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For: Bielejec F, Lemey P, Baele G, Rambaut A, Suchard MA. Inferring heterogeneous evolutionary processes through time: from sequence substitution to phylogeography. Syst Biol 2014;63:493-504. [PMID: 24627184 PMCID: PMC4055869 DOI: 10.1093/sysbio/syu015] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
1
Parino F, Gustani-Buss E, Bedford T, Suchard MA, Trovão NS, Rambaut A, Colizza V, Poletto C, Lemey P. Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation. PNAS NEXUS 2025;4:pgae561. [PMID: 39737444 PMCID: PMC11683419 DOI: 10.1093/pnasnexus/pgae561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 11/21/2024] [Indexed: 01/01/2025]
2
Arias JS. Phylogenetic Biogeography Inference Using Dynamic Paleogeography Models and Explicit Geographic Ranges. Syst Biol 2024;73:995-1014. [PMID: 39177659 DOI: 10.1093/sysbio/syae051] [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: 10/20/2023] [Revised: 08/15/2024] [Accepted: 08/20/2024] [Indexed: 08/24/2024]  Open
3
Li YT, Ko HY, Hughes J, Liu MT, Lin YL, Hampson K, Brunker K. From emergence to endemicity of highly pathogenic H5 avian influenza viruses in Taiwan. Nat Commun 2024;15:9348. [PMID: 39472594 PMCID: PMC11522503 DOI: 10.1038/s41467-024-53816-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 10/22/2024] [Indexed: 11/02/2024]  Open
4
Clement AM, Cloutier R, Lee MSY, King B, Vanhaesebroucke O, Bradshaw CJA, Dutel H, Trinajstic K, Long JA. A Late Devonian coelacanth reconfigures actinistian phylogeny, disparity, and evolutionary dynamics. Nat Commun 2024;15:7529. [PMID: 39266502 PMCID: PMC11392942 DOI: 10.1038/s41467-024-51238-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 08/02/2024] [Indexed: 09/14/2024]  Open
5
Magee AF, Holbrook AJ, Pekar JE, Caviedes-Solis IW, Matsen IV FA, Baele G, Wertheim JO, Ji X, Lemey P, Suchard MA. Random-Effects Substitution Models for Phylogenetics via Scalable Gradient Approximations. Syst Biol 2024;73:562-578. [PMID: 38712512 PMCID: PMC11498053 DOI: 10.1093/sysbio/syae019] [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: 03/24/2023] [Revised: 02/26/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]  Open
6
Langedijk AC, Vrancken B, Lebbink RJ, Wilkins D, Kelly EJ, Baraldi E, Mascareñas de Los Santos AH, Danilenko DM, Choi EH, Palomino MA, Chi H, Keller C, Cohen R, Papenburg J, Pernica J, Greenough A, Richmond P, Martinón-Torres F, Heikkinen T, Stein RT, Hosoya M, Nunes MC, Verwey C, Evers A, Kragten-Tabatabaie L, Suchard MA, Kosakovsky Pond SL, Poletto C, Colizza V, Lemey P, Bont LJ. The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus. Nat Commun 2024;15:3083. [PMID: 38600104 PMCID: PMC11006891 DOI: 10.1038/s41467-024-47118-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 03/14/2024] [Indexed: 04/12/2024]  Open
7
Parino F, Gustani-Buss E, Bedford T, Suchard MA, Trovão NS, Rambaut A, Colizza V, Poletto C, Lemey P. Integrating dynamical modeling and phylogeographic inference to characterize global influenza circulation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.14.24303719. [PMID: 38559244 PMCID: PMC10980132 DOI: 10.1101/2024.03.14.24303719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
8
Gräf T, Martinez AA, Bello G, Dellicour S, Lemey P, Colizza V, Mazzoli M, Poletto C, Cardoso VLO, da Silva AF, Motta FC, Resende PC, Siqueira MM, Franco L, Gresh L, Gabastou JM, Rodriguez A, Vicari A, Aldighieri S, Mendez-Rico J, Leite JA. Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean. Nat Commun 2024;15:1837. [PMID: 38418815 PMCID: PMC10902334 DOI: 10.1038/s41467-024-46143-9] [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: 10/11/2023] [Accepted: 02/15/2024] [Indexed: 03/02/2024]  Open
9
