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Volumn 6, Issue , 2014, Pages

Approximate Bayesian inference for complex ecosystems

Author keywords

[No Author keywords available]

Indexed keywords

APPROXIMATE BAYESIAN COMPUTATION; DEMOGRAPHY; ECOLOGY; MATHEMATICAL MODEL; POPULATION BIOLOGY; REVIEW; SYNTHETIC BIOLOGY;

EID: 84904917407     PISSN: None     EISSN: 20517599     Source Type: Journal    
DOI: 10.12703/P6-60     Document Type: Review
Times cited : (14)

References (55)
  • 2
    • 0001620238 scopus 로고
    • Analytical Note on Certain Rhythmic Relations in Organic Systems
    • Lotka AJ: Analytical Note on Certain Rhythmic Relations in Organic Systems. Proc Natl Acad Sci USA 1920, 6:410-5.
    • (1920) Proc Natl Acad Sci USA , vol.6 , pp. 410-415
    • Lotka, A.J.1
  • 3
    • 0006170098 scopus 로고
    • Fluctuations in the abundance of a species considered mathematically
    • Volterra V: Fluctuations in the abundance of a species considered mathematically. Nature 1926, 118:558-60, 1926.
    • (1926) Nature , vol.1926 , Issue.118 , pp. 558-560
    • Volterra, V.1
  • 5
    • 44949242883 scopus 로고    scopus 로고
    • Computational ecology: From the complex to the simple and back
    • Pascual M: Computational ecology: from the complex to the simple and back. PLoS Comput Biol 2005, 1:101-5.
    • (2005) PLoS Comput Biol , vol.1 , pp. 101-105
    • Pascual, M.1
  • 7
    • 19644400040 scopus 로고    scopus 로고
    • Stem-cell niches: It's the ecology, stupid!
    • Powell K: Stem-cell niches: it's the ecology, stupid!. Nature 2005, 435:268-70.
    • (2005) Nature , vol.435 , pp. 268-270
    • Powell, K.1
  • 8
    • 84875708161 scopus 로고    scopus 로고
    • Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled
    • MacLean AL, Lo Celso C, Stumpf MPH: Population dynamics of normal and leukaemia stem cells in the haematopoietic stem cell niche show distinct regimes where leukaemia will be controlled. J R Soc Interface 2013, 10:20120968.
    • (2013) J R Soc Interface , vol.10 , pp. 20120968
    • MacLean, A.L.1    Lo Celso, C.2    Stumpf, M.P.H.3
  • 9
    • 77951683871 scopus 로고    scopus 로고
    • Systemic risk: The dynamics of model banking systems
    • May RM, Arinaminpathy N: Systemic risk: the dynamics of model banking systems. J R Soc Interface 2010, 7:823-38.
    • (2010) J R Soc Interface , vol.7 , pp. 823-838
    • May, R.M.1    Arinaminpathy, N.2
  • 10
    • 78751671623 scopus 로고    scopus 로고
    • Systemic risk in banking ecosystems
    • Haldane AG, May RM: Systemic risk in banking ecosystems. Nature 2011, 469:351-5.
    • (2011) Nature , vol.469 , pp. 351-355
    • Haldane, A.G.1    May, R.M.2
  • 11
    • 0021607939 scopus 로고
    • The complexity and stability of ecosystems
    • Pimm SL: The complexity and stability of ecosystems. Nature 1984, 307:321-26.
    • (1984) Nature , vol.307 , pp. 321-326
    • Pimm, S.L.1
  • 12
    • 0038050538 scopus 로고    scopus 로고
    • Complexity and stability revisited
    • DOI 10.1046/j.1461-0248.2003.00464.x
    • Jansen VAA, Kokkoris GD: Complexity and stability revisited. Ecology Letters 2003, 6:498-502. (Pubitemid 36658663)
    • (2003) Ecology Letters , vol.6 , Issue.6 , pp. 498-502
    • Jansen, V.A.A.1    Kokkoris, G.D.2
  • 13
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • DOI 10.1101/gr.1262503
    • Moles CG, Mendes P, Banga JR: Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 2003, 13:2467-74. (Pubitemid 37428271)
    • (2003) Genome Research , vol.13 , Issue.11 , pp. 2467-2474
    • Moles, C.G.1    Mendes, P.2    Banga, J.R.3
  • 16
    • 84881526872 scopus 로고    scopus 로고
    • Approximate Bayesian computation (ABC) gives exact results under the assumption of model error
    • Wilkinson RD: Approximate Bayesian computation (ABC) gives exact results under the assumption of model error. Stat Appl Genet Mol Biol 2013, 12:129-41.
