메뉴 건너뛰기




Volumn 8, Issue 9, 2013, Pages

Correction: Bayesian parameter inference by Markov Chain Monte Carlo with hybrid fitness measures: Theory and test in apoptosis signal transduction network (PLoS ONE (2013) 8, 9, (e74178) DOI: 10.1371/journal.pone.0074178);Bayesian Parameter Inference by Markov Chain Monte Carlo with Hybrid Fitness Measures: Theory and Test in Apoptosis Signal Transduction Network

Author keywords

[No Author keywords available]

Indexed keywords

APOPTOTIC PROTEASE ACTIVATING FACTOR 1; CASPASE 3; CASPASE 9;

EID: 84884687789     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0097961     Document Type: Erratum
Times cited : (6)

References (52)
  • 1
    • 33745780500 scopus 로고    scopus 로고
    • Network motifs: structure does not determine function
    • Ingram PJ, Stumpf MP, Stark J, (2006) Network motifs: structure does not determine function. BMC Genomics 7: 108.
    • (2006) BMC Genomics , vol.7 , pp. 108
    • Ingram, P.J.1    Stumpf, M.P.2    Stark, J.3
  • 3
    • 0035892558 scopus 로고    scopus 로고
    • An overview of evolutionary algorithms: practical issues and common pitfalls
    • Whitley D, (2001) An overview of evolutionary algorithms: practical issues and common pitfalls. Information and Software Technology 43: 817-831.
    • (2001) Information and Software Technology , vol.43 , pp. 817-831
    • Whitley, D.1
  • 4
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: a comparison of global optimization methods
    • Moles CG, Mendes P, Banga JR, (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res 13: 2467-2474.
    • (2003) Genome Res , vol.13 , pp. 2467-2474
    • Moles, C.G.1    Mendes, P.2    Banga, J.R.3
  • 5
    • 33846085492 scopus 로고    scopus 로고
    • A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9
    • Zeilinger MN, Farre EM, Taylor SR, Kay SA, Doyle FJ, (2006) A novel computational model of the circadian clock in Arabidopsis that incorporates PRR7 and PRR9. Mol Syst Biol 2: 58.
    • (2006) Mol Syst Biol , vol.2 , pp. 58
    • Zeilinger, M.N.1    Farre, E.M.2    Taylor, S.R.3    Kay, S.A.4    Doyle, F.J.5
  • 8
    • 0032406131 scopus 로고    scopus 로고
    • Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation
    • Mendes P, Kell D, (1998) Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation. Bioinformatics 14: 869-883.
    • (1998) Bioinformatics , vol.14 , pp. 869-883
    • Mendes, P.1    Kell, D.2
  • 10
    • 77956890234 scopus 로고
    • Monte Carlo sampling methods using Markov chains and their applications
    • Hastings WK, (1970) Monte Carlo sampling methods using Markov chains and their applications. Biometrika 57: 97-109.
    • (1970) Biometrika , vol.57 , pp. 97-109
    • Hastings, W.K.1
  • 11
    • 0036964474 scopus 로고    scopus 로고
    • Approximate Bayesian computation in population genetics
    • Beaumont MA, Zhang W, Balding DJ, (2002) Approximate Bayesian computation in population genetics. Genetics 162: 2025-2035.
    • (2002) Genetics , vol.162 , pp. 2025-2035
    • Beaumont, M.A.1    Zhang, W.2    Balding, D.J.3
  • 14
    • 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 MP, (2009) Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J R Soc Interface 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, M.P.5
  • 15
    • 79952110708 scopus 로고    scopus 로고
    • Parameter inference and model selection in signaling pathway models
    • Toni T, Stumpf MP, (2010) Parameter inference and model selection in signaling pathway models. Methods Mol Biol 673: 283-295.
    • (2010) Methods Mol Biol , vol.673 , pp. 283-295
    • Toni, T.1    Stumpf, M.P.2
  • 16
    • 75249088572 scopus 로고    scopus 로고
    • Simulation-based model selection for dynamical systems in systems and population biology
    • Toni T, Stumpf MP, (2010) Simulation-based model selection for dynamical systems in systems and population biology. Bioinformatics 26: 104-110.
    • (2010) Bioinformatics , vol.26 , pp. 104-110
