메뉴 건너뛰기




Volumn 11, Issue 101, 2014, Pages

Sampling through time and phylodynamic inference with coalescent and birth-death models

Author keywords

Coalescent; Infectious diseases; Phylodynamics

Indexed keywords

ESTIMATION; SAMPLING;

EID: 84928911008     PISSN: 17425689     EISSN: 17425662     Source Type: Journal    
DOI: 10.1098/rsif.2014.0945     Document Type: Review
Times cited : (54)

References (33)
  • 2
    • 84903717811 scopus 로고    scopus 로고
    • Bayesian inference of infectious disease transmission from whole genome sequence data
    • Didelot X, Gardy J, Colijn C. 2014 Bayesian inference of infectious disease transmission from whole genome sequence data. Mol. Biol. Evol. 31, 1869-1879. (doi:10.1093/molbev/msu121)
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 1869-1879
    • Didelot, X.1    Gardy, J.2    Colijn, C.3
  • 3
    • 84055176877 scopus 로고    scopus 로고
    • Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data
    • Ypma R, Bataille A, Stegeman A, Koch G, Wallinga J, Van Ballegooijen W. 2011 Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data. Proc. R. Soc. B 279, 444-450. (doi:10.1098/rspb.2011.0913)
    • (2011) Proc. R. Soc. B , vol.279 , pp. 444-450
    • Ypma, R.1    Bataille, A.2    Stegeman, A.3    Koch, G.4    Wallinga, J.5    Van Ballegooijen, W.6
  • 4
    • 84865323065 scopus 로고    scopus 로고
    • Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with wholegenome sequencing
    • Snitkin ES, Zelazny AM, Thomas PJ, Stock F, Henderson DK, Palmore TN, Segre JA, NISC Comparative Sequencing Program Group. 2012 Tracking a hospital outbreak of carbapenem-resistant Klebsiella pneumoniae with wholegenome sequencing. Sci. Transl. Med. 4, 148ra116. (doi:10.1126/scitranslmed.3004129)
    • (2012) Sci. Transl. Med. , vol.4 , pp. 148ra116
    • Snitkin, E.S.1    Zelazny, A.M.2    Thomas, P.J.3    Stock, F.4    Henderson, D.K.5    Palmore, T.N.6    Segre, J.A.7
  • 5
    • 33845412091 scopus 로고
    • The coalescent
    • Kingman JFC. 1982 The coalescent. Stoch. Process. Appl. 13, 235-248. (doi:10.1016/0304-4149(82)90011-4)
    • (1982) Stoch. Process. Appl. , vol.13 , pp. 235-248
    • Kingman, J.F.C.1
  • 6
    • 85020718366 scopus 로고    scopus 로고
    • Greenwood Village, CO: Roberts & Company Publishers
    • Wakeley J. 2009 Coalescent theory: an introduction, vol. 1. Greenwood Village, CO: Roberts & Company Publishers.
    • (2009) Coalescent Theory: An Introduction , vol.1
    • Wakeley, J.1
  • 7
    • 0029818407 scopus 로고    scopus 로고
    • Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference
    • Rannala B, Yang Z. 1996 Probability distribution of molecular evolutionary trees: a new method of phylogenetic inference. J. Mol. Evol. 43, 304-311. (doi:10.1007/BF02338839)
    • (1996) J. Mol. Evol. , vol.43 , pp. 304-311
    • Rannala, B.1    Yang, Z.2
  • 8
    • 0002024701 scopus 로고
    • On the generalized 'birth-anddeath' process
    • Kendall DG. 1948 On the generalized 'birth-anddeath' process. Ann. Math. Stat. 19, 1-15. (doi:10.1214/aoms/1177730285)
    • (1948) Ann. Math. Stat. , vol.19 , pp. 1-15
    • Kendall, D.G.1
  • 9
    • 77958152206 scopus 로고    scopus 로고
    • Sampling-through-time in birth-death trees
    • Stadler T. 2010 Sampling-through-time in birth-death trees. J. Theor. Biol. 267, 396-404. (doi:10.1016/j.jtbi.2010.09.010)
    • (2010) J. Theor. Biol. , vol.267 , pp. 396-404
    • Stadler, T.1
  • 10
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • Rosenberg NA, Nordborg M. 2002 Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 3, 380-390. (doi:10.1038/nrg795)
    • (2002) Nat. Rev. Genet. , vol.3 , pp. 380-390
    • Rosenberg, N.A.1    Nordborg, M.2
  • 11
    • 77950806408 scopus 로고    scopus 로고
    • New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0
    • Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010 New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst. Biol. 59, 307-321. (doi:10.1093/sysbio/syq010)
