메뉴 건너뛰기




Volumn , Issue PART 2, 2013, Pages 1020-1028

Hierarchically-coupled hidden Markov models for learning kinetic rates from single-molecule data

Author keywords

[No Author keywords available]

Indexed keywords

HIDDEN MARKOV MODELS; LEARNING SYSTEMS;

EID: 84897550050     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper
Times cited : (11)

References (26)
  • 2
    • 34147143884 scopus 로고    scopus 로고
    • DNA looping kinetics analyzed using diffusive hidden Markov model
    • DOI 10.1529/biophysj.107.104828
    • Beausang, J.F., Zurla, C., Manzo, C., Dunlap, D., Finzi, L., and Nelson, P.C. DNA looping kinetics analyzed using diffusive hidden Markov model. Biophys. J., 92(8):L64-6, May 2007. (Pubitemid 46557838)
    • (2007) Biophysical Journal , vol.92 , Issue.8
    • Beausang, J.F.1    Zurla, C.2    Manzo, C.3    Dunlap, D.4    Finzi, L.5    Nelson, P.C.6
  • 3
    • 0011451154 scopus 로고
    • Bayesian Robustness and the Stein Effect
    • June
    • Berger, J. Bayesian Robustness and the Stein Effect. JASA, 77(378):358-368, June 1982.
    • (1982) JASA , vol.77 , Issue.378 , pp. 358-368
    • Berger, J.1
  • 5
    • 50649092124 scopus 로고    scopus 로고
    • Single-molecule studies of protein folding
    • January
    • Borgia, A., Williams, P.M., and Clarke, J. Single-molecule studies of protein folding. Ann. Rev. Biochem., 77:101-25, January 2008.
    • (2008) Ann. Rev. Biochem. , vol.77 , pp. 101-125
    • Borgia, A.1    Williams, P.M.2    Clarke, J.3
  • 6
    • 73449090455 scopus 로고    scopus 로고
    • Learning rates and states from biophysical time series: A Bayesian approach to model selection and single-molecule FRET data
    • December
    • Bronson, J.E., Fei, J., Hofman, J.M., Gonzalez, R.L., and Wiggins, C.H. Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data. Biophys. J., 97(12):3196-205, December 2009.
    • (2009) Biophys. J. , vol.97 , Issue.12 , pp. 3196-3205
    • Bronson, J.E.1    Fei, J.2    Hofman, J.M.3    Gonzalez, R.L.4    Wiggins, C.H.5
  • 7
    • 78049524429 scopus 로고    scopus 로고
    • Graphical models for inferring single molecule dynamics
    • (Suppl 8): January
    • Bronson, J.E., Hofman, J.M., Fei, J., Gonzalez, R.L., and Wiggins, C.H. Graphical models for inferring single molecule dynamics. BMC Bioinf., 11 Suppl 8 (Suppl 8):S2, January 2010.
    • (2010) BMC Bioinf. , vol.11 , Issue.SUPPL. 8
    • Bronson, J.E.1    Hofman, J.M.2    Fei, J.3    Gonzalez, R.L.4    Wiggins, C.H.5
  • 9
    • 0002632234 scopus 로고
    • An introduction to empirical Bayes data analysis
    • Casella, G. An introduction to empirical Bayes data analysis. Am. Statistician, 39(2):83-87, 1985.
    • (1985) Am. Statistician , vol.39 , Issue.2 , pp. 83-87
    • Casella, G.1
  • 10
    • 4043061882 scopus 로고    scopus 로고
    • Variational Bayesian model selection for mixture distributions
    • Corduneanu, Adrian and Bishop, CM. Variational Bayesian model selection for mixture distributions. AISTATS, 2001.
    • (2001) AISTATS
    • Corduneanu, A.1    Bishop, C.M.2
  • 11
    • 33947517676 scopus 로고    scopus 로고
    • A survey of single-molecule techniques in chemical biology
    • DOI 10.1021/cb600342a
    • Cornish, P.V. and Ha, T. A survey of single-molecule techniques in chemical biology. ACS Chem. Biol., 2(1):53-61, January 2007. (Pubitemid 47490242)
    • (2007) ACS Chemical Biology , vol.2 , Issue.1 , pp. 53-61
    • Cornish, P.V.1    Ha, T.2
  • 12
    • 70349470607 scopus 로고    scopus 로고
    • Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation
    • September
    • Fei, J., Bronson, J.E., Hofman, J.M., Srinivas, R.L., Wiggins, C.H., and Gonzalez, R.L. Allosteric collaboration between elongation factor G and the ribosomal L1 stalk directs tRNA movements during translation. Proc. Nat. Acad. Sci. USA, 106(37):15702-7, September 2009.
    • (2009) Proc. Nat. Acad. Sci. USA , vol.106 , Issue.37 , pp. 15702-15707
    • Fei, J.1    Bronson, J.E.2    Hofman, J.M.3    Srinivas, R.L.4    Wiggins, C.H.5    Gonzalez, R.L.6
  • 13
    • 0031268341 scopus 로고    scopus 로고
    • Factorial Hidden Markov Models
    • Ghahramani, Z. and Jordan, M.I. Factorial Hidden Markov Models. Machine Learning, 29(2-3):245-273, 1997. (Pubitemid 127510040)
    • (1997) Machine Learning , vol.29 , Issue.2-3 , pp. 245-273
    • Ghahramani, Z.1    Jordan, M.I.2
  • 14
    • 84857382006 scopus 로고    scopus 로고
    • Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data
    • January
    • Greenfeld, M., Pavlichin, D.S., Mabuchi, H., and Herschlag, D. Single Molecule Analysis Research Tool (SMART): An Integrated Approach for Analyzing Single Molecule Data. PloS One, 7(2):e30024, January 2012.
