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For: Simmonds P, Tuplin A, Evans DJ. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence. RNA 2004;10:1337-51. [PMID: 15273323 PMCID: PMC1370621 DOI: 10.1261/rna.7640104] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2004] [Accepted: 06/01/2004] [Indexed: 05/20/2023]
Number Cited by Other Article(s)
51
Virome Analysis of Transfusion Recipients Reveals a Novel Human Virus That Shares Genomic Features with Hepaciviruses and Pegiviruses. mBio 2015;6:e01466-15. [PMID: 26396247 PMCID: PMC4600124 DOI: 10.1128/mbio.01466-15] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
52
Tubiana L, Božič AL, Micheletti C, Podgornik R. Synonymous mutations reduce genome compactness in icosahedral ssRNA viruses. Biophys J 2015;108:194-202. [PMID: 25564866 DOI: 10.1016/j.bpj.2014.10.070] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 09/29/2014] [Accepted: 10/08/2014] [Indexed: 12/15/2022]  Open
53
Sachdeva M, Chawla YK, Arora SK. Dendritic cells: The warriors upfront-turned defunct in chronic hepatitis C infection. World J Hepatol 2015;7:2202-2208. [PMID: 26380045 PMCID: PMC4561774 DOI: 10.4254/wjh.v7.i19.2202] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 08/14/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023]  Open
54
Characterization of Hepatitis C Virus Recombination in Cameroon by Use of Nonspecific Next-Generation Sequencing. J Clin Microbiol 2015. [PMID: 26202126 PMCID: PMC4572555 DOI: 10.1128/jcm.00483-15] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
55
Moss WN, Steitz JA. In silico discovery and modeling of non-coding RNA structure in viruses. Methods 2015;91:48-56. [PMID: 26116541 DOI: 10.1016/j.ymeth.2015.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/17/2015] [Accepted: 06/22/2015] [Indexed: 11/30/2022]  Open
56
Mutso M, Nikonov A, Pihlak A, Žusinaite E, Viru L, Selyutina A, Reintamm T, Kelve M, Saarma M, Karelson M, Merits A. RNA Interference-Guided Targeting of Hepatitis C Virus Replication with Antisense Locked Nucleic Acid-Based Oligonucleotides Containing 8-oxo-dG Modifications. PLoS One 2015;10:e0128686. [PMID: 26039055 PMCID: PMC4454572 DOI: 10.1371/journal.pone.0128686] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 04/29/2015] [Indexed: 12/23/2022]  Open
57
Rima BK. Nucleotide sequence conservation in paramyxoviruses; the concept of codon constellation. J Gen Virol 2015;96:939-955. [DOI: 10.1099/vir.0.070789-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
58
Garmann RF, Gopal A, Athavale SS, Knobler CM, Gelbart WM, Harvey SC. Visualizing the global secondary structure of a viral RNA genome with cryo-electron microscopy. RNA (NEW YORK, N.Y.) 2015;21:877-886. [PMID: 25752599 PMCID: PMC4408795 DOI: 10.1261/rna.047506.114] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 12/30/2014] [Indexed: 05/29/2023]
59
Highly divergent hepaciviruses from African cattle. J Virol 2015;89:5876-82. [PMID: 25787289 DOI: 10.1128/jvi.00393-15] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 03/13/2015] [Indexed: 12/30/2022]  Open
60
Functionally conserved architecture of hepatitis C virus RNA genomes. Proc Natl Acad Sci U S A 2015;112:3692-7. [PMID: 25775547 DOI: 10.1073/pnas.1416266112] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
61
Tuplin A, Struthers M, Cook J, Bentley K, Evans DJ. Inhibition of HCV translation by disrupting the structure and interactions of the viral CRE and 3' X-tail. Nucleic Acids Res 2015;43:2914-26. [PMID: 25712095 PMCID: PMC4357731 DOI: 10.1093/nar/gkv142] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
62
Tuplin A. Diverse roles and interactions of RNA structures during the replication of positive-stranded RNA viruses of humans and animals. J Gen Virol 2015;96:1497-503. [PMID: 25626680 DOI: 10.1099/vir.0.000066] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
63