    • (2013) Stat Appl Genet Mol Biol , vol.12 , pp. 129-141
    • Wilkinson, R.D.1
  • 17
    • 0001135785 scopus 로고
    • Sampling and Bayes' inference in scientific modelling and robustness
    • Box G: Sampling and Bayes' inference in scientific modelling and robustness. J R Stat Soc Series B Stat Methodol 1980 143:383-430.
    • (1980) J R Stat Soc Series B Stat Methodol , vol.143 , pp. 383-430
    • Box, G.1
  • 20
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont MA, Zhang W, Balding DJ: Approximate Bayesian computation in population genetics. Genetics 2002, 162:2025-35. (Pubitemid 36114682)
    • (2002) Genetics , vol.162 , Issue.4 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 22
    • 58149142997 scopus 로고    scopus 로고
    • Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems
    • Toni T, Welch D, Strelkowa N, Ipsen A, Stumpf Michael P H: Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J R Soc Interface 2009, 6:187-202.
    • (2009) J R Soc Interface , vol.6 , pp. 187-202
    • Toni, T.1    Welch, D.2    Strelkowa, N.3    Ipsen, A.4    Stumpf Michael, P.H.5
  • 24
    • 33646483919 scopus 로고    scopus 로고
    • Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA
    • Chan YL, Anderson, Christian N K, Hadly EA: Bayesian estimation of the timing and severity of a population bottleneck from ancient DNA. PLoS Genet 2006, 2:e59.
    • (2006) PLoS Genet , vol.2
    • Chan, Y.L.1    Anderson, C.N.K.2    Hadly, E.A.3
  • 25
    • 34548065664 scopus 로고    scopus 로고
    • msBayes: Pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation
    • Hickerson MJ, Stahl E, Takebayashi N: msBayes: pipeline for testing comparative phylogeographic histories using hierarchical approximate Bayesian computation. BMC Bioinformatics 2007, 8:268.
    • (2007) BMC Bioinformatics , vol.8 , pp. 268
    • Hickerson, M.J.1    Stahl, E.2    Takebayashi, N.3
  • 26
    • 70350136774 scopus 로고    scopus 로고
    • Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood
    • Wegmann D, Leuenberger C, Excoffier L: Efficient approximate Bayesian computation coupled with Markov chain Monte Carlo without likelihood. Genetics 2009, 182:1207-18.
    • (2009) Genetics , vol.182 , pp. 1207-1218
    • Wegmann, D.1    Leuenberger, C.2    Excoffier, L.3
  • 27
    • 84866551549 scopus 로고    scopus 로고
    • Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA
    • Rosvold J, Røed KH, Hufthammer AK, Andersen R, Stenøien HK: Reconstructing the history of a fragmented and heavily exploited red deer population using ancient and contemporary DNA. BMC Evol Biol 2012, 12:191.
    • (2012) BMC Evol Biol , vol.12 , pp. 191
    • Rosvold, J.1    Røed, K.H.2    Hufthammer, A.K.3    Andersen, R.4    Stenøien, H.K.5
  • 29
    • 77957728670 scopus 로고    scopus 로고
    • On optimal selection of summary statistics for approximate Bayesian computation
    • Nunes MA, Balding DJ: On optimal selection of summary statistics for approximate Bayesian computation. Stat Appl Genet Mol Biol 2010, 9:Article34.
    • (2010) Stat Appl Genet Mol Biol , vol.9 , pp. 34
    • Nunes, M.A.1    Balding, D.J.2
  • 30
    • 80053490318 scopus 로고    scopus 로고
    • Choice of summary statistic weights in approximate Bayesian computation
    • Jung H, Marjoram P: Choice of summary statistic weights in approximate Bayesian computation. Stat Appl Genet Mol Biol 2011, 10.
    • (2011) Stat Appl Genet Mol Biol , pp. 10
    • Jung, H.1    Marjoram, P.2
  • 31
    • 84861111043 scopus 로고    scopus 로고
    • Constructing summary statistics for approximate Bayesian computation: Semi-automatic approximate Bayesian computation
    • Fearnhead P, Prangle D: Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation. J R Stat Soc Series B Stat Methodol 2012, 74:419-74.
    • (2012) J R Stat Soc Series B Stat Methodol , vol.74 , pp. 419-474