    • Toni, T.1    Stumpf, M.P.2
  • 17
    • 84862188059 scopus 로고    scopus 로고
    • Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection
    • Toni T, Ozaki Y, Kirk P, Kuroda S, Stumpf MP, (2012) Elucidating the in vivo phosphorylation dynamics of the ERK MAP kinase using quantitative proteomics data and Bayesian model selection. Mol Biosyst 8: 1921-1929.
    • (2012) Mol Biosyst , vol.8 , pp. 1921-1929
    • Toni, T.1    Ozaki, Y.2    Kirk, P.3    Kuroda, S.4    Stumpf, M.P.5
  • 19
    • 33749370199 scopus 로고    scopus 로고
    • Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability
    • Legewie S, Bluthgen N, Herzel H, (2006) Mathematical modeling identifies inhibitors of apoptosis as mediators of positive feedback and bistability. PLoS Comput Biol 2: e120.
    • (2006) PLoS Comput Biol , vol.2
    • Legewie, S.1    Bluthgen, N.2    Herzel, H.3
  • 21
    • 84873622581 scopus 로고    scopus 로고
    • Properties of cell death models calibrated and compared using Bayesian approaches
    • Eydgahi H, Chen WW, Muhlich JL, Vitkup D, Tsitsiklis JN, et al. (2013) Properties of cell death models calibrated and compared using Bayesian approaches. Mol Syst Biol 9: 644.
    • (2013) Mol Syst Biol , vol.9 , pp. 644
    • Eydgahi, H.1    Chen, W.W.2    Muhlich, J.L.3    Vitkup, D.4    Tsitsiklis, J.N.5
  • 22
    • 0037376655 scopus 로고    scopus 로고
    • Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
    • Tyson JJ, Chen KC, Novak B, (2003) Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Current Opinion in Cell Biology 15: 221-231.
    • (2003) Current Opinion in Cell Biology , vol.15 , pp. 221-231
    • Tyson, J.J.1    Chen, K.C.2    Novak, B.3
  • 24
    • 56749160113 scopus 로고    scopus 로고
    • Design principles of biochemical oscillators
    • Novak B, Tyson JJ, (2008) Design principles of biochemical oscillators. Nat Rev Mol Cell Biol 9: 981-991.
    • (2008) Nat Rev Mol Cell Biol , vol.9 , pp. 981-991
    • Novak, B.1    Tyson, J.J.2
  • 25
    • 77951681944 scopus 로고    scopus 로고
    • Functional motifs in biochemical reaction networks
    • Tyson JJ, Novak B, (2010) Functional motifs in biochemical reaction networks. Annu Rev Phys Chem 61: 219-240.
    • (2010) Annu Rev Phys Chem , vol.61 , pp. 219-240
    • Tyson, J.J.1    Novak, B.2
  • 26
    • 85038385321 scopus 로고    scopus 로고
    • Likelihood-Free Markov chain Monte Carlo
    • In: Brooks S, Gelman A, Jones G, Meng XL, Chapman & Hall/CRC Press
    • Sisson SA, Fan Y (2011) Likelihood-Free Markov chain Monte Carlo. In: Brooks S, Gelman A, Jones G, Meng XL, Handbook of Markov Chain Monte Carlo: Chapman & Hall/CRC Press. pp 313-335.
    • (2011) Handbook of Markov Chain Monte Carlo , pp. 313-335
    • Sisson, S.A.1    Fan, Y.2
  • 27
    • 31144431501 scopus 로고    scopus 로고
    • Robustness properties of apoptosis models with respect to parameter variations and intrinsic noise
    • Eißing T, Allgöwer F, Bullinger E, (2005) Robustness properties of apoptosis models with respect to parameter variations and intrinsic noise. IEE Proceedings- Systems Biology 152: 221-228.
    • (2005) IEE Proceedings - Systems Biology , vol.152 , pp. 221-228
    • Eißing, T.1    Allgöwer, F.2    Bullinger, E.3
  • 28
    • 32944481448 scopus 로고    scopus 로고
    • Robustness Analysis of the IFN-γ Induced JAK-STAT Signaling Pathway
    • Zi Z, Sun Z, (2005) Robustness Analysis of the IFN-γ Induced JAK-STAT Signaling Pathway. Journal of Computer Science and Technology 20: 491-495.
    • (2005) Journal of Computer Science and Technology , vol.20 , pp. 491-495
    • Zi, Z.1    Sun, Z.2
  • 29
    • 34250350056 scopus 로고    scopus 로고
    • Modeling of the role of a Bax-activation switch in the mitochondrial apoptosis decision
    • Chen C, Cui J, Lu H, Wang R, Zhang S, et al. (2007) Modeling of the role of a Bax-activation switch in the mitochondrial apoptosis decision. Biophys J 92: 4304-4315.
    • (2007) Biophys J , vol.92 , pp. 4304-4315
