Literature DB >> 27067018

EMPIAR: a public archive for raw electron microscopy image data.

Andrii Iudin1, Paul K Korir1, José Salavert-Torres1, Gerard J Kleywegt1, Ardan Patwardhan1.   

Abstract

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Year:  2016        PMID： 27067018     DOI： 10.1038/nmeth.3806

Source DB:  PubMed          Journal:  Nat Methods        ISSN： 1548-7091            Impact factor:   28.547


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  6 in total

1.  New electron microscopy database and deposition system.

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2.  The field that came in from the cold.

Authors:  Michael Eisenstein
Journal:  Nat Methods       Date:  2016-01       Impact factor: 28.547

3.  Outcome of the first electron microscopy validation task force meeting.

Authors:  Richard Henderson; Andrej Sali; Matthew L Baker; Bridget Carragher; Batsal Devkota; Kenneth H Downing; Edward H Egelman; Zukang Feng; Joachim Frank; Nikolaus Grigorieff; Wen Jiang; Steven J Ludtke; Ohad Medalia; Pawel A Penczek; Peter B Rosenthal; Michael G Rossmann; Michael F Schmid; Gunnar F Schröder; Alasdair C Steven; David L Stokes; John D Westbrook; Willy Wriggers; Huanwang Yang; Jasmine Young; Helen M Berman; Wah Chiu; Gerard J Kleywegt; Catherine L Lawson
Journal:  Structure       Date:  2012-02-08       Impact factor: 5.006

4.  Data management challenges in three-dimensional EM.

Authors:  Ardan Patwardhan; José-Maria Carazo; Bridget Carragher; Richard Henderson; J Bernard Heymann; Emma Hill; Grant J Jensen; Ingvar Lagerstedt; Catherine L Lawson; Steven J Ludtke; David Mastronarde; William J Moore; Alan Roseman; Peter Rosenthal; Carlos-Oscar S Sorzano; Eduardo Sanz-García; Sjors H W Scheres; Sriram Subramaniam; John Westbrook; Martyn Winn; Jason R Swedlow; Gerard J Kleywegt
Journal:  Nat Struct Mol Biol       Date:  2012-12       Impact factor: 15.369

5.  A 3D cellular context for the macromolecular world.

Authors:  Ardan Patwardhan; Alun Ashton; Robert Brandt; Sarah Butcher; Raffaella Carzaniga; Wah Chiu; Lucy Collinson; Pascal Doux; Elizabeth Duke; Mark H Ellisman; Erik Franken; Kay Grünewald; Jean-Karim Heriche; Abraham Koster; Werner Kühlbrandt; Ingvar Lagerstedt; Carolyn Larabell; Catherine L Lawson; Helen R Saibil; Eduardo Sanz-García; Sriram Subramaniam; Paul Verkade; Jason R Swedlow; Gerard J Kleywegt
Journal:  Nat Struct Mol Biol       Date:  2014-10       Impact factor: 15.369

6.  EMDataBank unified data resource for 3DEM.

Authors:  Catherine L Lawson; Ardan Patwardhan; Matthew L Baker; Corey Hryc; Eduardo Sanz Garcia; Brian P Hudson; Ingvar Lagerstedt; Steven J Ludtke; Grigore Pintilie; Raul Sala; John D Westbrook; Helen M Berman; Gerard J Kleywegt; Wah Chiu
Journal:  Nucleic Acids Res       Date:  2015-11-17       Impact factor: 16.971
  6 in total
  99 in total

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Journal:  Structure       Date:  2018-04-12       Impact factor: 5.006

2.  MBIR: A cryo-ET 3D reconstruction method that effectively minimizes missing wedge artifacts and restores missing information.

Authors:  Rui Yan; Singanallur V Venkatakrishnan; Jun Liu; Charles A Bouman; Wen Jiang
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3.  Computational Tools for Serial Block Electron Microscopy Reveal Plasmodesmata Distributions and Wall Environments.

Authors:  Andrea Paterlini; Ilya Belevich; Eija Jokitalo; Yrjö Helariutta
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4.  Image Processing in Cryo-Electron Microscopy of Single Particles: The Power of Combining Methods.

Authors:  Carlos Oscar S Sorzano; Amaya Jiménez-Moreno; David Maluenda; Erney Ramírez-Aportela; Marta Martínez; Ana Cuervo; Robert Melero; Jose Javier Conesa; Ruben Sánchez-García; David Strelak; Jiri Filipovic; Estrella Fernández-Giménez; Federico de Isidro-Gómez; David Herreros; Pablo Conesa; Laura Del Caño; Yunior Fonseca; Jorge Jiménez de la Morena; Jose Ramon Macías; Patricia Losana; Roberto Marabini; Jose-Maria Carazo
Journal:  Methods Mol Biol       Date:  2021

5.  The Protein Data Bank Archive.

Authors:  Sameer Velankar; Stephen K Burley; Genji Kurisu; Jeffrey C Hoch; John L Markley
Journal:  Methods Mol Biol       Date:  2021

6.  Multi-body Refinement of Cryo-EM Images in RELION.

Authors:  Takanori Nakane; Sjors H W Scheres
Journal:  Methods Mol Biol       Date:  2021

7.  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

Review 8.  Present and Emerging Methodologies in Cryo-EM Single-Particle Analysis.

Authors:  Mengyu Wu; Gabriel C Lander
Journal:  Biophys J       Date:  2020-09-01       Impact factor: 4.033

9.  Real-time detection and single-pass minimization of TEM objective lens astigmatism.

Authors:  Rui Yan; Kunpeng Li; Wen Jiang
Journal:  J Struct Biol       Date:  2016-11-10       Impact factor: 2.867

10.  Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets.

Authors:  Germán González; Conor L Evans
Journal:  Bioessays       Date:  2019-05-16       Impact factor: 4.345
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