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For: Wu GA, Jun SR, Sims GE, Kim SH. Whole-proteome phylogeny of large dsDNA virus families by an alignment-free method. Proc Natl Acad Sci U S A 2009;106:12826-31. [PMID: 19553209 DOI: 10.1073/pnas.0905115106] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Islam R, Rahman A. An alignment-free method for detection of missing regions for phylogenetic analysis. Heliyon 2024;10:e32227. [PMID: 38933968 PMCID: PMC11200290 DOI: 10.1016/j.heliyon.2024.e32227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Revised: 05/17/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024]  Open
2
Wang T, Yu ZG, Li J. CGRWDL: alignment-free phylogeny reconstruction method for viruses based on chaos game representation weighted by dynamical language model. Front Microbiol 2024;15:1339156. [PMID: 38572227 PMCID: PMC10987876 DOI: 10.3389/fmicb.2024.1339156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/23/2024] [Indexed: 04/05/2024]  Open
3
Thind AS, Sinha S. Using Chaos-Game-Representation for Analysing the SARS-CoV-2 Lineages, Newly Emerging Strains and Recombinants. Curr Genomics 2023;24:187-195. [PMID: 38178984 PMCID: PMC10761335 DOI: 10.2174/0113892029264990231013112156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 08/09/2023] [Accepted: 09/15/2023] [Indexed: 01/06/2024]  Open
4
Zhang W, Wang R, Zou X, Gu C, Yang Q, He M, Xiao W, He L, Zhao M, Yu Z. Comparative genomic analysis of alloherpesviruses: Exploring an available genus/species demarcation proposal and method. Virus Res 2023;334:199163. [PMID: 37364814 PMCID: PMC10410580 DOI: 10.1016/j.virusres.2023.199163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/22/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
5
van Oers MM, Herniou EA, Jehle JA, Krell PJ, Abd-Alla AMM, Ribeiro BM, Theilmann DA, Hu Z, Harrison RL. Developments in the classification and nomenclature of arthropod-infecting large DNA viruses that contain pif genes. Arch Virol 2023;168:182. [PMID: 37322175 PMCID: PMC10271883 DOI: 10.1007/s00705-023-05793-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
6
Perico CP, De Pierri CR, Neto GP, Fernandes DR, Pedrosa FO, de Souza EM, Raittz RT. Genomic landscape of the SARS-CoV-2 pandemic in Brazil suggests an external P.1 variant origin. Front Microbiol 2022;13:1037455. [PMID: 36620039 PMCID: PMC9814972 DOI: 10.3389/fmicb.2022.1037455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]  Open
7
Rachtman E, Sarmashghi S, Bafna V, Mirarab S. Quantifying the uncertainty of assembly-free genome-wide distance estimates and phylogenetic relationships using subsampling. Cell Syst 2022;13:817-829.e3. [PMID: 36265468 PMCID: PMC9589918 DOI: 10.1016/j.cels.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/14/2022] [Accepted: 06/28/2022] [Indexed: 01/26/2023]
8
Balaban M, Bristy NA, Faisal A, Bayzid MS, Mirarab S. Genome-wide alignment-free phylogenetic distance estimation under a no strand-bias model. BIOINFORMATICS ADVANCES 2022;2:vbac055. [PMID: 35992043 PMCID: PMC9383262 DOI: 10.1093/bioadv/vbac055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
9
He L, Sun S, Zhang Q, Bao X, Li PK. Alignment-free sequence comparison for virus genomes based on location correlation coefficient. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021;96:105106. [PMID: 34626822 PMCID: PMC8493760 DOI: 10.1016/j.meegid.2021.105106] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 09/08/2021] [Accepted: 10/03/2021] [Indexed: 12/18/2022]
10
Saleh M, Sellyei B, Kovács G, Székely C. Viruses Infecting the European Catfish (Silurus glanis). Viruses 2021;13:1865. [PMID: 34578446 PMCID: PMC8473376 DOI: 10.3390/v13091865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/13/2021] [Accepted: 09/15/2021] [Indexed: 12/23/2022]  Open
11
Mahapatra A, Mukherjee J. Taxonomy classification using genomic footprint of mitochondrial sequences. Comb Chem High Throughput Screen 2021;25:401-413. [PMID: 34382517 DOI: 10.2174/1386207324666210811102109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 07/07/2021] [Accepted: 07/12/2021] [Indexed: 11/22/2022]
12
