A citation-based method for searching scientific literature

J R Kremer, D N Mastronarde, J R McIntosh. J Struct Biol 1996
Times Cited: 3180







List of co-cited articles
317 articles co-cited >1



Times Cited
  Times     Co-cited
Similarity



Fiji: an open-source platform for biological-image analysis.
Johannes Schindelin, Ignacio Arganda-Carreras, Erwin Frise, Verena Kaynig, Mark Longair, Tobias Pietzsch, Stephan Preibisch, Curtis Rueden, Stephan Saalfeld, Benjamin Schmid,[...]. Nat Methods 2012
24

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy.
Shawn Q Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A Verba, Yifan Cheng, David A Agard. Nat Methods 2017
21

UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
20


CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
11

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
329
11

Highly accurate protein structure prediction with AlphaFold.
John Jumper, Richard Evans, Alexander Pritzel, Tim Green, Michael Figurnov, Olaf Ronneberger, Kathryn Tunyasuvunakool, Russ Bates, Augustin Žídek, Anna Potapenko,[...]. Nature 2021
10


Automated tilt series alignment and tomographic reconstruction in IMOD.
David N Mastronarde, Susannah R Held. J Struct Biol 2017
233
10

Multi-particle cryo-EM refinement with M visualizes ribosome-antibiotic complex at 3.5 Å in cells.
Dimitry Tegunov, Liang Xue, Christian Dienemann, Patrick Cramer, Julia Mahamid. Nat Methods 2021
87
10

UCSF ChimeraX: Meeting modern challenges in visualization and analysis.
Thomas D Goddard, Conrad C Huang, Elaine C Meng, Eric F Pettersen, Gregory S Couch, John H Morris, Thomas E Ferrin. Protein Sci 2018
9

New tools for automated high-resolution cryo-EM structure determination in RELION-3.
Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim Jh Hagen, Erik Lindahl, Sjors Hw Scheres. Elife 2018
9

Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments.
Daniel Castaño-Díez, Mikhail Kudryashev, Marcel Arheit, Henning Stahlberg. J Struct Biol 2012
192
8

A complete data processing workflow for cryo-ET and subtomogram averaging.
Muyuan Chen, James M Bell, Xiaodong Shi, Stella Y Sun, Zhao Wang, Steven J Ludtke. Nat Methods 2019
66
12

EMAN2: an extensible image processing suite for electron microscopy.
Guang Tang, Liwei Peng, Philip R Baldwin, Deepinder S Mann, Wen Jiang, Ian Rees, Steven J Ludtke. J Struct Biol 2007
8

UCSF ChimeraX: Structure visualization for researchers, educators, and developers.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Elaine C Meng, Gregory S Couch, Tristan I Croll, John H Morris, Thomas E Ferrin. Protein Sci 2021
8


Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
7

Efficient 3D-CTF correction for cryo-electron tomography using NovaCTF improves subtomogram averaging resolution to 3.4Å.
Beata Turoňová, Florian K M Schur, William Wan, John A G Briggs. J Struct Biol 2017
122
7

NIH Image to ImageJ: 25 years of image analysis.
Caroline A Schneider, Wayne S Rasband, Kevin W Eliceiri. Nat Methods 2012
7



Visualizing the molecular sociology at the HeLa cell nuclear periphery.
Julia Mahamid, Stefan Pfeffer, Miroslava Schaffer, Elizabeth Villa, Radostin Danev, Luis Kuhn Cuellar, Friedrich Förster, Anthony A Hyman, Jürgen M Plitzko, Wolfgang Baumeister. Science 2016
290
6

Tomo3D 2.0--exploitation of advanced vector extensions (AVX) for 3D reconstruction.
Jose-Ignacio Agulleiro, Jose-Jesus Fernandez. J Struct Biol 2015
79
7


Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM.
Xueming Li, Paul Mooney, Shawn Zheng, Christopher R Booth, Michael B Braunfeld, Sander Gubbens, David A Agard, Yifan Cheng. Nat Methods 2013
6

Focused-ion-beam thinning of frozen-hydrated biological specimens for cryo-electron microscopy.
Michael Marko, Chyongere Hsieh, Richard Schalek, Joachim Frank, Carmen Mannella. Nat Methods 2007
271
6

