3204–3223. Published online 2010 December 15. doi: 10.1093/nar/gkq1228
PMCID:
PMC3082918
Abstract Full Text PDF–3.5M Supplementary Material
Genes optimized by evolution for accurate and fast translation encode in Archaea and Bacteria a broad and characteristic spectrum of protein functions
Conrad von Mandach, Rainer Merkl
BMC Genomics. 2010; 11: 617. Published online 2010 November 4. doi: 10.1186/1471-2164-11-617
PMCID:
PMC3091758
Abstract Full Text PDF–610K 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
Replication-biased genome organisation in the crenarchaeon Sulfolobus
Anders F Andersson, Erik A Pelve, Stefan Lindeberg, Magnus Lundgren, Peter Nilsson, Rolf Bernander
BMC Genomics. 2010; 11: 454. Published online 2010 July 28. doi: 10.1186/1471-2164-11-454
PMCID:
PMC3091651
Abstract Full Text PDF–513K Supplementary Material
Nitrosopumilus maritimus genome reveals unique mechanisms for nitrification and autotrophy in globally distributed marine crenarchaea
C. B. Walker, J. R. de la Torre, M. G. Klotz, H. Urakawa, N. Pinel, D. J. Arp, C. Brochier-Armanet, P. S. G. Chain, P. P. Chan, A. Gollabgir, J. Hemp, M. Hügler, E. A. Karr, M. Könneke, M. Shin, T. J. Lawton, T. Lowe, W. Martens-Habbena, L. A. Sayavedra-Soto, D. Lang, S. M. Sievert, A. C. Rosenzweig, G. Manning, D. A. Stahl
Proc Natl Acad Sci U S A. 2010 May 11; 107(19): 8818–8823. Published online 2010 April 26. doi: 10.1073/pnas.0913533107
PMCID:
PMC2889351
Abstract Full Text PDF–631K Supplementary Material
eggNOG v2.0: extending the evolutionary genealogy of genes with enhanced non-supervised orthologous groups, species and functional annotations
J. Muller, D. Szklarczyk, P. Julien, I. Letunic, A. Roth, M. Kuhn, S. Powell, C. von Mering, T. Doerks, L. J. Jensen, P. Bork
Nucleic Acids Res. 2010 January; 38(Database issue): D190–D195. Published online 2010 January. doi: 10.1093/nar/gkp951
PMCID:
PMC2808932
Abstract Full Text PDF–1.5M
Molecular evolution of the hyperthermophilic archaea of the Pyrococcus genus: analysis of adaptation to different environmental conditions
Konstantin V Gunbin, Dmitry A Afonnikov, Nikolay A Kolchanov
BMC Genomics. 2009; 10: 639. Published online 2009 December 30. doi: 10.1186/1471-2164-10-639
PMCID:
PMC2816203
Abstract Full Text PDF–565K Supplementary Material
Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution
Natalya Yutin, Yuri I Wolf, Didier Raoult, Eugene V Koonin
Virol J. 2009; 6: 223. Published online 2009 December 17. doi: 10.1186/1743-422X-6-223
PMCID:
PMC2806869
Abstract Full Text PDF–1.1M Supplementary Material
Prokaryotic homologs of Argonaute proteins are predicted to function as key components of a novel system of defense against mobile genetic elements
Kira S Makarova, Yuri I Wolf, John van der Oost, Eugene V Koonin
Biol Direct. 2009; 4: 29. Published online 2009 August 25. doi: 10.1186/1745-6150-4-29
PMCID:
PMC2743648
Abstract Full Text PDF–579K Supplementary Material
Pantoate Kinase and Phosphopantothenate Synthetase, Two Novel Enzymes Necessary for CoA Biosynthesis in the Archaea
Yuusuke Yokooji, Hiroya Tomita, Haruyuki Atomi, Tadayuki Imanaka
J Biol Chem. 2009 October 9; 284(41): 28137–28145. Published online 2009 August 7. doi: 10.1074/jbc.M109.009696
PMCID:
PMC2788864
Abstract Full Text Supplementary Material
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
Autotrophic Carbon Dioxide Assimilation in Thermoproteales Revisited
W. Hugo Ramos-Vera, Ivan A. Berg, Georg Fuchs
J Bacteriol. 2009 July; 191(13): 4286–4297. Published online 2009 May 1. doi: 10.1128/JB.00145-09
PMCID:
PMC2698501
Abstract Full Text PDF–1.4M
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