Pornputtapong N, Acheampong DA, Patumcharoenpol P, Jenjaroenpun P, Wongsurawat T, Jun SR, Yongkiettrakul S, Chokesajjawatee N, Nookaew I. KITSUNE: A Tool for Identifying Empirically Optimal K-mer Length for Alignment-Free Phylogenomic Analysis. Front Bioeng Biotechnol 2020;8:556413. [PMID: 33072720 PMCID: PMC7538862 DOI: 10.3389/fbioe.2020.556413] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/24/2020] [Indexed: 12/22/2022]  Open
13
Wang W, Ren J, Tang K, Dart E, Ignacio-Espinoza JC, Fuhrman JA, Braun J, Sun F, Ahlgren NA. A network-based integrated framework for predicting virus-prokaryote interactions. NAR Genom Bioinform 2020;2:lqaa044. [PMID: 32626849 PMCID: PMC7324143 DOI: 10.1093/nargab/lqaa044] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 03/12/2020] [Accepted: 06/05/2020] [Indexed: 12/12/2022]  Open
14
Positional Correlation Natural Vector: A Novel Method for Genome Comparison. Int J Mol Sci 2020;21:ijms21113859. [PMID: 32485813 PMCID: PMC7312176 DOI: 10.3390/ijms21113859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/17/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022]  Open
15
De Pierri CR, Voyceik R, Santos de Mattos LGC, Kulik MG, Camargo JO, Repula de Oliveira AM, de Lima Nichio BT, Marchaukoski JN, da Silva Filho AC, Guizelini D, Ortega JM, Pedrosa FO, Raittz RT. SWeeP: representing large biological sequences datasets in compact vectors. Sci Rep 2020;10:91. [PMID: 31919449 PMCID: PMC6952362 DOI: 10.1038/s41598-019-55627-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/02/2019] [Indexed: 12/25/2022]  Open
16
Maabar M, Davison AJ, Vučak M, Thorburn F, Murcia PR, Gunson R, Palmarini M, Hughes J. DisCVR: Rapid viral diagnosis from high-throughput sequencing data. Virus Evol 2019;5:vez033. [PMID: 31528358 PMCID: PMC6735924 DOI: 10.1093/ve/vez033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
17
An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes. PLoS One 2018;13:e0206409. [PMID: 30427878 PMCID: PMC6235296 DOI: 10.1371/journal.pone.0206409] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2018] [Accepted: 10/14/2018] [Indexed: 01/11/2023]  Open
18
Ren J, Bai X, Lu YY, Tang K, Wang Y, Reinert G, Sun F. Alignment-Free Sequence Analysis and Applications. Annu Rev Biomed Data Sci 2018;1:93-114. [PMID: 31828235 PMCID: PMC6905628 DOI: 10.1146/annurev-biodatasci-080917-013431] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
19
Nishimura Y, Yoshida T, Kuronishi M, Uehara H, Ogata H, Goto S. ViPTree: the viral proteomic tree server. Bioinformatics 2018;33:2379-2380. [PMID: 28379287 DOI: 10.1093/bioinformatics/btx157] [Citation(s) in RCA: 418] [Impact Index Per Article: 69.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/21/2017] [Indexed: 11/12/2022]  Open
20
Chinchar V, Waltzek TB, Subramaniam K. Ranaviruses and other members of the family Iridoviridae: Their place in the virosphere. Virology 2017. [DOI: 10.1016/j.virol.2017.06.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
21
A novel fast vector method for genetic sequence comparison. Sci Rep 2017;7:12226. [PMID: 28939913 PMCID: PMC5610321 DOI: 10.1038/s41598-017-12493-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 09/07/2017] [Indexed: 11/08/2022]  Open
22
Zhang Q, Jun SR, Leuze M, Ussery D, Nookaew I. Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep 2017;7:40712. [PMID: 28102365 PMCID: PMC5244389 DOI: 10.1038/srep40712] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 12/08/2016] [Indexed: 11/25/2022]  Open
23
Li Y, He L, He RL, Yau SST. Zika and Flaviviruses Phylogeny Based on the Alignment-Free Natural Vector Method. DNA Cell Biol 2016;36:109-116. [PMID: 27977308 DOI: 10.1089/dna.2016.3532] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
24
Chen S, Deng LY, Bowman D, Shiau JJH, Wong TY, Madahian B, Lu HHS. Phylogenetic tree construction using trinucleotide usage profile (TUP). BMC Bioinformatics 2016;17:381. [PMID: 27766939 PMCID: PMC5073869 DOI: 10.1186/s12859-016-1222-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
25