New insights into the evolutionary rate of hepatitis B virus at different biological scales. J Virol 2015;89:3512-22. [PMID: 25589664 DOI: 10.1128/jvi.03131-14] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
64
Sagan SM, Chahal J, Sarnow P. cis-Acting RNA elements in the hepatitis C virus RNA genome. Virus Res 2015;206:90-8. [PMID: 25576644 DOI: 10.1016/j.virusres.2014.12.029] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Revised: 12/12/2014] [Accepted: 12/24/2014] [Indexed: 12/22/2022]
65
Firth AE. Mapping overlapping functional elements embedded within the protein-coding regions of RNA viruses. Nucleic Acids Res 2014;42:12425-39. [PMID: 25326325 PMCID: PMC4227794 DOI: 10.1093/nar/gku981] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2014] [Revised: 09/20/2014] [Accepted: 10/04/2014] [Indexed: 12/29/2022]  Open
66
Gould N, Hendy O, Papamichail D. Computational tools and algorithms for designing customized synthetic genes. Front Bioeng Biotechnol 2014;2:41. [PMID: 25340050 PMCID: PMC4186344 DOI: 10.3389/fbioe.2014.00041] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 09/16/2014] [Indexed: 11/13/2022]  Open
67
Cloete LJ, Tanov EP, Muhire BM, Martin DP, Harkins GW. The influence of secondary structure, selection and recombination on rubella virus nucleotide substitution rate estimates. Virol J 2014;11:166. [PMID: 25224517 PMCID: PMC4175276 DOI: 10.1186/1743-422x-11-166] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 09/11/2014] [Indexed: 01/21/2023]  Open
68
Candresse T, Filloux D, Muhire B, Julian C, Galzi S, Fort G, Bernardo P, Daugrois JH, Fernandez E, Martin DP, Varsani A, Roumagnac P. Appearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine context. PLoS One 2014;9:e102945. [PMID: 25061967 PMCID: PMC4111361 DOI: 10.1371/journal.pone.0102945] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 06/24/2014] [Indexed: 12/21/2022]  Open
69
Gultyaev AP, Tsyganov-Bodounov A, Spronken MIJ, van der Kooij S, Fouchier RAM, Olsthoorn RCL. RNA structural constraints in the evolution of the influenza A virus genome NP segment. RNA Biol 2014;11:942-52. [PMID: 25180940 DOI: 10.4161/rna.29730] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
70
Lowry K, Woodman A, Cook J, Evans DJ. Recombination in enteroviruses is a biphasic replicative process involving the generation of greater-than genome length 'imprecise' intermediates. PLoS Pathog 2014;10:e1004191. [PMID: 24945141 PMCID: PMC4055744 DOI: 10.1371/journal.ppat.1004191] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 05/02/2014] [Indexed: 01/29/2023]  Open
71
Romero-López C, Berzal-Herranz A. Structure-function relationship in viral RNA genomes: The case of hepatitis C virus. World J Med Genet 2014;4:6-18. [DOI: 10.5496/wjmg.v4.i2.6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 01/23/2014] [Accepted: 04/03/2014] [Indexed: 02/06/2023]  Open
72
Witteveldt J, Blundell R, Maarleveld JJ, McFadden N, Evans DJ, Simmonds P. The influence of viral RNA secondary structure on interactions with innate host cell defences. Nucleic Acids Res 2014;42:3314-29. [PMID: 24335283 PMCID: PMC3950689 DOI: 10.1093/nar/gkt1291] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 12/21/2022]  Open
73
Atkinson NJ, Witteveldt J, Evans DJ, Simmonds P. The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication. Nucleic Acids Res 2014;42:4527-45. [PMID: 24470146 PMCID: PMC3985648 DOI: 10.1093/nar/gku075] [Citation(s) in RCA: 137] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
74
Evidence of pervasive biologically functional secondary structures within the genomes of eukaryotic single-stranded DNA viruses. J Virol 2013;88:1972-89. [PMID: 24284329 DOI: 10.1128/jvi.03031-13] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]  Open
75
Analysis of serine codon conservation reveals diverse phenotypic constraints on hepatitis C virus glycoprotein evolution. J Virol 2013;88:667-78. [PMID: 24173227 DOI: 10.1128/jvi.01745-13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