Yang Q, Wang B, Lemey P, Dong L, Mu T, Wiebe RA, Guo F, Trovão NS, Park SW, Lewis N, Tsui JLH, Bajaj S, Cheng Y, Yang L, Haba Y, Li B, Zhang G, Pybus OG, Tian H, Grenfell B. Synchrony of Bird Migration with Global Dispersal of Avian Influenza Reveals Exposed Bird Orders. Nat Commun 2024;15:1126. [PMID: 38321046 PMCID: PMC10847442 DOI: 10.1038/s41467-024-45462-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 01/23/2024] [Indexed: 02/08/2024]  Open
10
Goldberg EE, Lundgren EJ, Romero-Severson EO, Leitner T. Inferring Viral Transmission Time from Phylogenies for Known Transmission Pairs. Mol Biol Evol 2024;41:msad282. [PMID: 38149995 PMCID: PMC10776241 DOI: 10.1093/molbev/msad282] [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: 09/12/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 12/28/2023]  Open
11
Guimarães Fabreti L, Höhna S. Nucleotide Substitution Model Selection Is Not Necessary for Bayesian Inference of Phylogeny With Well-Behaved Priors. Syst Biol 2023;72:1418-1432. [PMID: 37455495 DOI: 10.1093/sysbio/syad041] [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: 02/17/2023] [Revised: 06/02/2023] [Accepted: 07/02/2023] [Indexed: 07/18/2023]  Open
12
Goldberg EE, Lundgren EJ, Romero-Severson EO, Leitner T. Inferring viral transmission time from phylogenies for known transmission pairs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.12.557404. [PMID: 37745490 PMCID: PMC10515827 DOI: 10.1101/2023.09.12.557404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
13
Ramirez-Mata AS, Ostrov D, Salemi M, Marini S, Magalis BR. Machine Learning Prediction and Phyloanatomic Modeling of Viral Neuroadaptive Signatures in the Macaque Model of HIV-Mediated Neuropathology. Microbiol Spectr 2023;11:e0308622. [PMID: 36847516 PMCID: PMC10100676 DOI: 10.1128/spectrum.03086-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 02/06/2023] [Indexed: 03/01/2023]  Open
14
Zhang G, Li B, Raghwani J, Vrancken B, Jia R, Hill SC, Fournié G, Cheng Y, Yang Q, Wang Y, Wang Z, Dong L, Pybus OG, Tian H. Bidirectional Movement of Emerging H5N8 Avian Influenza Viruses Between Europe and Asia via Migratory Birds Since Early 2020. Mol Biol Evol 2023;40:msad019. [PMID: 36703230 PMCID: PMC9922686 DOI: 10.1093/molbev/msad019] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/22/2022] [Accepted: 11/28/2022] [Indexed: 01/28/2023]  Open
15
Salis AT, Bray SCE, Lee MSY, Heiniger H, Barnett R, Burns JA, Doronichev V, Fedje D, Golovanova L, Harington CR, Hockett B, Kosintsev P, Lai X, Mackie Q, Vasiliev S, Weinstock J, Yamaguchi N, Meachen JA, Cooper A, Mitchell KJ. Lions and brown bears colonized North America in multiple synchronous waves of dispersal across the Bering Land Bridge. Mol Ecol 2022;31:6407-6421. [PMID: 34748674 DOI: 10.1111/mec.16267] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 01/13/2023]
16
Rahman S, Hasan M, Alam MS, Uddin KMM, Moni S, Rahman M. The evolutionary footprint of influenza A subtype H3N2 strains in Bangladesh: implication of vaccine strain selection. Sci Rep 2022;12:16186. [PMID: 36171388 PMCID: PMC9519982 DOI: 10.1038/s41598-022-20179-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 09/09/2022] [Indexed: 11/09/2022]  Open
17
Gao J, May MR, Rannala B, Moore BR. New Phylogenetic Models Incorporating Interval-Specific Dispersal Dynamics Improve Inference of Disease Spread. Mol Biol Evol 2022;39:msac159. [PMID: 35861314 PMCID: PMC9384482 DOI: 10.1093/molbev/msac159] [Citation(s) in RCA: 1] [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] [Indexed: 12/02/2022]  Open
18
Cross-reactive immunity potentially drives global oscillation and opposed alternation patterns of seasonal influenza A viruses. Sci Rep 2022;12:8883. [PMID: 35614123 PMCID: PMC9131982 DOI: 10.1038/s41598-022-08233-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 03/02/2022] [Indexed: 11/08/2022]  Open
