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The ancient Virus World and evolution of cells
Eugene V Koonin, Tatiana G Senkevich, Valerian V Dolja
Biol Direct. 2006; 1: 29. Published online 2006 September 19. doi: 10.1186/1745-6150-1-29
PMCID:
PMC1594570
Abstract Full Text PDF–2.0M

Is Cited by the Following 55 Articles in this Archive:

Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs
Benjamin Bolduc, Daniel P. Shaughnessy, Yuri I. Wolf, Eugene V. Koonin, Francisco F. Roberto, Mark Young
J Virol. 2012 May; 86(10): 5562–5573. doi: 10.1128/JVI.07196-11
PMCID:
PMC3347303
Free in PMC on 2012/11/01
Vehicles, Replicators, and Intercellular Movement of Genetic Information: Evolutionary Dissection of a Bacterial Cell
Matti Jalasvuori
Int J Evol Biol. 2012; 2012: 874153. Published online 2012 April 10. doi: 10.1155/2012/874153
PMCID:
PMC3332184
Abstract Full Text PDF–768K
Origin of first cells at terrestrial, anoxic geothermal fields
Armen Y. Mulkidjanian, Andrew Yu. Bychkov, Daria V. Dibrova, Michael Y. Galperin, Eugene V. Koonin
Proc Natl Acad Sci U S A. 2012 April 3; 109(14): E821–E830. Published online 2012 February 13. doi: 10.1073/pnas.1117774109
Includes additional comments & authors
PMCID:
PMC3325685
Abstract Full Text PDF–754K Supplementary Material
Viral Proteins Acquired from a Host Converge to Simplified Domain Architectures
Nadav Rappoport, Michal Linial
PLoS Comput Biol. 2012 February; 8(2): e1002364. Published online 2012 February 2. doi: 10.1371/journal.pcbi.1002364
PMCID:
PMC3271019
Abstract Full Text PDF–1.4M Supplementary Material
Genomics of Bacterial and Archaeal Viruses: Dynamics within the Prokaryotic Virosphere
Mart Krupovic, David Prangishvili, Roger W. Hendrix, Dennis H. Bamford
Microbiol Mol Biol Rev. 2011 December; 75(4): 610–635. doi: 10.1128/MMBR.00011-11
PMCID:
PMC3232739
Free in PMC on 2012/12/01
Common Origins and Host-Dependent Diversity of Plant and Animal Viromes
Valerian V. Dolja, Eugene V. Koonin
Curr Opin Virol. Author manuscript; available in PMC 2012 November 1.
Published in final edited form as: Curr Opin Virol. 2011 November 1; 1(5): 322–331. doi: 10.1016/j.coviro.2011.09.007
PMCID:
PMC3293486
Free in PMC on 2012/11/01
Widespread Horizontal Gene Transfer from Circular Single-stranded DNA Viruses to Eukaryotic Genomes
Huiquan Liu, Yanping Fu, Bo Li, Xiao Yu, Jiatao Xie, Jiasen Cheng, Said A Ghabrial, Guoqing Li, Xianhong Yi, Daohong Jiang
BMC Evol Biol. 2011; 11: 276. Published online 2011 September 26. doi: 10.1186/1471-2148-11-276
PMCID:
PMC3198968
Abstract Full Text PDF–2.5M Supplementary Material
Recombination in Eukaryotic Single Stranded DNA Viruses
Darren P. Martin, Philippe Biagini, Pierre Lefeuvre, Michael Golden, Philippe Roumagnac, Arvind Varsani
Viruses. 2011 September; 3(9): 1699–1738. Published online 2011 September 13. doi: 10.3390/v3091699
PMCID:
PMC3187698
Abstract Full Text PDF–3.7M
Evolution in Revolution: A Paradigm shift in our understanding of life and biological evolution
František Baluška
Commun Integr Biol. 2011 Sep-Oct; 4(5): 521–523. Published online 2011 September 1. doi: 10.4161/cib.4.5.17702
PMCID:
PMC3204118
Abstract Full Text PDF–107K
Severe Hindrance of Viral Infection Propagation in Spatially Extended Hosts
José A. Capitán, José A. Cuesta, Susanna C. Manrubia, Jacobo Aguirre
PLoS One. 2011; 6(8): e23358. Published online 2011 August 23. doi: 10.1371/journal.pone.0023358
PMCID:
PMC3160299
Abstract Full Text PDF–821K Supplementary Material
Domain-Domain Interactions Underlying Herpesvirus-Human Protein-Protein Interaction Networks
Zohar Itzhaki
PLoS One. 2011; 6(7): e21724. Published online 2011 July 7. doi: 10.1371/journal.pone.0021724
PMCID:
PMC3131297
Abstract Full Text PDF–170K Supplementary Material
What Does Virus Evolution Tell Us about Virus Origins?
Edward C. Holmes
J Virol. 2011 June; 85(11): 5247–5251. doi: 10.1128/JVI.02203-10
Correction in:
J Virol. 2011 September; 85(18): 9655.
PMCID:
PMC3094976
Abstract Full Text PDF–137K Correction
HCV: Written in our DNA
Darja Kanduc
Self Nonself. 2011 Apr-Jun; 2(2): 108–113. Published online 2011 April 1. doi: 10.4161/self.2.2.15795
PMCID:
PMC3268996
Abstract Full Text PDF–161K Supplementary Material
Cellular Decision-Making and Biological Noise: From Microbes to Mammals
Gábor Balázsi, Alexander van Oudenaarden, James J. Collins
Cell. Author manuscript; available in PMC 2011 September 18.
