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For: Twarock R, Leonov G, Stockley PG. Hamiltonian path analysis of viral genomes. Nat Commun 2018;9:2021. [PMID: 29789600 PMCID: PMC5964074 DOI: 10.1038/s41467-018-03713-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 03/02/2018] [Indexed: 12/25/2022]  Open
Number Cited by Other Article(s)
1
Neil C, Newman J, Stonehouse NJ, Rowlands DJ, Belsham GJ, Tuthill TJ. The pseudoknot region and poly-(C) tract comprise an essential RNA packaging signal for assembly of foot-and-mouth disease virus. PLoS Pathog 2024;20:e1012283. [PMID: 39715215 PMCID: PMC11734982 DOI: 10.1371/journal.ppat.1012283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 01/15/2025] [Accepted: 12/04/2024] [Indexed: 12/25/2024]  Open
2
Bukina V, Božič A. Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA. Biophys J 2024;123:3397-3407. [PMID: 39118324 PMCID: PMC11480767 DOI: 10.1016/j.bpj.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/17/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]  Open
3
Twarock R, Towers GJ, Stockley PG. Molecular frustration: a hypothesis for regulation of viral infections. Trends Microbiol 2024;32:17-26. [PMID: 37507296 DOI: 10.1016/j.tim.2023.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
4
Sung PY, Zhou Y, Kao CC, Aburigh AA, Routh A, Roy P. A multidisciplinary approach to the identification of the protein-RNA connectome in double-stranded RNA virus capsids. Nucleic Acids Res 2023;51:5210-5227. [PMID: 37070191 PMCID: PMC10250232 DOI: 10.1093/nar/gkad274] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023]  Open
5
Chandler-Bostock R, Bingham RJ, Clark S, Scott AJP, Wroblewski E, Barker A, White SJ, Dykeman EC, Mata CP, Bohon J, Farquhar E, Twarock R, Stockley PG. Genome-regulated Assembly of a ssRNA Virus May Also Prepare It for Infection. J Mol Biol 2022;434:167797. [PMID: 35998704 DOI: 10.1016/j.jmb.2022.167797] [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: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/15/2022] [Indexed: 11/17/2022]
6
Adlhart M, Poetsch F, Hlevnjak M, Hoogmoed M, Polyansky A, Zagrovic B. Compositional complementarity between genomic RNA and coat proteins in positive-sense single-stranded RNA viruses. Nucleic Acids Res 2022;50:4054-4067. [PMID: 35357492 PMCID: PMC9023274 DOI: 10.1093/nar/gkac202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/29/2022] [Indexed: 02/02/2023]  Open
7
Mizrahi I, Bruinsma R, Rudnick J. Packaging contests between viral RNA molecules and kinetic selectivity. PLoS Comput Biol 2022;18:e1009913. [PMID: 35363785 PMCID: PMC9022832 DOI: 10.1371/journal.pcbi.1009913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 04/21/2022] [Accepted: 02/09/2022] [Indexed: 11/18/2022]  Open
8
Finding Hamiltonian and Longest (s,t)-Paths of C-Shaped Supergrid Graphs in Linear Time. ALGORITHMS 2022. [DOI: 10.3390/a15020061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
9
Biela AP, Naskalska A, Fatehi F, Twarock R, Heddle JG. Programmable polymorphism of a virus-like particle. COMMUNICATIONS MATERIALS 2022;3:7. [PMID: 35284827 PMCID: PMC7612486 DOI: 10.1038/s43246-022-00229-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
10
Dechant PP, He YH. Machine-learning a virus assembly fitness landscape. PLoS One 2021;16:e0250227. [PMID: 33951035 PMCID: PMC8099058 DOI: 10.1371/journal.pone.0250227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 04/01/2021] [Indexed: 02/05/2023]  Open
11
Bruinsma RF, Wuite GJL, Roos WH. Physics of viral dynamics. NATURE REVIEWS. PHYSICS 2021;3:76-91. [PMID: 33728406 PMCID: PMC7802615 DOI: 10.1038/s42254-020-00267-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 11/20/2020] [Indexed: 05/12/2023]
12
Blaas D. Individual subunits of a rhinovirus causing common cold exhibit largely different protein-RNA contact site conformations. Commun Biol 2020;3:537. [PMID: 32994533 PMCID: PMC7525237 DOI: 10.1038/s42003-020-01269-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 08/27/2020] [Indexed: 11/09/2022]  Open
13
Bellomo N, Bingham R, Chaplain MAJ, Dosi G, Forni G, Knopoff DA, Lowengrub J, Twarock R, Virgillito ME. A multiscale model of virus pandemic: Heterogeneous interactive entities in a globally connected world. MATHEMATICAL MODELS & METHODS IN APPLIED SCIENCES : M3AS 2020;30:1591-1651. [PMID: 35309741 PMCID: PMC8932953 DOI: 10.1142/s0218202520500323] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
14
Buzón P, Maity S, Roos WH. Physical virology: From virus self-assembly to particle mechanics. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2020;12:e1613. [PMID: 31960585 PMCID: PMC7317356 DOI: 10.1002/wnan.1613] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 10/01/2019] [Accepted: 12/11/2019] [Indexed: 12/19/2022]
15
Twarock R, Luque A. Structural puzzles in virology solved with an overarching icosahedral design principle. Nat Commun 2019;10:4414. [PMID: 31562316 PMCID: PMC6765026 DOI: 10.1038/s41467-019-12367-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 09/03/2019] [Indexed: 11/09/2022]  Open
16
Indelicato G, Cermelli P, Twarock R. A coarse-grained model of the expansion of the human rhinovirus 2 capsid reveals insights in genome release. J R Soc Interface 2019;16:20190044. [PMID: 31409237 PMCID: PMC6731498 DOI: 10.1098/rsif.2019.0044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 07/11/2019] [Indexed: 12/02/2022]  Open
17
Curk T, Farrell JD, Dobnikar J, Podgornik R. Spontaneous Domain Formation in Spherically Confined Elastic Filaments. PHYSICAL REVIEW LETTERS 2019;123:047801. [PMID: 31491267 DOI: 10.1103/physrevlett.123.047801] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Indexed: 06/10/2023]
18
Twarock R, Stockley PG. RNA-Mediated Virus Assembly: Mechanisms and Consequences for Viral Evolution and Therapy. Annu Rev Biophys 2019;48:495-514. [PMID: 30951648 PMCID: PMC7612295 DOI: 10.1146/annurev-biophys-052118-115611] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
19
Twarock R, Bingham RJ, Dykeman EC, Stockley PG. A modelling paradigm for RNA virus assembly. Curr Opin Virol 2018;31:74-81. [PMID: 30078702 PMCID: PMC6281560 DOI: 10.1016/j.coviro.2018.07.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Accepted: 07/04/2018] [Indexed: 12/14/2022]
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