19
Dellicour S, Lemey P, Suchard MA, Gilbert M, Baele G. Accommodating sampling location uncertainty in continuous phylogeography. Virus Evol 2022;8:veac041. [PMID: 35795297 PMCID: PMC9248920 DOI: 10.1093/ve/veac041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 04/22/2022] [Accepted: 05/18/2022] [Indexed: 02/01/2023]  Open
20
Cornuault J, Sanmartín I. A road map for phylogenetic models of species trees. Mol Phylogenet Evol 2022;173:107483. [DOI: 10.1016/j.ympev.2022.107483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/09/2022] [Accepted: 04/05/2022] [Indexed: 10/18/2022]
21
He WT, Bollen N, Xu Y, Zhao J, Dellicour S, Yan Z, Gong W, Zhang C, Zhang L, Lu M, Lai A, Suchard MA, Ji X, Tu C, Lemey P, Baele G, Su S. Phylogeography reveals association between swine trade and the spread of porcine epidemic diarrhea virus in China and across the world. Mol Biol Evol 2021;39:6482749. [PMID: 34951645 PMCID: PMC8826572 DOI: 10.1093/molbev/msab364] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
22
Hackel J, Sanmartín I. Modelling the tempo and mode of lineage dispersal. Trends Ecol Evol 2021;36:1102-1112. [PMID: 34462154 DOI: 10.1016/j.tree.2021.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/09/2021] [Accepted: 07/19/2021] [Indexed: 11/16/2022]
23
Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Oude Munnink BB, Koopmans M, Sadilek A, Lai S, Tatem AJ, Baele G, Suchard MA, Dellicour S. Untangling introductions and persistence in COVID-19 resurgence in Europe. Nature 2021;595:713-717. [PMID: 34192736 PMCID: PMC8324533 DOI: 10.1038/s41586-021-03754-2] [Citation(s) in RCA: 122] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/22/2021] [Indexed: 11/09/2022]
24
Lemey P, Ruktanonchai N, Hong SL, Colizza V, Poletto C, Van den Broeck F, Gill MS, Ji X, Levasseur A, Sadilek A, Lai S, Tatem AJ, Baele G, Suchard MA, Dellicour S. SARS-CoV-2 European resurgence foretold: interplay of introductions and persistence by leveraging genomic and mobility data. RESEARCH SQUARE 2021:rs.3.rs-208849. [PMID: 33594355 PMCID: PMC7885927 DOI: 10.21203/rs.3.rs-208849/v1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
25
Worobey M, Pekar J, Larsen BB, Nelson MI, Hill V, Joy JB, Rambaut A, Suchard MA, Wertheim JO, Lemey P. The emergence of SARS-CoV-2 in Europe and North America. Science 2020;370:564-570. [PMID: 32912998 PMCID: PMC7810038 DOI: 10.1126/science.abc8169] [Citation(s) in RCA: 278] [Impact Index Per Article: 55.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
26
Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nat Commun 2020;11:5110. [PMID: 33037213 PMCID: PMC7547076 DOI: 10.1038/s41467-020-18877-9] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022]  Open
27
Landis M, Edwards EJ, Donoghue MJ. Modeling Phylogenetic Biome Shifts on a Planet with a Past. Syst Biol 2020;70:86-107. [PMID: 32514540 DOI: 10.1093/sysbio/syaa045] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]  Open
28
Kasson PM. Infectious Disease Research in the Era of Big Data. Annu Rev Biomed Data Sci 2020. [DOI: 10.1146/annurev-biodatasci-121219-025722] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
29
Allicock OM, Sahadeo N, Lemey P, Auguste AJ, Suchard MA, Rambaut A, Carrington CVF. Determinants of dengue virus dispersal in the Americas. Virus Evol 2020;6:veaa074. [PMID: 33408877 PMCID: PMC7772473 DOI: 10.1093/ve/veaa074] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
30
Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165464. [PMID: 32596695 PMCID: PMC7315996 DOI: 10.1101/2020.06.22.165464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
31
