Literature DB >> 25954869

A primer on Bayesian inference for biophysical systems.

Keegan E Hines1.   

Abstract

Bayesian inference is a powerful statistical paradigm that has gained popularity in many fields of science, but adoption has been somewhat slower in biophysics. Here, I provide an accessible tutorial on the use of Bayesian methods by focusing on example applications that will be familiar to biophysicists. I first discuss the goals of Bayesian inference and show simple examples of posterior inference using conjugate priors. I then describe Markov chain Monte Carlo sampling and, in particular, discuss Gibbs sampling and Metropolis random walk algorithms with reference to detailed examples. These Bayesian methods (with the aid of Markov chain Monte Carlo sampling) provide a generalizable way of rigorously addressing parameter inference and identifiability for arbitrarily complicated models.
Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Mesh:

Year:  2015        PMID: 25954869      PMCID: PMC4423066          DOI: 10.1016/j.bpj.2015.03.042

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  12 in total

1.  MCMC for hidden Markov models incorporating aggregation of states and filtering.

Authors:  Rafael A Rosales
Journal:  Bull Math Biol       Date:  2004-09       Impact factor: 1.758

2.  Stochastic relaxation, gibbs distributions, and the bayesian restoration of images.

Authors:  S Geman; D Geman
Journal:  IEEE Trans Pattern Anal Mach Intell       Date:  1984-06       Impact factor: 6.226

3.  Subunit counting in membrane-bound proteins.

Authors:  Maximilian H Ulbrich; Ehud Y Isacoff
Journal:  Nat Methods       Date:  2007-03-18       Impact factor: 28.547

4.  Bayesian approaches for mechanistic ion channel modeling.

Authors:  Ben Calderhead; Michael Epstein; Lucia Sivilotti; Mark Girolami
Journal:  Methods Mol Biol       Date:  2013

5.  Analyzing single-molecule time series via nonparametric Bayesian inference.

Authors:  Keegan E Hines; John R Bankston; Richard W Aldrich
Journal:  Biophys J       Date:  2015-02-03       Impact factor: 4.033

6.  MCMC can detect nonidentifiable models.

Authors:  Ivo Siekmann; James Sneyd; Edmund J Crampin
Journal:  Biophys J       Date:  2012-12-05       Impact factor: 4.033

7.  Data transformations for improved display and fitting of single-channel dwell time histograms.

Authors:  F J Sigworth; S M Sine
Journal:  Biophys J       Date:  1987-12       Impact factor: 4.033

8.  On the stochastic properties of single ion channels.

Authors:  D Colquhoun; A G Hawkes
Journal:  Proc R Soc Lond B Biol Sci       Date:  1981-03-06

9.  An empirical Bayesian approach for model-based inference of cellular signaling networks.

Authors:  David J Klinke
Journal:  BMC Bioinformatics       Date:  2009-11-09       Impact factor: 3.169

10.  Inferring subunit stoichiometry from single molecule photobleaching.

Authors:  Keegan E Hines
Journal:  J Gen Physiol       Date:  2013-06       Impact factor: 4.086

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  22 in total

1.  A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer.

Authors:  Ioannis Sgouralis; Shreya Madaan; Franky Djutanta; Rachael Kha; Rizal F Hariadi; Steve Pressé
Journal:  J Phys Chem B       Date:  2019-01-10       Impact factor: 2.991

2.  Analyzing single-molecule time series via nonparametric Bayesian inference.

Authors:  Keegan E Hines; John R Bankston; Richard W Aldrich
Journal:  Biophys J       Date:  2015-02-03       Impact factor: 4.033

3.  BEES: Bayesian Ensemble Estimation from SAS.

Authors:  Samuel Bowerman; Joseph E Curtis; Joseph Clayton; Emre H Brookes; Jeff Wereszczynski
Journal:  Biophys J       Date:  2019-07-18       Impact factor: 4.033

4.  Unraveling the Thousand Word Picture: An Introduction to Super-Resolution Data Analysis.

Authors:  Antony Lee; Konstantinos Tsekouras; Christopher Calderon; Carlos Bustamante; Steve Pressé
Journal:  Chem Rev       Date:  2017-04-17       Impact factor: 60.622

5.  Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation.

Authors:  Eri Nakatani-Webster; Abhinav Nath
Journal:  Biophys J       Date:  2017-03-14       Impact factor: 4.033

Review 6.  An Introduction to Infinite HMMs for Single-Molecule Data Analysis.

Authors:  Ioannis Sgouralis; Steve Pressé
Journal:  Biophys J       Date:  2017-05-23       Impact factor: 4.033

7.  ICON: An Adaptation of Infinite HMMs for Time Traces with Drift.

Authors:  Ioannis Sgouralis; Steve Pressé
Journal:  Biophys J       Date:  2017-05-23       Impact factor: 4.033

8.  A Bayesian approach to quantifying uncertainty from experimental noise in DEER spectroscopy.

Authors:  Thomas H Edwards; Stefan Stoll
Journal:  J Magn Reson       Date:  2016-07-02       Impact factor: 2.229

Review 9.  A Primer on the Bayesian Approach to High-Density Single-Molecule Trajectories Analysis.

Authors:  Mohamed El Beheiry; Silvan Türkcan; Maximilian U Richly; Antoine Triller; Antigone Alexandrou; Maxime Dahan; Jean-Baptiste Masson
Journal:  Biophys J       Date:  2016-03-29       Impact factor: 4.033

10.  MEMLET: An Easy-to-Use Tool for Data Fitting and Model Comparison Using Maximum-Likelihood Estimation.

Authors:  Michael S Woody; John H Lewis; Michael J Greenberg; Yale E Goldman; E Michael Ostap
Journal:  Biophys J       Date:  2016-07-26       Impact factor: 4.033

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