Li Y, Tian K, Yin C, He RL, Yau SST. Virus classification in 60-dimensional protein space. Mol Phylogenet Evol 2016;99:53-62. [PMID: 26988414 DOI: 10.1016/j.ympev.2016.03.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 01/24/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
26
Overstreet RM, Lotz JM. Host–Symbiont Relationships: Understanding the Change from Guest to Pest. ADVANCES IN ENVIRONMENTAL MICROBIOLOGY 2016. [PMCID: PMC7123458 DOI: 10.1007/978-3-319-28170-4_2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
27
Yang WF, Yu ZG, Anh V. Whole genome/proteome based phylogeny reconstruction for prokaryotes using higher order Markov model and chaos game representation. Mol Phylogenet Evol 2015;96:102-111. [PMID: 26724405 DOI: 10.1016/j.ympev.2015.12.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 12/17/2015] [Accepted: 12/18/2015] [Indexed: 01/18/2023]
28
Jun SR, Leuze MR, Nookaew I, Uberbacher EC, Land M, Zhang Q, Wanchai V, Chai J, Nielsen M, Trolle T, Lund O, Buzard GS, Pedersen TD, Wassenaar TM, Ussery DW. Ebolavirus comparative genomics. FEMS Microbiol Rev 2015;39:764-78. [PMID: 26175035 PMCID: PMC4551310 DOI: 10.1093/femsre/fuv031] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/08/2015] [Indexed: 12/17/2022]  Open
29
Xie XH, Yu ZG, Han GS, Yang WF, Anh V. Whole-proteome based phylogenetic tree construction with inter-amino-acid distances and the conditional geometric distribution profiles. Mol Phylogenet Evol 2015;89:37-45. [PMID: 25882834 DOI: 10.1016/j.ympev.2015.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 03/29/2015] [Accepted: 04/06/2015] [Indexed: 11/18/2022]
30
Yuan J, Zhu Q, Liu B. Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes. PLoS One 2014;9:e84330. [PMID: 24465405 PMCID: PMC3896360 DOI: 10.1371/journal.pone.0084330] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 11/14/2013] [Indexed: 12/29/2022]  Open
31
Wang JD. Comparing virus classification using genomic materials according to different taxonomic levels. J Bioinform Comput Biol 2013;11:1343003. [PMID: 24372032 DOI: 10.1142/s0219720013430038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
32
Song K, Ren J, Reinert G, Deng M, Waterman MS, Sun F. New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing. Brief Bioinform 2013;15:343-53. [PMID: 24064230 DOI: 10.1093/bib/bbt067] [Citation(s) in RCA: 112] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
33
Kariithi HM, van Oers MM, Vlak JM, Vreysen MJB, Parker AG, Abd-Alla AMM. Virology, Epidemiology and Pathology of Glossina Hytrosavirus, and Its Control Prospects in Laboratory Colonies of the Tsetse Fly, Glossina pallidipes (Diptera; Glossinidae). INSECTS 2013;4:287-319. [PMID: 26462422 PMCID: PMC4553466 DOI: 10.3390/insects4030287] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2013] [Revised: 06/13/2013] [Accepted: 06/13/2013] [Indexed: 01/03/2023]
34
New insights into the evolution of Entomopoxvirinae from the complete genome sequences of four entomopoxviruses infecting Adoxophyes honmai, Choristoneura biennis, Choristoneura rosaceana, and Mythimna separata. J Virol 2013;87:7992-8003. [PMID: 23678178 DOI: 10.1128/jvi.00453-13] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
35
Azad RK, Li J. Interpreting genomic data via entropic dissection. Nucleic Acids Res 2012;41:e23. [PMID: 23036836 PMCID: PMC3592408 DOI: 10.1093/nar/gks917] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
36
Phylogeny and evolution of Hytrosaviridae. J Invertebr Pathol 2012;112 Suppl:S62-7. [PMID: 22841640 DOI: 10.1016/j.jip.2012.07.015] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2012] [Revised: 05/21/2012] [Accepted: 05/22/2012] [Indexed: 11/21/2022]
37
Zhai Z, Reinert G, Song K, Waterman MS, Luan Y, Sun F. Normal and compound poisson approximations for pattern occurrences in NGS reads. J Comput Biol 2012;19:839-54. [PMID: 22697250 PMCID: PMC3375642 DOI: 10.1089/cmb.2012.0029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
38
Göke J, Schulz MH, Lasserre J, Vingron M. Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts. ACTA ACUST UNITED AC 2012;28:656-63. [PMID: 22247280 PMCID: PMC3289921 DOI: 10.1093/bioinformatics/bts028] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
39