Fast tomographic reconstruction on multicore computers.
J I Agulleiro, J J Fernandez. Bioinformatics 2011
142
6

The molecular architecture of axonemes revealed by cryoelectron tomography.
Daniela Nicastro, Cindi Schwartz, Jason Pierson, Richard Gaudette, Mary E Porter, J Richard McIntosh. Science 2006
557
6

SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM.
Thorsten Wagner, Felipe Merino, Markus Stabrin, Toshio Moriya, Claudia Antoni, Amir Apelbaum, Philine Hagel, Oleg Sitsel, Tobias Raisch, Daniel Prumbaum,[...]. Commun Biol 2019
402
6


Atomic-resolution protein structure determination by cryo-EM.
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark. Nature 2020
202
5

Single-particle cryo-EM at atomic resolution.
Takanori Nakane, Abhay Kotecha, Andrija Sente, Greg McMullan, Simonas Masiulis, Patricia M G E Brown, Ioana T Grigoras, Lina Malinauskaite, Tomas Malinauskas, Jonas Miehling,[...]. Nature 2020
274
5

Volta potential phase plate for in-focus phase contrast transmission electron microscopy.
Radostin Danev, Bart Buijsse, Maryam Khoshouei, Jürgen M Plitzko, Wolfgang Baumeister. Proc Natl Acad Sci U S A 2014
270
5

Real-space refinement in PHENIX for cryo-EM and crystallography.
Pavel V Afonine, Billy K Poon, Randy J Read, Oleg V Sobolev, Thomas C Terwilliger, Alexandre Urzhumtsev, Paul D Adams. Acta Crystallogr D Struct Biol 2018
924
5

CTF determination and correction for low dose tomographic tilt series.
Quanren Xiong, Mary K Morphew, Cindi L Schwartz, Andreas H Hoenger, David N Mastronarde. J Struct Biol 2009
133
5


SARS-CoV-2 structure and replication characterized by in situ cryo-electron tomography.
Steffen Klein, Mirko Cortese, Sophie L Winter, Moritz Wachsmuth-Melm, Christopher J Neufeldt, Berati Cerikan, Megan L Stanifer, Steeve Boulant, Ralf Bartenschlager, Petr Chlanda. Nat Commun 2020
278
5

An improved cryogen for plunge freezing.
William F Tivol, Ariane Briegel, Grant J Jensen. Microsc Microanal 2008
178
5

Optimized cryo-focused ion beam sample preparation aimed at in situ structural studies of membrane proteins.
Miroslava Schaffer, Julia Mahamid, Benjamin D Engel, Tim Laugks, Wolfgang Baumeister, Jürgen M Plitzko. J Struct Biol 2017
118
5

Cryo-electron microscopy of vitrified specimens.
J Dubochet, M Adrian, J J Chang, J C Homo, J Lepault, A W McDowall, P Schultz. Q Rev Biophys 1988
5

eC-CLEM: flexible multidimensional registration software for correlative microscopies.
Perrine Paul-Gilloteaux, Xavier Heiligenstein, Martin Belle, Marie-Charlotte Domart, Banafshe Larijani, Lucy Collinson, Graça Raposo, Jean Salamero. Nat Methods 2017
116
5


TOM software toolbox: acquisition and analysis for electron tomography.
Stephan Nickell, Friedrich Förster, Alexandros Linaroudis, William Del Net, Florian Beck, Reiner Hegerl, Wolfgang Baumeister, Jürgen M Plitzko. J Struct Biol 2005
305
5

Software tools for automated transmission electron microscopy.
Martin Schorb, Isabella Haberbosch, Wim J H Hagen, Yannick Schwab, David N Mastronarde. Nat Methods 2019
169
4


In situ structure determination at nanometer resolution using TYGRESS.
Kangkang Song, Zhiguo Shang, Xiaofeng Fu, Xiaochu Lou, Nikolaus Grigorieff, Daniela Nicastro. Nat Methods 2020
25
16


VMD: visual molecular dynamics.
W Humphrey, A Dalke, K Schulten. J Mol Graph 1996
4


Co-cited is the co-citation frequency, indicating how many articles cite the article together with the query article. Similarity is the co-citation as percentage of the times cited of the query article or the article in the search results, whichever is the lowest. These numbers are calculated for the last 100 citations when articles are cited more than 100 times.