    • (2012) PloS One , vol.7 , Issue.2
    • Greenfeld, M.1    Pavlichin, D.S.2    Mabuchi, H.3    Herschlag, D.4
  • 15
    • 50649121477 scopus 로고    scopus 로고
    • Advances in single-molecule fluorescence methods for molecular biology
    • January
    • Joo, C., Balci, H., Ishitsuka, Y., Buranachai, C., and Ha, T. Advances in single-molecule fluorescence methods for molecular biology. Ann. Rev. Biochem., 77:51-76, January 2008.
    • (2008) Ann. Rev. Biochem. , vol.77 , pp. 51-76
    • Joo, C.1    Balci, H.2    Ishitsuka, Y.3    Buranachai, C.4    Ha, T.5
  • 16
    • 0033225865 scopus 로고    scopus 로고
    • Introduction to variational methods for graphical models
    • DOI 10.1023/A:1007665907178
    • Jordan, M.I., Ghahramani, Z., and Jaakkola, T.S. An introduction to variational methods for graphical models. Machine Learning, 233:183-233, 1999. (Pubitemid 30544678)
    • (1999) Machine Learning , vol.37 , Issue.2 , pp. 183-233
    • Jordan, M.I.1    Ghahramani, Z.2    Jaakkola, T.S.3    Saul, L.K.4
  • 17
    • 80052029170 scopus 로고
    • Approximate Bayesian inference in conditionally independent hierarchical models (parametric empirical Bayes models)
    • Kass, R.E. and Steffey, D. Approximate Bayesian inference in conditionally independent hierarchical models (parametric empirical Bayes models). JASA, 84(407), 1989.
    • (1989) JASA , vol.84 , Issue.407
    • Kass, R.E.1    Steffey, D.2
  • 18
    • 33746747438 scopus 로고    scopus 로고
    • Analysis of single-molecule FRET trajectories using hidden Markov modeling
    • DOI 10.1529/biophysj.106.082487
    • McKinney, S.A, Joo, C., and Ha, T. Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophys. J., 91(5):1941-51, September 2006. (Pubitemid 44352455)
    • (2006) Biophysical Journal , vol.91 , Issue.5 , pp. 1941-1951
    • McKinney, S.A.1    Joo, C.2    Ha, T.3
  • 20
    • 84950432453 scopus 로고
    • Parametric Empirical Bayes Inference: Theory and Applications
    • March
    • Morris, C.N. Parametric Empirical Bayes Inference: Theory and Applications. JASA, 78(381):47-55, March 1983.
    • (1983) JASA , vol.78 , Issue.381 , pp. 47-55
    • Morris, C.N.1
  • 21
    • 44449087047 scopus 로고    scopus 로고
    • Single-molecule force spectroscopy: Optical tweezers, magnetic tweezers and atomic force microscopy
    • DOI 10.1038/nmeth.1218, PII NMETH.1218
    • Neuman, K.C. and Nagy, A. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat. Methods, 5(6):491-505, June 2008. (Pubitemid 351761756)
    • (2008) Nature Methods , vol.5 , Issue.6 , pp. 491-505
    • Neuman, K.C.1    Nagy, A.2
  • 22
    • 84866478835 scopus 로고    scopus 로고
    • Variational Bayes Analysis of a Photon-Based Hidden Markov Model for Single-Molecule FRET Trajectories
    • September
    • Okamoto, K. and Sako, Y. Variational Bayes Analysis of a Photon-Based Hidden Markov Model for Single-Molecule FRET Trajectories. Biophys. J., 103(6):1315-24, September 2012.
    • (2012) Biophys. J. , vol.103 , Issue.6 , pp. 1315-1324
    • Okamoto, K.1    Sako, Y.2
  • 23
    • 79751527778 scopus 로고    scopus 로고
    • Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor
    • February
    • Sorgenfrei, S., Chiu, C-Y., Gonzalez, R.L., Yu, Y-J., Kim, P., Nuckolls, C., and Shepard, K.L. Label-free single-molecule detection of DNA-hybridization kinetics with a carbon nanotube field-effect transistor. Nat. Nanotechnol, 6(2):126-32, February 2011.
    • (2011) Nat. Nanotechnol , vol.6 , Issue.2 , pp. 126-132
    • Sorgenfrei, S.1    Chiu, C.-Y.2    Gonzalez, R.L.3    Yu, Y.-J.4    Kim, P.5    Nuckolls, C.6    Shepard, K.L.7
  • 24
    • 0000169918 scopus 로고
    • Estimation of the Mean of a Multivariate Normal Distribution
    • November
    • Stein, C.M. Estimation of the Mean of a Multivariate Normal Distribution. Ann. Stat., 9(6):1135-1151, November 1981.
    • (1981) Ann. Stat. , vol.9 , Issue.6 , pp. 1135-1151
    • Stein, C.M.1
  • 25
    • 79959655626 scopus 로고    scopus 로고
    • Biological mechanisms, one molecule at a time
    • June
    • Tinoco, I. and Gonzalez, R.L. Biological mechanisms, one molecule at a time. Genes Dev., 25(12):1205-31, June 2011.
    • (2011) Genes Dev. , vol.25 , Issue.12 , pp. 1205-1231
    • Tinoco, I.1    Gonzalez, R.L.2
  • 26
    • 65749118363 scopus 로고    scopus 로고
    • Graphical Models, Exponential Families, and Variational Inference
    • Wainwright, M.J. and Jordan, M.I. Graphical Models, Exponential Families, and Variational Inference. Found. Trends Machine Learning, 1(12):1-305, 2008.
    • (2008) Found. Trends Machine Learning , vol.1 , Issue.12 , pp. 1-305
    • Wainwright, M.J.1    Jordan, M.I.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.