Gao Y, Luo L. Genome-based phylogeny of dsDNA viruses by a novel alignment-free method. Gene 2011;492:309-14. [PMID: 22100880 DOI: 10.1016/j.gene.2011.11.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2011] [Revised: 09/19/2011] [Accepted: 11/01/2011] [Indexed: 12/25/2022]
40
Hanson L, Dishon A, Kotler M. Herpesviruses that infect fish. Viruses 2011;3:2160-91. [PMID: 22163339 PMCID: PMC3230846 DOI: 10.3390/v3112160] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Revised: 10/15/2011] [Accepted: 10/22/2011] [Indexed: 11/25/2022]  Open
41
Paleozoic origin of insect large dsDNA viruses. Proc Natl Acad Sci U S A 2011;108:15931-5. [PMID: 21911395 DOI: 10.1073/pnas.1105580108] [Citation(s) in RCA: 102] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]  Open
42
Liu X, Wan L, Li J, Reinert G, Waterman MS, Sun F. New powerful statistics for alignment-free sequence comparison under a pattern transfer model. J Theor Biol 2011;284:106-16. [PMID: 21723298 DOI: 10.1016/j.jtbi.2011.06.020] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Revised: 05/30/2011] [Accepted: 06/17/2011] [Indexed: 12/15/2022]
43
Nagamine B, Jones L, Tellgren-Roth C, Cavender J, Bratanich AC. A novel gammaherpesvirus isolated from a black-tailed prairie dog (Cynomys ludovicianus). Arch Virol 2011;156:1835-40. [PMID: 21630099 DOI: 10.1007/s00705-011-1024-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2011] [Accepted: 05/06/2011] [Indexed: 11/27/2022]
44
Holmes EC. What does virus evolution tell us about virus origins? J Virol 2011;85:5247-51. [PMID: 21450811 PMCID: PMC3094976 DOI: 10.1128/jvi.02203-10] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
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Wang Y, Bininda-Emonds ORP, van Oers MM, Vlak JM, Jehle JA. The genome of Oryctes rhinoceros nudivirus provides novel insight into the evolution of nuclear arthropod-specific large circular double-stranded DNA viruses. Virus Genes 2011;42:444-56. [DOI: 10.1007/s11262-011-0589-5] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2010] [Accepted: 02/21/2011] [Indexed: 11/29/2022]
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Hendrickson RC, Wang C, Hatcher EL, Lefkowitz EJ. Orthopoxvirus genome evolution: the role of gene loss. Viruses 2010;2:1933-1967. [PMID: 21994715 PMCID: PMC3185746 DOI: 10.3390/v2091933] [Citation(s) in RCA: 146] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2010] [Revised: 08/25/2010] [Accepted: 09/01/2010] [Indexed: 12/26/2022]  Open
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Blanc G, Duncan G, Agarkova I, Borodovsky M, Gurnon J, Kuo A, Lindquist E, Lucas S, Pangilinan J, Polle J, Salamov A, Terry A, Yamada T, Dunigan DD, Grigoriev IV, Claverie JM, Van Etten JL. The Chlorella variabilis NC64A genome reveals adaptation to photosymbiosis, coevolution with viruses, and cryptic sex. THE PLANT CELL 2010;22:2943-55. [PMID: 20852019 PMCID: PMC2965543 DOI: 10.1105/tpc.110.076406] [Citation(s) in RCA: 337] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 07/15/2010] [Accepted: 09/01/2010] [Indexed: 05/18/2023]
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Eaton HE, Ring BA, Brunetti CR. The genomic diversity and phylogenetic relationship in the family iridoviridae. Viruses 2010;2:1458-1475. [PMID: 21994690 PMCID: PMC3185713 DOI: 10.3390/v2071458] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2010] [Revised: 07/12/2010] [Accepted: 07/13/2010] [Indexed: 01/13/2023]  Open
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Entropy and Information Approaches to Genetic Diversity and its Expression: Genomic Geography. ENTROPY 2010. [DOI: 10.3390/e12071765] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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Yu ZG, Chu KH, Li CP, Anh V, Zhou LQ, Wang RW. Whole-proteome phylogeny of large dsDNA viruses and parvoviruses through a composition vector method related to dynamical language model. BMC Evol Biol 2010;10:192. [PMID: 20565983 PMCID: PMC2898692 DOI: 10.1186/1471-2148-10-192] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Accepted: 06/22/2010] [Indexed: 11/24/2022]  Open
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