76
Priore SF, Moss WN, Turner DH. Influenza B virus has global ordered RNA structure in (+) and (-) strands but relatively less stable predicted RNA folding free energy than allowed by the encoded protein sequence. BMC Res Notes 2013;6:330. [PMID: 23958134 PMCID: PMC3765861 DOI: 10.1186/1756-0500-6-330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 07/03/2013] [Indexed: 12/03/2022]  Open
77
Moss WN, Steitz JA. Genome-wide analyses of Epstein-Barr virus reveal conserved RNA structures and a novel stable intronic sequence RNA. BMC Genomics 2013;14:543. [PMID: 23937650 PMCID: PMC3751371 DOI: 10.1186/1471-2164-14-543] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 08/07/2013] [Indexed: 02/08/2023]  Open
78
González-Candelas F, Bracho MA, Wróbel B, Moya A. Molecular evolution in court: analysis of a large hepatitis C virus outbreak from an evolving source. BMC Biol 2013;11:76. [PMID: 23870105 PMCID: PMC3717074 DOI: 10.1186/1741-7007-11-76] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Accepted: 05/24/2013] [Indexed: 02/07/2023]  Open
79
McFadden N, Arias A, Dry I, Bailey D, Witteveldt J, Evans DJ, Goodfellow I, Simmonds P. Influence of genome-scale RNA structure disruption on the replication of murine norovirus--similar replication kinetics in cell culture but attenuation of viral fitness in vivo. Nucleic Acids Res 2013;41:6316-31. [PMID: 23630317 PMCID: PMC3695492 DOI: 10.1093/nar/gkt334] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 01/08/2023]  Open
80
Simon-Loriere E, Holmes EC, Pagán I. The effect of gene overlapping on the rate of RNA virus evolution. Mol Biol Evol 2013;30:1916-28. [PMID: 23686658 DOI: 10.1093/molbev/mst094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
81
Archer EJ, Simpson MA, Watts NJ, O'Kane R, Wang B, Erie DA, McPherson A, Weeks KM. Long-range architecture in a viral RNA genome. Biochemistry 2013;52:3182-90. [PMID: 23614526 DOI: 10.1021/bi4001535] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
82
Identification of rodent homologs of hepatitis C virus and pegiviruses. mBio 2013;4:e00216-13. [PMID: 23572554 PMCID: PMC3622934 DOI: 10.1128/mbio.00216-13] [Citation(s) in RCA: 157] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]  Open
83
Knoepfel SA, Berkhout B. On the role of four small hairpins in the HIV-1 RNA genome. RNA Biol 2013;10:540-52. [PMID: 23535706 PMCID: PMC3710360 DOI: 10.4161/rna.24133] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]  Open
84
Monk SL, Simmonds P, Matthews KR. A short bifunctional element operates to positively or negatively regulate ESAG9 expression in different developmental forms of Trypanosoma brucei. J Cell Sci 2013;126:2294-304. [PMID: 23524999 DOI: 10.1242/jcs.126011] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
85
Systematic analysis of enhancer and critical cis-acting RNA elements in the protein-encoding region of the hepatitis C virus genome. J Virol 2013;87:5678-96. [PMID: 23487449 DOI: 10.1128/jvi.00840-12] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]  Open
86
Belalov IS, Lukashev AN. Causes and implications of codon usage bias in RNA viruses. PLoS One 2013;8:e56642. [PMID: 23451064 PMCID: PMC3581513 DOI: 10.1371/journal.pone.0056642] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2012] [Accepted: 01/15/2013] [Indexed: 12/03/2022]  Open
87
Lisowski L, Elazar M, Chu K, Glenn JS, Kay MA. The anti-genomic (negative) strand of Hepatitis C Virus is not targetable by shRNA. Nucleic Acids Res 2013;41:3688-98. [PMID: 23396439 PMCID: PMC3616702 DOI: 10.1093/nar/gkt068] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
88
Marton S, Romero-López C, Berzal-Herranz A. RNA aptamer-mediated interference of HCV replication by targeting the CRE-5BSL3.2 domain. J Viral Hepat 2013;20:103-112. [PMID: 23301545 DOI: 10.1111/j.1365-2893.2012.01629.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