    • Chen, C.1    Cui, J.2    Lu, H.3    Wang, R.4    Zhang, S.5
  • 30
    • 44849128902 scopus 로고    scopus 로고
    • Two independent positive feedbacks and bistability in the Bcl-2 apoptotic switch
    • Cui J, Chen C, Lu H, Sun T, Shen P, (2008) Two independent positive feedbacks and bistability in the Bcl-2 apoptotic switch. PLoS One 3: e1469.
    • (2008) PLoS One , vol.3
    • Cui, J.1    Chen, C.2    Lu, H.3    Sun, T.4    Shen, P.5
  • 31
    • 67651202705 scopus 로고    scopus 로고
    • Modeling the role of p53 pulses in DNA damage- induced cell death decision
    • Sun T, Chen C, Wu Y, Zhang S, Cui J, et al. (2009) Modeling the role of p53 pulses in DNA damage- induced cell death decision. BMC Bioinformatics 10: 190.
    • (2009) BMC Bioinformatics , vol.10 , pp. 190
    • Sun, T.1    Chen, C.2    Wu, Y.3    Zhang, S.4    Cui, J.5
  • 32
    • 76749131517 scopus 로고    scopus 로고
    • Evaluating bistability of Bax activation switch
    • Sun T, Lin X, Wei Y, Xu Y, Shen P, (2010) Evaluating bistability of Bax activation switch. FEBS Lett 584: 954-960.
    • (2010) FEBS Lett , vol.584 , pp. 954-960
    • Sun, T.1    Lin, X.2    Wei, Y.3    Xu, Y.4    Shen, P.5
  • 33
    • 41549132691 scopus 로고    scopus 로고
    • Quantitative analysis of pathways controlling extrinsic apoptosis in single cells
    • Albeck JG, Burke JM, Aldridge BB, Zhang M, Lauffenburger DA, et al. (2008) Quantitative analysis of pathways controlling extrinsic apoptosis in single cells. Mol Cell 30: 11-25.
    • (2008) Mol Cell , vol.30 , pp. 11-25
    • Albeck, J.G.1    Burke, J.M.2    Aldridge, B.B.3    Zhang, M.4    Lauffenburger, D.A.5
  • 35
    • 4544246088 scopus 로고    scopus 로고
    • Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis
    • Bentele M, Lavrik I, Ulrich M, Stosser S, Heermann DW, et al. (2004) Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J Cell Biol 166: 839-851.
    • (2004) J Cell Biol , vol.166 , pp. 839-851
    • Bentele, M.1    Lavrik, I.2    Ulrich, M.3    Stosser, S.4    Heermann, D.W.5
  • 36
    • 84857066223 scopus 로고    scopus 로고
    • Rigor of cell fate decision by variable p53 pulses and roles of cooperative gene expression by p53
    • Murakami Y, Takada S, (2012) Rigor of cell fate decision by variable p53 pulses and roles of cooperative gene expression by p53. BIOPHYSICS 8: 41-50.
    • (2012) BIOPHYSICS , vol.8 , pp. 41-50
    • Murakami, Y.1    Takada, S.2
  • 37
    • 68949136900 scopus 로고    scopus 로고
    • Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death
    • Zhang T, Brazhnik P, Tyson JJ, (2009) Computational analysis of dynamical responses to the intrinsic pathway of programmed cell death. Biophys J 97: 415-434.
    • (2009) Biophys J , vol.97 , pp. 415-434
    • Zhang, T.1    Brazhnik, P.2    Tyson, J.J.3
  • 39
    • 77957767333 scopus 로고    scopus 로고
    • Coordination between cell cycle progression and cell fate decision by the p53 and E2F1 pathways in response to DNA damage
    • Zhang XP, Liu F, Wang W, (2010) Coordination between cell cycle progression and cell fate decision by the p53 and E2F1 pathways in response to DNA damage. J Biol Chem 285: 31571-31580.
    • (2010) J Biol Chem , vol.285 , pp. 31571-31580
    • Zhang, X.P.1    Liu, F.2    Wang, W.3
  • 40
    • 77957375431 scopus 로고    scopus 로고
    • Coordination of the nuclear and cytoplasmic activities of p53 in response to DNA damage
    • Pu T, Zhang XP, Liu F, Wang W, (2010) Coordination of the nuclear and cytoplasmic activities of p53 in response to DNA damage. Biophys J 99: 1696-1705.
    • (2010) Biophys J , vol.99 , pp. 1696-1705
    • Pu, T.1    Zhang, X.P.2    Liu, F.3    Wang, W.4
  • 41
    • 84861910774 scopus 로고    scopus 로고
    • A two-step mechanism for cell fate decision by coordination of nuclear and mitochondrial p53 activities
    • Tian XJ, Liu F, Zhang XP, Li J, Wang W, (2012) A two-step mechanism for cell fate decision by coordination of nuclear and mitochondrial p53 activities. PLoS One 7: e38164.
