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Items: 1 to 20 of 125

1.

Graphical models for inferring single molecule dynamics.

Bronson JE, Hofman JM, Fei J, Gonzalez RL Jr, Wiggins CH.

BMC Bioinformatics. 2010 Oct 26;11 Suppl 8:S2. doi: 10.1186/1471-2105-11-S8-S2.

2.

Learning rates and states from biophysical time series: a Bayesian approach to model selection and single-molecule FRET data.

Bronson JE, Fei J, Hofman JM, Gonzalez RL Jr, Wiggins CH.

Biophys J. 2009 Dec 16;97(12):3196-205. doi: 10.1016/j.bpj.2009.09.031.

3.

Variational Bayes analysis of a photon-based hidden Markov model for single-molecule FRET trajectories.

Okamoto K, Sako Y.

Biophys J. 2012 Sep 19;103(6):1315-24. doi: 10.1016/j.bpj.2012.07.047.

4.

Latent-space variational bayes.

Sung J, Ghahramani Z, Bang SY.

IEEE Trans Pattern Anal Mach Intell. 2008 Dec;30(12):2236-42. doi: 10.1109/TPAMI.2008.157.

PMID:
18988955
5.

Bayesian inference of accurate population sizes and FRET efficiencies from single diffusing biomolecules.

Murphy RR, Danezis G, Horrocks MH, Jackson SE, Klenerman D.

Anal Chem. 2014 Sep 2;86(17):8603-12. doi: 10.1021/ac501188r. Epub 2014 Aug 18.

PMID:
25105347
6.

Analyzing Single Molecule FRET Trajectories Using HMM.

Okamoto K.

Methods Mol Biol. 2017;1552:103-113. doi: 10.1007/978-1-4939-6753-7_7.

PMID:
28224493
7.

Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.

van de Meent JW, Bronson JE, Wiggins CH, Gonzalez RL Jr.

Biophys J. 2014 Mar 18;106(6):1327-37. doi: 10.1016/j.bpj.2013.12.055.

8.

Superresolution with compound Markov random fields via the variational EM algorithm.

Kanemura A, Maeda S, Ishii S.

Neural Netw. 2009 Sep;22(7):1025-34. doi: 10.1016/j.neunet.2008.12.005. Epub 2009 Jan 7.

PMID:
19157777
9.

Denoising single-molecule FRET trajectories with wavelets and Bayesian inference.

Taylor JN, Makarov DE, Landes CF.

Biophys J. 2010 Jan 6;98(1):164-73. doi: 10.1016/j.bpj.2009.09.047.

10.

Expectation-maximization of the potential of mean force and diffusion coefficient in Langevin dynamics from single molecule FRET data photon by photon.

Haas KR, Yang H, Chu JW.

J Phys Chem B. 2013 Dec 12;117(49):15591-605. doi: 10.1021/jp405983d. Epub 2013 Sep 20.

PMID:
23937300
11.

Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data.

Zhang F, Flaherty P.

BMC Bioinformatics. 2017 Jan 19;18(1):45. doi: 10.1186/s12859-016-1451-5.

12.

Development of a variational scheme for model inversion of multi-area model of brain. Part II: VBEM method.

Babajani-Feremi A, Soltanian-Zadeh H.

Math Biosci. 2011 Jan;229(1):76-92. doi: 10.1016/j.mbs.2010.11.001. Epub 2010 Nov 16.

PMID:
21087617
13.

Mixed Bayesian networks: a mixture of Gaussian distributions.

Chevrolat JP, Rutigliano F, Golmard JL.

Methods Inf Med. 1994 Dec;33(5):535-42.

PMID:
7869953
14.

A Bayesian method for construction of Markov models to describe dynamics on various time-scales.

Rains EK, Andersen HC.

J Chem Phys. 2010 Oct 14;133(14):144113. doi: 10.1063/1.3496438.

PMID:
20949993
15.
16.

Analysis of complex single-molecule FRET time trajectories.

Blanco M, Walter NG.

Methods Enzymol. 2010;472:153-78. doi: 10.1016/S0076-6879(10)72011-5.

17.

Constructing gene networks using variational Bayesian variable selection.

Tienda-Luna IM, Yin Y, Huang Y, Padillo DP, Perez MC, Wang Y.

Artif Life. 2008 Winter;14(1):65-79. doi: 10.1162/artl.2008.14.1.65.

PMID:
18171131
18.

Structural Information from Single-molecule FRET Experiments Using the Fast Nano-positioning System.

Dörfler T, Eilert T, Röcker C, Nagy J, Michaelis J.

J Vis Exp. 2017 Feb 9;(120). doi: 10.3791/54782.

19.

Single Molecule Analysis Research Tool (SMART): an integrated approach for analyzing single molecule data.

Greenfeld M, Pavlichin DS, Mabuchi H, Herschlag D.

PLoS One. 2012;7(2):e30024. doi: 10.1371/journal.pone.0030024. Epub 2012 Feb 20.

20.

A constraint-based evolutionary learning approach to the expectation maximization for optimal estimation of the hidden Markov model for speech signal modeling.

Huda S, Yearwood J, Togneri R.

IEEE Trans Syst Man Cybern B Cybern. 2009 Feb;39(1):182-97. doi: 10.1109/TSMCB.2008.2004051. Epub 2008 Dec 9.

PMID:
19068441

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