Fields BN, Howley PM, Griffin DE, Lamb RA, Martin MA, Roizman B, Straus SE, Knipe DM, (eds.): Fields Virology. New York: Lippincott Williams & Wilkins; 2001.
Google Scholar
Forterre P: The origin of viruses and their possible roles in major evolutionary transitions. Virus Res 2006,117(1):5-16. 10.1016/j.virusres.2006.01.010
Article
CAS
PubMed
Google Scholar
Raoult D, Forterre P: Redefining viruses: lessons from Mimivirus. Nat Rev Microbiol 2008,6(4):315-319. 10.1038/nrmicro1858
Article
CAS
PubMed
Google Scholar
Koonin EV, Senkevich TG, Dolja VV: The ancient Virus World and evolution of cells. Biol Direct 2006, 1: 29. 10.1186/1745-6150-1-29
Article
PubMed Central
PubMed
Google Scholar
Iyer LM, Aravind L, Koonin EV: Common origin of four diverse families of large eukaryotic DNA viruses. J Virol 2001,75(23):11720-11734. 10.1128/JVI.75.23.11720-11734.2001
Article
PubMed Central
CAS
PubMed
Google Scholar
Iyer LM, Balaji S, Koonin EV, Aravind L: Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res 2006,117(1):156-184. 10.1016/j.virusres.2006.01.009
Article
CAS
PubMed
Google Scholar
Van Etten JL: Unusual life style of giant chlorella viruses. Annu Rev Genet 2003, 37: 153-195. 10.1146/annurev.genet.37.110801.143915
Article
CAS
PubMed
Google Scholar
Filee J: Lateral gene transfer, lineage-specific gene expansion and the evolution of Nucleo Cytoplasmic Large DNA viruses. J Invertebr Pathol 2009,101(3):169-171. 10.1016/j.jip.2009.03.010
Article
CAS
PubMed
Google Scholar
La Scola B, Desnues C, Pagnier I, Robert C, Barrassi L, Fournous G, Merchat M, Suzan-Monti M, Forterre P, Koonin E, Raoult D: The virophage as a unique parasite of the giant mimivirus. Nature 2008,455(7209):100-104. 10.1038/nature07218
Article
CAS
PubMed
Google Scholar
Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, La Scola B, Suzan M, Claverie JM: The 1.2-megabase genome sequence of Mimivirus. Science 2004,306(5700):1344-1350. 10.1126/science.1101485
Article
CAS
PubMed
Google Scholar
Claverie JM, Abergel C: Mimivirus and its Virophage. Annu Rev Genet 2009, 43: 49-66. 10.1146/annurev-genet-102108-134255
Article
CAS
PubMed
Google Scholar
Claverie JM, Abergel C, Ogata H: Mimivirus. Curr Top Microbiol Immunol 2009, 328: 89-121. full_text
CAS
PubMed
Google Scholar
Suzan-Monti M, La Scola B, Raoult D: Genomic and evolutionary aspects of Mimivirus. Virus Res 2006,117(1):145-155. 10.1016/j.virusres.2005.07.011
Article
CAS
PubMed
Google Scholar
Claverie JM, Ogata H, Audic S, Abergel C, Suhre K, Fournier PE: Mimivirus and the emerging concept of "giant" virus. Virus Res 2006,117(1):133-144. 10.1016/j.virusres.2006.01.008
Article
CAS
PubMed
Google Scholar
Koonin EV: Virology: Gulliver among the Lilliputians. Curr Biol 2005,15(5):R167-169. 10.1016/j.cub.2005.02.042
Article
CAS
PubMed
Google Scholar
Filee J, Pouget N, Chandler M: Phylogenetic evidence for extensive lateral acquisition of cellular genes by Nucleocytoplasmic large DNA viruses. BMC Evol Biol 2008, 8: 320. 10.1186/1471-2148-8-320
Article
PubMed Central
PubMed
Google Scholar
Moreira D, Brochier-Armanet C: Giant viruses, giant chimeras: the multiple evolutionary histories of Mimivirus genes. BMC Evol Biol 2008, 8: 12. 10.1186/1471-2148-8-12
Article
PubMed Central
PubMed
Google Scholar
Filee J, Siguier P, Chandler M: I am what I eat and I eat what I am: acquisition of bacterial genes by giant viruses. Trends Genet 2007,23(1):10-15. 10.1016/j.tig.2006.11.002
Article
CAS
PubMed
Google Scholar
Boyer M, Yutin N, Pagnier I, Barrassi L, Fournous G, Espinosa M, Robert C, Azza A, Sun S, Rossmann MG, Suzan-Monti M, La Scola B, Koonin EV, Raoult D: Giant Marseillevirus highlights the role of amoebae as a melting pot in emergence of chimaeric microorganisms. Proc Natl Acad Sci USA 2009, in press.