Membrebe JV, Suchard MA, Rambaut A, Baele G, Lemey P. Bayesian Inference of Evolutionary Histories under Time-Dependent Substitution Rates. Mol Biol Evol 2020;36:1793-1803. [PMID: 31004175 PMCID: PMC6657730 DOI: 10.1093/molbev/msz094] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
32
Hicks JT, Lee DH, Duvvuri VR, Kim Torchetti M, Swayne DE, Bahl J. Agricultural and geographic factors shaped the North American 2015 highly pathogenic avian influenza H5N2 outbreak. PLoS Pathog 2020;16:e1007857. [PMID: 31961906 PMCID: PMC7004387 DOI: 10.1371/journal.ppat.1007857] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 02/06/2020] [Accepted: 01/04/2020] [Indexed: 11/18/2022]  Open
33
Müller NF, Dudas G, Stadler T. Inferring time-dependent migration and coalescence patterns from genetic sequence and predictor data in structured populations. Virus Evol 2019;5:vez030. [PMID: 31428459 PMCID: PMC6693038 DOI: 10.1093/ve/vez030] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]  Open
34
Yang J, Müller NF, Bouckaert R, Xu B, Drummond AJ. Bayesian phylodynamics of avian influenza A virus H9N2 in Asia with time-dependent predictors of migration. PLoS Comput Biol 2019;15:e1007189. [PMID: 31386651 PMCID: PMC6684064 DOI: 10.1371/journal.pcbi.1007189] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Accepted: 06/17/2019] [Indexed: 11/25/2022]  Open
35
Reconstruction of the Genetic History and the Current Spread of HIV-1 Subtype A in Germany. J Virol 2019;93:JVI.02238-18. [PMID: 30944175 DOI: 10.1128/jvi.02238-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Accepted: 03/13/2019] [Indexed: 12/15/2022]  Open
36
Ali A, Melcher U. Modeling of Mutational Events in the Evolution of Viruses. Viruses 2019;11:v11050418. [PMID: 31060293 PMCID: PMC6563203 DOI: 10.3390/v11050418] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/27/2019] [Accepted: 05/02/2019] [Indexed: 11/24/2022]  Open
37
Dellicour S, Vrancken B, Trovão NS, Fargette D, Lemey P. On the importance of negative controls in viral landscape phylogeography. Virus Evol 2018;4:vey023. [PMID: 30151241 PMCID: PMC6101606 DOI: 10.1093/ve/vey023] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
38
Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018;5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
39
Dellicour S, Baele G, Dudas G, Faria NR, Pybus OG, Suchard MA, Rambaut A, Lemey P. Phylodynamic assessment of intervention strategies for the West African Ebola virus outbreak. Nat Commun 2018;9:2222. [PMID: 29884821 PMCID: PMC5993714 DOI: 10.1038/s41467-018-03763-2] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 03/12/2018] [Indexed: 01/25/2023]  Open
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Brunker K, Lemey P, Marston DA, Fooks AR, Lugelo A, Ngeleja C, Hampson K, Biek R. Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs. Mol Ecol 2018;27:773-788. [PMID: 29274171 PMCID: PMC5900915 DOI: 10.1111/mec.14470] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 11/15/2017] [Accepted: 11/20/2017] [Indexed: 12/24/2022]
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King B, Qiao T, Lee MSY, Zhu M, Long JA. Bayesian Morphological Clock Methods Resurrect Placoderm Monophyly and Reveal Rapid Early Evolution in Jawed Vertebrates. Syst Biol 2018;66:499-516. [PMID: 27920231 DOI: 10.1093/sysbio/syw107] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/18/2016] [Indexed: 11/13/2022]  Open
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Molecular epidemiology reveals the role of war in the spread of HIV in Ukraine. Proc Natl Acad Sci U S A 2018;115:1051-1056. [PMID: 29339468 DOI: 10.1073/pnas.1701447115] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