    • Fearnhead, P.1    Prangle, D.2
  • 32
    • 84869057921 scopus 로고    scopus 로고
    • A novel approach for choosing summary statistics in approximate Bayesian computation
    • Aeschbacher S, Beaumont MA, Futschik A: A novel approach for choosing summary statistics in approximate Bayesian computation. Genetics 2012, 192:1027-47.
    • (2012) Genetics , vol.192 , pp. 1027-1047
    • Aeschbacher, S.1    Beaumont, M.A.2    Futschik, A.3
  • 33
    • 84888158892 scopus 로고    scopus 로고
    • Kernel approximate Bayesian computation in population genetic inferences
    • Nakagome S, Fukumizu K, Mano S: Kernel approximate Bayesian computation in population genetic inferences. Stat Appl Genet Mol Biol 2013, 12:667-78.
    • (2013) Stat Appl Genet Mol Biol , vol.12 , pp. 667-678
    • Nakagome, S.1    Fukumizu, K.2    Mano, S.3
  • 35
    • 84893308174 scopus 로고    scopus 로고
    • A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation
    • Liepe J, Kirk P, Filippi S, Toni T, Barnes CP, Stumpf Michael P H: A framework for parameter estimation and model selection from experimental data in systems biology using approximate Bayesian computation. Nat Protoc 2014, 9:439-56.
    • (2014) Nat Protoc , vol.9 , pp. 439-456
    • Liepe, J.1    Kirk, P.2    Filippi, S.3    Toni, T.4    Barnes, C.P.5    Stumpf Michael, P.H.6
  • 36
    • 84888166132 scopus 로고    scopus 로고
    • Optimizing thresholdschedules for sequential approximate Bayesian computation: Applications to molecular systems
    • Silk D, Filippi S, Stumpf Michael P H: Optimizing thresholdschedules for sequential approximate Bayesian computation: applications to molecular systems. Stat Appl Genet Mol Biol 2013, 12:603-18.
    • (2013) Stat Appl Genet Mol Biol , vol.12 , pp. 603-618
    • Silk, D.1    Filippi, S.2    Stumpf Michael, P.H.3
  • 37
    • 84879208026 scopus 로고    scopus 로고
    • On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo
    • Filippi S, Barnes CP, Cornebise J, Stumpf Michael P H: On optimality of kernels for approximate Bayesian computation using sequential Monte Carlo. Stat Appl Genet Mol Biol 2013, 12:87-107.
    • (2013) Stat Appl Genet Mol Biol , vol.12 , pp. 87-107
    • Filippi, S.1    Barnes, C.P.2    Cornebise, J.3    Stumpf Michael, P.H.4
  • 38
    • 75249088572 scopus 로고    scopus 로고
    • Simulation-based model selection for dynamical systems in systems and population biology
    • Toni T, Stumpf Michael P H: Simulation-based model selection for dynamical systems in systems and population biology. Bioinformatics 2010, 26:104-10.
    • (2010) Bioinformatics , vol.26 , pp. 104-110
    • Toni, T.1    Stumpf Michael, P.H.2
  • 39
    • 74249110200 scopus 로고    scopus 로고
    • Bayesian computation and model selection without likelihoods
    • Leuenberger C, Wegmann D: Bayesian computation and model selection without likelihoods. Genetics 2010, 184:243-52.
    • (2010) Genetics , vol.184 , pp. 243-252
    • Leuenberger, C.1    Wegmann, D.2
  • 40
    • 78149423210 scopus 로고    scopus 로고
    • Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure
    • Peter BM, Wegmann D, Excoffier L: Distinguishing between population bottleneck and population subdivision by a Bayesian model choice procedure. Mol Ecol 2010, 19:4648-60.
    • (2010) Mol Ecol , vol.19 , pp. 4648-4660
    • Peter, B.M.1    Wegmann, D.2    Excoffier, L.3
  • 42
    • 84865301018 scopus 로고    scopus 로고
    • Estimation of demo-genetic model probabilities with Approximate Bayesian Computation using linear discriminant analysis on summary statistics
    • Estoup A, Lombaert E, Marin J, Guillemaud T, Pudlo P, Robert CP, Cornuet J: Estimation of demo-genetic model probabilities with Approximate Bayesian Computation using linear discriminant analysis on summary statistics. Mol Ecol Resour 2012, 12:846-55.
