Literature DB >> 20888965

An introduction to maximum-likelihood methods in cryo-EM.

Fred J Sigworth1, Peter C Doerschuk, Jose-Maria Carazo, Sjors H W Scheres.   

Abstract

The maximum-likelihood method provides a powerful approach to many problems in cryo-electron microscopy (cryo-EM) image processing. This contribution aims to provide an accessible introduction to the underlying theory and reviews existing applications in the field. In addition, current developments to reduce computational costs and to improve the statistical description of cryo-EM images are discussed. Combined with the increasing power of modern computers and yet unexplored possibilities provided by theory, these developments are expected to turn the statistical approach into an essential image-processing tool for the electron microscopist.
Copyright © 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 20888965      PMCID: PMC3051286          DOI: 10.1016/S0076-6879(10)82011-7

Source DB:  PubMed          Journal:  Methods Enzymol        ISSN: 0076-6879            Impact factor:   1.600


  33 in total

1.  An ab initio algorithm for low-resolution 3-D reconstructions from cryoelectron microscopy images.

Authors:  Z Yin; Y Zheng; P C Doerschuk
Journal:  J Struct Biol       Date:  2001 Feb-Mar       Impact factor: 2.867

2.  A statistical approach to computer processing of cryo-electron microscope images: virion classification and 3-D reconstruction.

Authors:  Zhye Yin; Yili Zheng; Peter C Doerschuk; Padmaja Natarajan; John E Johnson
Journal:  J Struct Biol       Date:  2003 Oct-Nov       Impact factor: 2.867

3.  On the three-dimensional reconstruction of icosahedral particles.

Authors:  Jorge Navaza
Journal:  J Struct Biol       Date:  2003 Oct-Nov       Impact factor: 2.867

4.  Quantitative self-organizing maps for clustering electron tomograms.

Authors:  A Pascual-Montano; K A Taylor; H Winkler; R D Pascual-Marqui; J-M Carazo
Journal:  J Struct Biol       Date:  2002 Apr-May       Impact factor: 2.867

5.  Classical detection theory and the cryo-EM particle selection problem.

Authors:  Fred J Sigworth
Journal:  J Struct Biol       Date:  2004 Jan-Feb       Impact factor: 2.867

6.  The molecular architecture of cadherins in native epidermal desmosomes.

Authors:  Ashraf Al-Amoudi; Daniel Castaño Díez; Matthew J Betts; Achilleas S Frangakis
Journal:  Nature       Date:  2007-12-06       Impact factor: 49.962

7.  Exact reduced-complexity maximum likelihood reconstruction of multiple 3-D objects from unlabeled unoriented 2-D projections and electron microscopy of viruses.

Authors:  Junghoon Lee; Peter C Doerschuk; John E Johnson
Journal:  IEEE Trans Image Process       Date:  2007-12       Impact factor: 10.856

8.  Three-dimensional reconstruction of the shape of human wart virus using spatial correlations.

Authors:  Z Kam; I Gafni
Journal:  Ultramicroscopy       Date:  1985       Impact factor: 2.689

9.  Maximum likelihood refinement of electron microscopy data with normalization errors.

Authors:  Sjors H W Scheres; Mikel Valle; Patricia Grob; Eva Nogales; José-María Carazo
Journal:  J Struct Biol       Date:  2009-02-21       Impact factor: 2.867

10.  Introducing robustness to maximum-likelihood refinement of electron-microscopy data.

Authors:  Sjors H W Scheres; José María Carazo
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-06-20
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  19 in total

1.  COVARIANCE ESTIMATION USING CONJUGATE GRADIENT FOR 3D CLASSIFICATION IN CRYO-EM.

Authors:  Joakim Andén; Eugene Katsevich; Amit Singer
Journal:  Proc IEEE Int Symp Biomed Imaging       Date:  2015-04

Review 2.  Single-particle cryo-electron microscopy of macromolecular complexes.

Authors:  Georgios Skiniotis; Daniel R Southworth
Journal:  Microscopy (Oxf)       Date:  2015-11-25       Impact factor: 1.571

3.  SubspaceEM: A fast maximum-a-posteriori algorithm for cryo-EM single particle reconstruction.

Authors:  Nicha C Dvornek; Fred J Sigworth; Hemant D Tagare
Journal:  J Struct Biol       Date:  2015-03-31       Impact factor: 2.867

4.  Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Authors:  Massimiliano Bonomi; Samuel Hanot; Charles H Greenberg; Andrej Sali; Michael Nilges; Michele Vendruscolo; Riccardo Pellarin
Journal:  Structure       Date:  2018-11-01       Impact factor: 5.006

5.  Separating distinct structures of multiple macromolecular assemblies from cryo-EM projections.

Authors:  Eric J Verbeke; Yi Zhou; Andrew P Horton; Anna L Mallam; David W Taylor; Edward M Marcotte
Journal:  J Struct Biol       Date:  2019-11-11       Impact factor: 2.867

6.  Covariance Matrix Estimation for the Cryo-EM Heterogeneity Problem.

Authors:  E Katsevich; A Katsevich; A Singer
Journal:  SIAM J Imaging Sci       Date:  2015-01-22       Impact factor: 2.867

Review 7.  Single-Particle Cryo-EM at Crystallographic Resolution.

Authors:  Yifan Cheng
Journal:  Cell       Date:  2015-04-23       Impact factor: 41.582

8.  Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps.

Authors:  Qiu Wang; Tsutomu Matsui; Tatiana Domitrovic; Yili Zheng; Peter C Doerschuk; John E Johnson
Journal:  J Struct Biol       Date:  2012-12-12       Impact factor: 2.867

9.  An approach to improve the resolution of helical filaments with a large axial rise and flexible subunits.

Authors:  Shixin Yang; John L Woodhead; Fa-Qing Zhao; Guidenn Sulbarán; Roger Craig
Journal:  J Struct Biol       Date:  2015-11-22       Impact factor: 2.867

10.  Bayesian analysis of individual electron microscopy images: towards structures of dynamic and heterogeneous biomolecular assemblies.

Authors:  Pilar Cossio; Gerhard Hummer
Journal:  J Struct Biol       Date:  2013-10-24       Impact factor: 2.867

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