Google Scholar
Ghedin E, Claverie JM: Mimivirus relatives in the Sargasso sea. Virol J 2005, 2: 62. 10.1186/1743-422X-2-62
Article
PubMed Central
PubMed
Google Scholar
Monier A, Claverie JM, Ogata H: Taxonomic distribution of large DNA viruses in the sea. Genome Biol 2008,9(7):R106. 10.1186/gb-2008-9-7-r106
Article
PubMed Central
PubMed
Google Scholar
Monier A, Larsen JB, Sandaa RA, Bratbak G, Claverie JM, Ogata H: Marine mimivirus relatives are probably large algal viruses. Virol J 2008, 5: 12. 10.1186/1743-422X-5-12
Article
PubMed Central
PubMed
Google Scholar
Kristensen DM, Mushegian AR, Dolja VV, Koonin EV: New dimensions of the virus world discovered through metagenomics. Trends Microbiol 2010, in press.
Google Scholar
Claverie JM, Grzela R, Lartigue A, Bernadac A, Nitsche S, Vacelet J, Ogata H, Abergel C: Mimivirus and Mimiviridae: giant viruses with an increasing number of potential hosts, including corals and sponges. J Invertebr Pathol 2009,101(3):172-180. 10.1016/j.jip.2009.03.011
Article
CAS
PubMed
Google Scholar
Fitch WM: Distinguishing homologous from analogous proteins. Systematic Zoology 1970, 19: 99-106. 10.2307/2412448
Article
CAS
PubMed
Google Scholar
Koonin EV: Orthologs, Paralogs and Evolutionary Genomics. Annu Rev Genet 2005, 39: 309-338. 10.1146/annurev.genet.39.073003.114725
Article
CAS
PubMed
Google Scholar
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, et al.: The COG database: an updated version includes eukaryotes. BMC Bioinformatics 2003, 4: 41. 10.1186/1471-2105-4-41
Article
PubMed Central
PubMed
Google Scholar
Tatusov RL, Koonin EV, Lipman DJ: A genomic perspective on protein families. Science 1997,278(5338):631-637. 10.1126/science.278.5338.631
Article
CAS
PubMed
Google Scholar
Mulkidjanian AY, Koonin EV, Makarova KS, Mekhedov SL, Sorokin A, Wolf YI, Dufresne A, Partensky F, Burd H, Kaznadzey D, Haselkorn R, Galperin MY: The cyanobacterial genome core and the origin of photosynthesis. Proc Natl Acad Sci USA 2006,103(35):13126-13131. 10.1073/pnas.0605709103
Article
PubMed Central
CAS
PubMed
Google Scholar
Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV: Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea. Biol Direct 2007, 2: 33. 10.1186/1745-6150-2-33
Article
PubMed Central
PubMed
Google Scholar
Koonin EV: Comparative genomics, minimal gene-sets and the last universal common ancestor. Nat Rev Microbiol 2003,1(2):127-136. 10.1038/nrmicro751
Article
CAS
PubMed
Google Scholar
Charlebois RL, Doolittle WF: Computing prokaryotic gene ubiquity: rescuing the core from extinction. Genome Res 2004,14(12):2469-2477. 10.1101/gr.3024704
Article
PubMed Central
CAS
PubMed
Google Scholar
Koonin EV, Mushegian AR, Bork P: Non-orthologous gene displacement. Trends Genet 1996,12(9):334-336. 10.1016/0168-9525(96)20010-1
Article
CAS
PubMed
Google Scholar
Shimodaira H: An approximately unbiased test of phylogenetic tree selection. Syst Biol 2002,51(3):492-508. 10.1080/10635150290069913
Article
PubMed
Google Scholar
Ogata H, Toyoda K, Tomaru Y, Nakayama N, Shirai Y, Claverie JM, Nagasaki K: Remarkable sequence similarity between the dinoflagellate-infecting marine girus and the terrestrial pathogen African swine fever virus. Virol J 2009, 6: 178. 10.1186/1743-422X-6-178
Article
PubMed Central
PubMed
Google Scholar
Wolf YI, Rogozin IB, Grishin NV, Koonin EV: Genome trees and the tree of life. Trends Genet 2002,18(9):472-479. 10.1016/S0168-9525(02)02744-0