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Troupin C, Picard-Meyer E, Dellicour S, Casademont I, Kergoat L, Lepelletier A, Dacheux L, Baele G, Monchâtre-Leroy E, Cliquet F, Lemey P, Bourhy H. Host Genetic Variation Does Not Determine Spatio-Temporal Patterns of European Bat 1 Lyssavirus. Genome Biol Evol 2017;9:3202-3213. [PMID: 29165566 PMCID: PMC5721339 DOI: 10.1093/gbe/evx236] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2017] [Indexed: 12/22/2022]  Open
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The evolution of seasonal influenza viruses. Nat Rev Microbiol 2017;16:47-60. [DOI: 10.1038/nrmicro.2017.118] [Citation(s) in RCA: 470] [Impact Index Per Article: 58.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Jacquot M, Nomikou K, Palmarini M, Mertens P, Biek R. Bluetongue virus spread in Europe is a consequence of climatic, landscape and vertebrate host factors as revealed by phylogeographic inference. Proc Biol Sci 2017;284:20170919. [PMID: 29021180 PMCID: PMC5647287 DOI: 10.1098/rspb.2017.0919] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/08/2017] [Indexed: 01/13/2023]  Open
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Hölzer M, Marz M. Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral". Adv Virus Res 2017;99:233-257. [PMID: 29029728 PMCID: PMC7172532 DOI: 10.1016/bs.aivir.2017.08.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Andrews SM, Rowland-Jones S. Recent advances in understanding HIV evolution. F1000Res 2017;6:597. [PMID: 28529718 PMCID: PMC5414815 DOI: 10.12688/f1000research.10876.1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/24/2017] [Indexed: 11/20/2022]  Open
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Dudas G, Carvalho LM, Bedford T, Tatem AJ, Baele G, Faria NR, Park DJ, Ladner JT, Arias A, Asogun D, Bielejec F, Caddy SL, Cotten M, D’Ambrozio J, Dellicour S, Di Caro A, Diclaro J, Duraffour S, Elmore MJ, Fakoli LS, Faye O, Gilbert ML, Gevao SM, Gire S, Gladden-Young A, Gnirke A, Goba A, Grant DS, Haagmans BL, Hiscox JA, Jah U, Kargbo B, Kugelman JR, Liu D, Lu J, Malboeuf CM, Mate S, Matthews DA, Matranga CB, Meredith LW, Qu J, Quick J, Pas SD, Phan MVT, Pollakis G, Reusken CB, Sanchez-Lockhart M, Schaffner SF, Schieffelin JS, Sealfon RS, Simon-Loriere E, Smits SL, Stoecker K, Thorne L, Tobin EA, Vandi MA, Watson SJ, West K, Whitmer S, Wiley MR, Winnicki SM, Wohl S, Wölfel R, Yozwiak NL, Andersen KG, Blyden SO, Bolay F, Carroll M, Dahn B, Diallo B, Formenty P, Fraser C, Gao GF, Garry RF, Goodfellow I, Günther S, Happi CT, Holmes EC, Kargbo B, Keïta S, Kellam P, Koopmans MPG, Kuhn JH, Loman NJ, Magassouba N, Naidoo D, Nichol ST, Nyenswah T, Palacios G, Pybus OG, Sabeti PC, Sall A, Ströher U, Wurie I, Suchard MA, Lemey P, Rambaut A. Virus genomes reveal factors that spread and sustained the Ebola epidemic. Nature 2017;544:309-315. [PMID: 28405027 PMCID: PMC5712493 DOI: 10.1038/nature22040] [Citation(s) in RCA: 273] [Impact Index Per Article: 34.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Accepted: 03/02/2017] [Indexed: 01/03/2023]
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Landis MJ. Biogeographic Dating of Speciation Times Using Paleogeographically Informed Processes. Syst Biol 2017;66:128-144. [PMID: 27155009 PMCID: PMC5837510 DOI: 10.1093/sysbio/syw040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 04/28/2016] [Indexed: 11/13/2022]  Open
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Silvestro D, Zizka A, Bacon CD, Cascales-Miñana B, Salamin N, Antonelli A. Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data. Philos Trans R Soc Lond B Biol Sci 2016;371:20150225. [PMID: 26977065 PMCID: PMC4810818 DOI: 10.1098/rstb.2015.0225] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]  Open
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