Published in final edited form as: Cell. 2011 March 18; 144(6): 910–925. doi: 10.1016/j.cell.2011.01.030
PMCID:
PMC3068611
Abstract Full Text PDF–680K
Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses
Tong Zhou, Claus O Wilke
BMC Evol Biol. 2011; 11: 59. Published online 2011 March 7. doi: 10.1186/1471-2148-11-59
PMCID:
PMC3072339
Abstract Full Text PDF–315K Supplementary Material
The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon
Ruben E Valas, Philip E Bourne
Biol Direct. 2011; 6: 16. Published online 2011 February 28. doi: 10.1186/1745-6150-6-16
PMCID:
PMC3056875
Abstract Full Text PDF–1.0M Supplementary Material
Another Really, Really Big Virus
James L. Van Etten
Viruses. 2011 January; 3(1): 32–46. Published online 2011 January 18. doi: 10.3390/v3010032
PMCID:
PMC3187590
Abstract Full Text PDF–217K
Structural analysis of bacteriophage T4 DNA replication: a review in the Virology Journal series on bacteriophage T4 and its relatives
Timothy C Mueser, Jennifer M Hinerman, Juliette M Devos, Ryan A Boyer, Kandace J Williams
Virol J. 2010; 7: 359. Published online 2010 December 3. doi: 10.1186/1743-422X-7-359
PMCID:
PMC3012046
Abstract Full Text PDF–3.4M
Biocommunication and natural genome editing
Guenther Witzany
World J Biol Chem. 2010 November 26; 1(11): 348–352. Published online 2010 November 26. doi: 10.4331/wjbc.v1.i11.348
PMCID:
PMC3083936
Abstract Full Text PDF–615K
Giant virus with a remarkable complement of genes infects marine zooplankton
Matthias G. Fischer, Michael J. Allen, William H. Wilson, Curtis A. Suttle
Proc Natl Acad Sci U S A. 2010 November 9; 107(45): 19508–19513. Published online 2010 October 25. doi: 10.1073/pnas.1007615107
PMCID:
PMC2984142
Abstract Full Text PDF–935K Supplementary Material
DNA Viruses: The Really Big Ones (Giruses)
James L. Van Etten, Leslie C. Lane, David D. Dunigan
Annu Rev Microbiol. Author manuscript; available in PMC 2010 October 1.
Published in final edited form as: Annu Rev Microbiol. 2010 October 13; 64: 83–99. doi: 10.1146/annurev.micro.112408.134338
PMCID:
PMC2936810
Abstract Full Text PDF–503K
The wonder world of microbial viruses
Eugene V Koonin
Expert Rev Anti Infect Ther. Author manuscript; available in PMC 2012 March 5.
Published in final edited form as: Expert Rev Anti Infect Ther. 2010 October; 8(10): 1097–1099. doi: 10.1586/eri.10.96
PMCID:
PMC3293457
Abstract Full Text PDF–30K
Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses
Eugene V. Koonin, Natalya Yutin
Intervirology. 2010 June; 53(5): 284–292. Published online 2010 June 15. doi: 10.1159/000312913
PMCID:
PMC2895762
Abstract Full Text PDF–207K
Two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins
Nicolas Soler, Evelyne Marguet, Diego Cortez, Nicole Desnoues, Jenny Keller, Herman van Tilbeurgh, Guennadi Sezonov, Patrick Forterre
Nucleic Acids Res. 2010 August; 38(15): 5088–5104. Published online 2010 April 19. doi: 10.1093/nar/gkq236
PMCID:
PMC2926602
Abstract Full Text PDF–1.7M Supplementary Material
Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity
Natalya Yutin, Eugene V Koonin
Biol Direct. 2009; 4: 51. Published online 2009 December 18. doi: 10.1186/1745-6150-4-51
PMCID:
PMC2806865
Abstract Full Text PDF–399K 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
New dimensions of the virus world discovered through metagenomics
David M. Kristensen, Arcady R. Mushegian, Valerian V. Dolja, Eugene V. Koonin
Trends Microbiol. Author manuscript; available in PMC 2012 March 5.
Published in final edited form as: Trends Microbiol. 2010 January; 18(1): 11–19. Published online 2009 November 26. doi: 10.1016/j.tim.2009.11.003
PMCID:
PMC3293453
Abstract Full Text PDF–1.3M
Acidianus filamentous virus 1 coat proteins display a helical fold spanning the filamentous archaeal viruses lineage
Adeline Goulet, Stéphanie Blangy, Peter Redder, David Prangishvili, Catarina Felisberto-Rodrigues, Patrick Forterre, Valérie Campanacci, Christian Cambillau
Proc Natl Acad Sci U S A. 2009 December 15; 106(50): 21155–21160. Published online 2009 November 23. doi: 10.1073/pnas.0909893106
PMCID:
PMC2795548
Abstract Full Text PDF–1.1M Supplementary Material
Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences
Iris Bahir, Menachem Fromer, Yosef Prat, Michal Linial
Mol Syst Biol. 2009; 5: 311. Published online 2009 October 13. doi: 10.1038/msb.2009.71
PMCID:
PMC2779085
Abstract Full Text PDF–1.8M Supplementary Material
The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum
Eugene V Koonin, Yuri I Wolf
Biol Direct. 2009; 4: 33. Published online 2009 September 29. doi: 10.1186/1745-6150-4-33
PMCID:
PMC2761301
Abstract Full Text PDF–647K
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