    • (2010) Syst. Biol. , vol.59 , pp. 307-321
    • Guindon, S.1    Dufayard, J.F.2    Lefort, V.3    Anisimova, M.4    Hordijk, W.5    Gascuel, O.6
  • 12
    • 84864530626 scopus 로고    scopus 로고
    • Bayesian phylogenetics with BEAUti and the BEAST 1.7
    • Drummond AJ, Suchard MA, Xie D, Rambaut A. 2012 Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol. Biol. Evol. 29, 1969-1973. (doi:10.1093/molbev/mss075)
    • (2012) Mol. Biol. Evol. , vol.29 , pp. 1969-1973
    • Drummond, A.J.1    Suchard, M.A.2    Xie, D.3    Rambaut, A.4
  • 13
    • 0033911330 scopus 로고    scopus 로고
    • An integrated framework for the inference of viral population history from reconstructed genealogies
    • Pybus OG, Rambaut A, Harvey PH. 2000 An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics 155, 1429-1437.
    • (2000) Genetics , vol.155 , pp. 1429-1437
    • Pybus, O.G.1    Rambaut, A.2    Harvey, P.H.3
  • 14
    • 0035211479 scopus 로고    scopus 로고
    • Exploring the demographic history of DNA sequences using the generalized e plot
    • Strimmer K, Pybus OG. 2001 Exploring the demographic history of DNA sequences using the generalized e plot. Mol. Biol. Evol. 18, 2298-2305. (doi:10.1093/oxfordjournals.molbev.a003776)
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2298-2305
    • Strimmer, K.1    Pybus, O.G.2
  • 15
    • 14344259235 scopus 로고    scopus 로고
    • Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo
    • Opgen-Rhein R, Fahrmeir L, Strimmer K. 2005 Inference of demographic history from genealogical trees using reversible jump Markov chain Monte Carlo. BMC Evol. Biol. 5, 6. (doi:10.1186/1471-2148-5-6)
    • (2005) BMC Evol. Biol. , vol.5 , pp. 6
    • Opgen-Rhein, R.1    Fahrmeir, L.2    Strimmer, K.3
  • 16
    • 0029559462 scopus 로고
    • Coalescents and genealogical structure under neutrality
    • Donnelly P, Tavare S. 1995 Coalescents and genealogical structure under neutrality. Annu. Rev. Genet. 29, 401-421. (doi:10.1146/annurev.ge.29.120195.002153)
    • (1995) Annu. Rev. Genet. , vol.29 , pp. 401-421
    • Donnelly, P.1    Tavare, S.2
  • 17
    • 84855467207 scopus 로고    scopus 로고
    • Complex population dynamics and the coalescent under neutrality
    • Volz EM. 2012 Complex population dynamics and the coalescent under neutrality. Genetics 190, 187-201. (doi:10.1534/genetics.111.134627)
    • (2012) Genetics , vol.190 , pp. 187-201
    • Volz, E.M.1
  • 18
    • 80052336720 scopus 로고    scopus 로고
    • Inference for nonlinear epidemiological models using genealogies and time series
    • Rasmussen DA, Ratmann O, Koelle K. 2011 Inference for nonlinear epidemiological models using genealogies and time series. PLoS Comp. Biol. 7, e1002136. (doi:10.1371/journal.pcbi.1002136)
    • (2011) PLoS Comp. Biol. , vol.7 , pp. e1002136
    • Rasmussen, D.A.1    Ratmann, O.2    Koelle, K.3
  • 19
    • 84901339626 scopus 로고    scopus 로고
    • Phylodynamic inference for structured epidemiological models
    • Rasmussen DA, Volz EM, Koelle K. 2014 Phylodynamic inference for structured epidemiological models. PLoS Comput. Biol. 10, e1003570. (doi:10.1371/journal.pcbi.1003570)
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003570
    • Rasmussen, D.A.1    Volz, E.M.2    Koelle, K.3
  • 21
    • 48049107322 scopus 로고    scopus 로고
    • The conditioned reconstructed process
    • Gernhard T. 2008 The conditioned reconstructed process. J. Theor. Biol. 253, 769-778. (doi:10.1016/j.jtbi.2008.04.005)
    • (2008) J. Theor. Biol. , vol.253 , pp. 769-778
    • Gernhard, T.1
  • 22
    • 84871983084 scopus 로고    scopus 로고
    • Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV)
    • Stadler T, Kühnert D, Bonhoeffer S, Drummond AJ. 2013 Birth-death skyline plot reveals temporal changes of epidemic spread in HIV and hepatitis C virus (HCV). Proc. Natl Acad. Sci. USA 110, 228-233. (doi:10.1073/pnas.1207965110)
    • (2013) Proc. Natl Acad. Sci. USA , vol.110 , pp. 228-233