    • (2012) PLoS One , vol.7
    • Tian, X.J.1    Liu, F.2    Zhang, X.P.3    Li, J.4    Wang, W.5
  • 42
    • 33846594408 scopus 로고    scopus 로고
    • Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis
    • Zhang T, Brazhnik P, Tyson JJ, (2007) Exploring mechanisms of the DNA-damage response: p53 pulses and their possible relevance to apoptosis. Cell Cycle 6: 85-94.
    • (2007) Cell Cycle , vol.6 , pp. 85-94
    • Zhang, T.1    Brazhnik, P.2    Tyson, J.J.3
  • 43
    • 79959343390 scopus 로고    scopus 로고
    • Two-phase dynamics of p53 in the DNA damage response
    • Zhang XP, Liu F, Wang W, (2011) Two-phase dynamics of p53 in the DNA damage response. Proc Natl Acad Sci U S A 108: 8990-8995.
    • (2011) Proc Natl Acad Sci U S A , vol.108 , pp. 8990-8995
    • Zhang, X.P.1    Liu, F.2    Wang, W.3
  • 44
    • 84861138484 scopus 로고    scopus 로고
    • Regulation of the DNA damage response by p53 cofactors
    • Zhang XP, Liu F, Wang W, (2012) Regulation of the DNA damage response by p53 cofactors. Biophys J 102: 2251-2260.
    • (2012) Biophys J , vol.102 , pp. 2251-2260
    • Zhang, X.P.1    Liu, F.2    Wang, W.3
  • 45
    • 0040298568 scopus 로고    scopus 로고
    • Caspase-3 is required for DNA fragmentation and morphological changes associated with apoptosis
    • Janicke RU, Sprengart ML, Wati MR, Porter AG, (1998) Caspase-3 is required for DNA fragmentation and morphological changes associated with apoptosis. J Biol Chem 273: 9357-9360.
    • (1998) J Biol Chem , vol.273 , pp. 9357-9360
    • Janicke, R.U.1    Sprengart, M.L.2    Wati, M.R.3    Porter, A.G.4
  • 46
    • 0035831473 scopus 로고    scopus 로고
    • Executioner caspase-3, -6, and -7 perform distinct, non-redundant roles during the demolition phase of apoptosis
    • Slee EA, Adrain C, Martin SJ, (2001) Executioner caspase-3,-6, and-7 perform distinct, non-redundant roles during the demolition phase of apoptosis. J Biol Chem 276: 7320-7326.
    • (2001) J Biol Chem , vol.276 , pp. 7320-7326
    • Slee, E.A.1    Adrain, C.2    Martin, S.J.3
  • 47
    • 0032724653 scopus 로고    scopus 로고
    • Caspase-3 is the primary activator of apoptotic DNA fragmentation via DNA fragmentation factor-45/inhibitor of caspase-activated DNase inactivation
    • Wolf BB, Schuler M, Echeverri F, Green DR, (1999) Caspase-3 is the primary activator of apoptotic DNA fragmentation via DNA fragmentation factor-45/inhibitor of caspase-activated DNase inactivation. J Biol Chem 274: 30651-30656.
    • (1999) J Biol Chem , vol.274 , pp. 30651-30656
    • Wolf, B.B.1    Schuler, M.2    Echeverri, F.3    Green, D.R.4
  • 48
    • 79952635820 scopus 로고    scopus 로고
    • Measuring and modeling apoptosis in single cells
    • Spencer SL, Sorger PK, (2011) Measuring and modeling apoptosis in single cells. Cell 144: 926-939.
    • (2011) Cell , vol.144 , pp. 926-939
    • Spencer, S.L.1    Sorger, P.K.2
  • 49
    • 0034978467 scopus 로고    scopus 로고
    • Log-normal Distributions across the Sciences: Keys and Clues
    • Limpert E, Stahel WA, Abbt M, (2001) Log-normal Distributions across the Sciences: Keys and Clues. BioScience 51: 341-352.
    • (2001) BioScience , vol.51 , pp. 341-352
    • Limpert, E.1    Stahel, W.A.2    Abbt, M.3
  • 50
    • 0035831019 scopus 로고    scopus 로고
    • Structural basis for the inhibition of caspase-3 by XIAP
    • Riedl SJ, Renatus M, Schwarzenbacher R, Zhou Q, Sun C, et al. (2001) Structural basis for the inhibition of caspase-3 by XIAP. Cell 104: 791-800.
    • (2001) Cell , vol.104 , pp. 791-800
    • Riedl, S.J.1    Renatus, M.2    Schwarzenbacher, R.3    Zhou, Q.4    Sun, C.5
  • 51
    • 0036088471 scopus 로고    scopus 로고
    • IAP proteins: blocking the road to death's door
    • Salvesen GS, Duckett CS, (2002) IAP proteins: blocking the road to death's door. Nat Rev Mol Cell Biol 3: 401-410.
    • (2002) Nat Rev Mol Cell Biol , vol.3 , pp. 401-410
    • Salvesen, G.S.1    Duckett, C.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.