    • (2012) Mol Ecol Resour , vol.12 , pp. 846-855
    • Estoup, A.1    Lombaert, E.2    Marin, J.3    Guillemaud, T.4    Pudlo, P.5    Robert, C.P.6    Cornuet, J.7
  • 43
    • 84866249585 scopus 로고    scopus 로고
    • Graph spectral analysis of protein interaction network evolution
    • Thorne T, Stumpf Michael P H: Graph spectral analysis of protein interaction network evolution. J R Soc Interface 2012, 9:2653-66.
    • (2012) J R Soc Interface , vol.9 , pp. 2653-2666
    • Thorne, T.1    Stumpf Michael, P.H.2
  • 44
    • 84872013113 scopus 로고    scopus 로고
    • Phylodynamic inference and model assessment with approximate bayesian computation: Influenza as a case study
    • Ratmann O, Donker G, Meijer A, Fraser C, Koelle K: Phylodynamic inference and model assessment with approximate bayesian computation: influenza as a case study. PLoS Comput Biol 2012, 8:e1002835.
    • (2012) PLoS Comput Biol , vol.8
    • Ratmann, O.1    Donker, G.2    Meijer, A.3    Fraser, C.4    Koelle, K.5
  • 45
    • 84876681820 scopus 로고    scopus 로고
    • Climate change and the spread of vector-borne diseases: Using approximate Bayesian computation to compare invasion scenarios for the bluetongue virus vector Culicoides imicola in Italy
    • Mardulyn P, Goffredo M, Conte A, Hendrickx G, Meiswinkel R, Balenghien T, Sghaier S, Lohr Y, Gilbert M: Climate change and the spread of vector-borne diseases: using approximate Bayesian computation to compare invasion scenarios for the bluetongue virus vector Culicoides imicola in Italy. Mol Ecol 2013, 22:2456-66.
    • (2013) Mol Ecol , vol.22 , pp. 2456-2466
    • Mardulyn, P.1    Goffredo, M.2    Conte, A.3    Hendrickx, G.4    Meiswinkel, R.5    Balenghien, T.6    Sghaier, S.7    Lohr, Y.8    Gilbert, M.9
  • 47
    • 80053069153 scopus 로고    scopus 로고
    • Lack of confidence in approximate Bayesian computation model choice
    • Robert CP, Cornuet J, Marin J, Pillai NS: Lack of confidence in approximate Bayesian computation model choice. Proc Natl Acad Sci USA 2011, 108:15112-7.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 15112-15117
    • Robert, C.P.1    Cornuet, J.2    Marin, J.3    Pillai, N.S.4
  • 48
    • 84867996819 scopus 로고    scopus 로고
    • Considerate approaches to constructing summary statistics for ABC model selection
    • Barnes CP, Filippi S, Stumpf MPH, Thorne T: Considerate approaches to constructing summary statistics for ABC model selection. Statistics and Computing 2012, 22:1181-97.
    • (2012) Statistics and Computing , vol.22 , pp. 1181-1197
    • Barnes, C.P.1    Filippi, S.2    Stumpf, M.P.H.3    Thorne, T.4
  • 50
    • 84890309642 scopus 로고    scopus 로고
    • Bayesian experimental design for models with intractable likelihoods
    • Drovandi CC, Pettitt AN: Bayesian experimental design for models with intractable likelihoods. Biometrics 2013, 69:937-48.
    • (2013) Biometrics , vol.69 , pp. 937-948
    • Drovandi, C.C.1    Pettitt, A.N.2
  • 51
    • 67649819681 scopus 로고    scopus 로고
    • Model criticism based on likelihood-free inference, with an application to protein network evolution
    • Ratmann O, Andrieu C, Wiuf C, Richardson S: Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc Natl Acad Sci USA 2009, 106:10576-81.
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 10576-10581
    • Ratmann, O.1    Andrieu, C.2    Wiuf, C.3    Richardson, S.4
  • 55
    • 79956002338 scopus 로고    scopus 로고
    • Assessing wastewater micropollutant loads with approximate Bayesian computations
    • Rieckermann J, Anta J, Scheidegger A, Ort C: Assessing wastewater micropollutant loads with approximate Bayesian computations. Environ Sci Technol 2011, 45:4399-406.
    • (2011) Environ Sci Technol , vol.45 , pp. 4399-4406
    • Rieckermann, J.1    Anta, J.2    Scheidegger, A.3    Ort, C.4


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