89
Palmer BA, Moreau I, Levis J, Harty C, Crosbie O, Kenny-Walsh E, Fanning LJ. Insertion and recombination events at hypervariable region 1 over 9.6 years of hepatitis C virus chronic infection. J Gen Virol 2012;93:2614-2624. [PMID: 22971825 DOI: 10.1099/vir.0.045344-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]  Open
90
Ng TFF, Marine R, Wang C, Simmonds P, Kapusinszky B, Bodhidatta L, Oderinde BS, Wommack KE, Delwart E. High variety of known and new RNA and DNA viruses of diverse origins in untreated sewage. J Virol 2012;86:12161-75. [PMID: 22933275 PMCID: PMC3486453 DOI: 10.1128/jvi.00869-12] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 08/22/2012] [Indexed: 12/17/2022]  Open
91
Lukashev AN, Drexler JF, Belalov IS, Eschbach-Bludau M, Baumgarte S, Drosten C. Genetic variation and recombination in Aichi virus. J Gen Virol 2012;93:1226-1235. [DOI: 10.1099/vir.0.040311-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]  Open
92
Tuplin A, Struthers M, Simmonds P, Evans DJ. A twist in the tail: SHAPE mapping of long-range interactions and structural rearrangements of RNA elements involved in HCV replication. Nucleic Acids Res 2012;40:6908-21. [PMID: 22561372 PMCID: PMC3413155 DOI: 10.1093/nar/gks370] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
93
Priore SF, Moss WN, Turner DH. Influenza A virus coding regions exhibit host-specific global ordered RNA structure. PLoS One 2012;7:e35989. [PMID: 22558296 PMCID: PMC3338493 DOI: 10.1371/journal.pone.0035989] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/25/2012] [Indexed: 12/26/2022]  Open
94
Serology-enabled discovery of genetically diverse hepaciviruses in a new host. J Virol 2012;86:6171-8. [PMID: 22491452 DOI: 10.1128/jvi.00250-12] [Citation(s) in RCA: 205] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
95
Sharp PM, Simmonds P. Evaluating the evidence for virus/host co-evolution. Curr Opin Virol 2011;1:436-41. [DOI: 10.1016/j.coviro.2011.10.018] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2011] [Accepted: 10/19/2011] [Indexed: 01/04/2023]
96
Pang PS, Elazar M, Pham EA, Glenn JS. Simplified RNA secondary structure mapping by automation of SHAPE data analysis. Nucleic Acids Res 2011;39:e151. [PMID: 21965531 PMCID: PMC3239176 DOI: 10.1093/nar/gkr773] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
97
Belshaw R, Sanjuán R, Pybus OG. Viral mutation and substitution: units and levels. Curr Opin Virol 2011;1:430-5. [PMID: 22440847 DOI: 10.1016/j.coviro.2011.08.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Accepted: 08/11/2011] [Indexed: 01/11/2023]
98
Martin DP, Lefeuvre P, Varsani A, Hoareau M, Semegni JY, Dijoux B, Vincent C, Reynaud B, Lett JM. Complex recombination patterns arising during geminivirus coinfections preserve and demarcate biologically important intra-genome interaction networks. PLoS Pathog 2011;7:e1002203. [PMID: 21949649 PMCID: PMC3174254 DOI: 10.1371/journal.ppat.1002203] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Accepted: 06/24/2011] [Indexed: 02/05/2023]  Open
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Semegni JY, Wamalwa M, Gaujoux R, Harkins GW, Gray A, Martin DP. NASP: a parallel program for identifying evolutionarily conserved nucleic acid secondary structures from nucleotide sequence alignments. ACTA ACUST UNITED AC 2011;27:2443-5. [PMID: 21757466 DOI: 10.1093/bioinformatics/btr417] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Tuplin A, Evans DJ, Buckley A, Jones IM, Gould EA, Gritsun TS. Replication enhancer elements within the open reading frame of tick-borne encephalitis virus and their evolution within the Flavivirus genus. Nucleic Acids Res 2011;39:7034-48. [PMID: 21622960 PMCID: PMC3303483 DOI: 10.1093/nar/gkr237] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]  Open
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