    • Stadler, T.1    Kühnert, D.2    Bonhoeffer, S.3    Drummond, A.J.4
  • 23
    • 84880494351 scopus 로고    scopus 로고
    • Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods
    • Stadler T, Bonhoeffer S. 2013 Uncovering epidemiological dynamics in heterogeneous host populations using phylogenetic methods. Phil. Trans. R. Soc. B 368, 20120198. (doi:10.1098/rstb.2012.0198)
    • (2013) Phil. Trans. R. Soc. B , vol.368 , pp. 20120198
    • Stadler, T.1    Bonhoeffer, S.2
  • 25
    • 84877761231 scopus 로고    scopus 로고
    • A stochastic simulator of birth-death master equations with application to phylodynamics
    • Vaughan TG, Drummond AJ. 2013 A stochastic simulator of birth-death master equations with application to phylodynamics. Mol. Biol. Evol. 30, 1480-1493. (doi:10.1093/molbev/mst057)
    • (2013) Mol. Biol. Evol. , vol.30 , pp. 1480-1493
    • Vaughan, T.G.1    Drummond, A.J.2
  • 26
    • 84891749257 scopus 로고    scopus 로고
    • Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission
    • Leventhal GE, Günthard HF, Bonhoeffer S, Stadler T. 2014 Using an epidemiological model for phylogenetic inference reveals density dependence in HIV transmission. Mol. Biol. Evol. 31, 6-17. (doi:10.1093/molbev/mst172)
    • (2014) Mol. Biol. Evol. , vol.31 , pp. 6-17
    • Leventhal, G.E.1    Günthard, H.F.2    Bonhoeffer, S.3    Stadler, T.4
  • 27
    • 77954337309 scopus 로고    scopus 로고
    • Viral phylodynamics and the search for an effective number of infections
    • Frost SD, Volz EM. 2010 Viral phylodynamics and the search for an effective number of infections. Phil. Trans. R. Soc. B 365, 1879-1890. (doi:10.1098/rstb.2010.0060)
    • (2010) Phil. Trans. R. Soc. B , vol.365 , pp. 1879-1890
    • Frost, S.D.1    Volz, E.M.2
  • 28
    • 79955371587 scopus 로고    scopus 로고
    • Recovering population parameters from a single gene genealogy: An unbiased estimator of the growth rate
    • Maruvka YE, Shnerb NM, Bar-Yam Y, Wakeley J. 2011 Recovering population parameters from a single gene genealogy: an unbiased estimator of the growth rate. Mol. Biol. Evol. 28, 1617-1631. (doi:10.1093/molbev/msq331)
    • (2011) Mol. Biol. Evol. , vol.28 , pp. 1617-1631
    • Maruvka, Y.E.1    Shnerb, N.M.2    Bar-Yam, Y.3    Wakeley, J.4
  • 29
    • 84896541526 scopus 로고    scopus 로고
    • Theory and applications of a deterministic approximation to the coalescent model
    • Jewett EM, Rosenberg NA. 2014 Theory and applications of a deterministic approximation to the coalescent model. Theor. Popul. Biol. 93, 14-29. (doi:10.1016/j.tpb.2013.12.007)
    • (2014) Theor. Popul. Biol. , vol.93 , pp. 14-29
    • Jewett, E.M.1    Rosenberg, N.A.2
  • 30
    • 84879764213 scopus 로고    scopus 로고
    • Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size
    • Chen H, Chen K. 2013 Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. Genetics 194, 721-736. (doi:10.1534/genetics.113.151522)
    • (2013) Genetics , vol.194 , pp. 721-736
    • Chen, H.1    Chen, K.2
  • 32
    • 84896986112 scopus 로고    scopus 로고
    • Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model
    • Kühnert D, Stadler T, Vaughan TG, Drummond AJ. 2014 Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model. J. R. Soc. Interface 11, 20131106. (doi:10.1098/rsif.2013.1106)
    • (2014) J. R. Soc. Interface , vol.11 , pp. 20131106
    • Kühnert, D.1    Stadler, T.2    Vaughan, T.G.3    Drummond, A.J.4
  • 33
    • 80053427855 scopus 로고    scopus 로고
    • Transmission network parameters estimated from HIV sequences for a nationwide epidemic
    • Brown AJL, Lycett SJ, Weinert L, Hughes GJ, Fearnhill E, Dunn DT. 2011 Transmission network parameters estimated from HIV sequences for a nationwide epidemic. J. Infect. Dis. 204, 1463-1469. (doi:10.1093/infdis/jir550)
    • (2011) J. Infect. Dis. , vol.204 , pp. 1463-1469
    • Brown, A.J.L.1    Lycett, S.J.2    Weinert, L.3    Hughes, G.J.4    Fearnhill, E.5    Dunn, D.T.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.