Article
CAS
PubMed
Google Scholar
Csuros M, Miklos I: Streamlining and large ancestral genomes in Archaea inferred with a phylogenetic birth-and-death model. Mol Biol Evol 2009,26(9):2087-2095. 10.1093/molbev/msp123
Article
PubMed Central
PubMed
Google Scholar
Senkevich TG, Koonin EV, Bugert JJ, Darai G, Moss B: The genome of molluscum contagiosum virus: analysis and comparison with other poxviruses. Virology 1997,233(1):19-42. 10.1006/viro.1997.8607
Article
CAS
PubMed
Google Scholar
Yutin N, Koonin EV: Evolution of DNA ligases of Nucleo-Cytoplasmic Large DNA viruses of eukaryotes: a case of hidden complexity. Biology Direct 2009,4(1):51. 10.1186/1745-6150-4-51
Article
PubMed Central
PubMed
Google Scholar
Banerji S, Aurass P, Flieger A: The manifold phospholipases A of Legionella pneumophila - identification, export, regulation, and their link to bacterial virulence. Int J Med Microbiol 2008,298(3-4):169-181. 10.1016/j.ijmm.2007.11.004
Article
CAS
PubMed
Google Scholar
Koonin EV: A duplicated catalytic motif in a new superfamily of phosphohydrolases and phospholipid synthases that includes poxvirus envelope proteins. Trends Biochem Sci 1996,21(7):242-243.
Article
CAS
PubMed
Google Scholar
Husain M, Moss B: Similarities in the induction of post-Golgi vesicles by the vaccinia virus F13L protein and phospholipase D. J Virol 2002,76(15):7777-7789. 10.1128/JVI.76.15.7777-7789.2002
Article
PubMed Central
CAS
PubMed
Google Scholar
Koonin EV, Wolf YI, Nagasaki K, Dolja VV: The Big Bang of picorna-like virus evolution antedates the radiation of eukaryotic supergroups. Nat Rev Microbiol 2008,6(12):925-939. 10.1038/nrmicro2030
Article
CAS
PubMed
Google Scholar
Lukashin AV, Borodovsky M: GeneMark.hmm: new solutions for gene finding. Nucleic Acids Res 1998,26(4):1107-1115. 10.1093/nar/26.4.1107
Article
PubMed Central
CAS
PubMed
Google Scholar
Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 1997,25(17):3389-3402. 10.1093/nar/25.17.3389
Article
PubMed Central
CAS
PubMed
Google Scholar
Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004,32(5):1792-1797. 10.1093/nar/gkh340
Article
PubMed Central
CAS
PubMed
Google Scholar
Marchler-Bauer A, Bryant SH: CD-Search: protein domain annotations on the fly. Nucleic Acids Res 2004, (32 Web Server):W327-331. 10.1093/nar/gkh454
Jobb G, von Haeseler A, Strimmer K: TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 2004, 4: 18. 10.1186/1471-2148-4-18
Article
PubMed Central
PubMed
Google Scholar
Whelan S, Goldman N: A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol 2001,18(5):691-699.
Article
CAS
PubMed
Google Scholar
Puigbo P, Garcia-Vallve S, McInerney JO: TOPD/FMTS: a new software to compare phylogenetic trees. Bioinformatics 2007,23(12):1556-1558. 10.1093/bioinformatics/btm135
Article
CAS
PubMed
Google Scholar
Puigbo P, Wolf YI, Koonin EV: Search for a 'Tree of Life' in the thicket of the phylogenetic forest. J Biol 2009,8(6):59. 10.1186/jbiol159
Article
PubMed Central
PubMed
Google Scholar
Felsenstein J: Inferring phylogenies from protein sequences by parsimony, distance, and likelihood methods. Methods Enzymol 1996, 266: 418-427. full_text
Article
CAS
PubMed
Google Scholar
Csuros M, Miklos I: A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer. Lecture Notes in Computer Science 2006, 3909: 206-220. full_text
Article
Google Scholar