Literature DB >> 29100109

Big data in cryoEM: automated collection, processing and accessibility of EM data.

Philip R Baldwin1, Yong Zi Tan2, Edward T Eng1, William J Rice1, Alex J Noble1, Carl J Negro1, Michael A Cianfrocco3, Clinton S Potter2, Bridget Carragher4.   

Abstract

The scope and complexity of cryogenic electron microscopy (cryoEM) data has greatly increased, and will continue to do so, due to recent and ongoing technical breakthroughs that have led to much improved resolutions for macromolecular structures solved using this method. This big data explosion includes single particle data as well as tomographic tilt series, both generally acquired as direct detector movies of ∼10-100 frames per image or per tilt-series. We provide a brief survey of the developments leading to the current status, and describe existing cryoEM pipelines, with an emphasis on the scope of data acquisition, methods for automation, and use of cloud storage and computing.
Copyright © 2017 Elsevier Ltd. All rights reserved.

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Year:  2017        PMID: 29100109      PMCID: PMC6067001          DOI: 10.1016/j.mib.2017.10.005

Source DB:  PubMed          Journal:  Curr Opin Microbiol        ISSN: 1369-5274            Impact factor:   7.934


  90 in total

1.  FindEM--a fast, efficient program for automatic selection of particles from electron micrographs.

Authors:  A M Roseman
Journal:  J Struct Biol       Date:  2004 Jan-Feb       Impact factor: 2.867

2.  A novel approximation method of CTF amplitude correction for 3D single particle reconstruction.

Authors:  Linhua Jiang; Zunfeng Liu; Dilyana Georgieva; Maxim E Kuil; Jan Pieter Abrahams
Journal:  Ultramicroscopy       Date:  2010-02-01       Impact factor: 2.689

3.  SIGNATURE: a single-particle selection system for molecular electron microscopy.

Authors:  James Z Chen; Nikolaus Grigorieff
Journal:  J Struct Biol       Date:  2006-06-17       Impact factor: 2.867

4.  Cryo-electron tomography of microtubules assembled in vitro from purified components.

Authors:  Frédéric M Coquelle; Sophie Blestel; Claire Heichette; Isabelle Arnal; Charles Kervrann; Denis Chrétien
Journal:  Methods Mol Biol       Date:  2011

5.  Multidimensional persistence in biomolecular data.

Authors:  Kelin Xia; Guo-Wei Wei
Journal:  J Comput Chem       Date:  2015-05-30       Impact factor: 3.376

6.  Best practices for managing large CryoEM facilities.

Authors:  Bart Alewijnse; Alun W Ashton; Melissa G Chambers; Songye Chen; Anchi Cheng; Mark Ebrahim; Edward T Eng; Wim J H Hagen; Abraham J Koster; Claudia S López; Natalya Lukoyanova; Joaquin Ortega; Ludovic Renault; Steve Reyntjens; William J Rice; Giovanna Scapin; Raymond Schrijver; Alistair Siebert; Scott M Stagg; Valerie Grum-Tokars; Elizabeth R Wright; Shenping Wu; Zhiheng Yu; Z Hong Zhou; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2017-08-04       Impact factor: 2.867

7.  Architectures of Lipid Transport Systems for the Bacterial Outer Membrane.

Authors:  Damian C Ekiert; Gira Bhabha; Georgia L Isom; Garrett Greenan; Sergey Ovchinnikov; Ian R Henderson; Jeffery S Cox; Ronald D Vale
Journal:  Cell       Date:  2017-04-06       Impact factor: 41.582

8.  Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6.

Authors:  Timothy Grant; Nikolaus Grigorieff
Journal:  Elife       Date:  2015-05-29       Impact factor: 8.140

9.  Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud.

Authors:  Michael A Cianfrocco; Andres E Leschziner
Journal:  Elife       Date:  2015-05-08       Impact factor: 8.140

10.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.

Authors:  Dari Kimanius; Björn O Forsberg; Sjors Hw Scheres; Erik Lindahl
Journal:  Elife       Date:  2016-11-15       Impact factor: 8.140

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  13 in total

1.  APPLE picker: Automatic particle picking, a low-effort cryo-EM framework.

Authors:  Ayelet Heimowitz; Joakim Andén; Amit Singer
Journal:  J Struct Biol       Date:  2018-08-19       Impact factor: 2.867

2.  Gum-Net: Unsupervised Geometric Matching for Fast and Accurate 3D Subtomogram Image Alignment and Averaging.

Authors:  Xiangrui Zeng; Min Xu
Journal:  Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit       Date:  2020-08-05

3.  Reducing cryoEM file storage using lossy image formats.

Authors:  Edward T Eng; Mykhailo Kopylov; Carl J Negro; Sarkis Dallaykan; William J Rice; Kelsey D Jordan; Kotaro Kelley; Bridget Carragher; Clinton S Potter
Journal:  J Struct Biol       Date:  2019-05-21       Impact factor: 2.867

Review 4.  Cryo-electron Microscopy of Adeno-associated Virus.

Authors:  Scott M Stagg; Craig Yoshioka; Omar Davulcu; Michael S Chapman
Journal:  Chem Rev       Date:  2022-05-16       Impact factor: 72.087

5.  High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines.

Authors:  Yilai Li; Jennifer N Cash; John J G Tesmer; Michael A Cianfrocco
Journal:  Structure       Date:  2020-04-14       Impact factor: 5.006

Review 6.  Understanding the invisible hands of sample preparation for cryo-EM.

Authors:  Giulia Weissenberger; Rene J M Henderikx; Peter J Peters
Journal:  Nat Methods       Date:  2021-05-07       Impact factor: 47.990

7.  Automated map sharpening by maximization of detail and connectivity.

Authors:  Thomas C Terwilliger; Oleg V Sobolev; Pavel V Afonine; Paul D Adams
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-05-18       Impact factor: 7.652

8.  ETDB-Caltech: A blockchain-based distributed public database for electron tomography.

Authors:  Davi R Ortega; Catherine M Oikonomou; H Jane Ding; Prudence Rees-Lee; Grant J Jensen
Journal:  PLoS One       Date:  2019-04-15       Impact factor: 3.240

9.  A collection of yeast cellular electron cryotomography data.

Authors:  Lu Gan; Cai Tong Ng; Chen Chen; Shujun Cai
Journal:  Gigascience       Date:  2019-06-01       Impact factor: 6.524

Review 10.  Advances in methods for atomic resolution macromolecular structure determination.

Authors:  Michael C Thompson; Todd O Yeates; Jose A Rodriguez
Journal:  F1000Res       Date:  2020-07-02
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