Most cited papers in Advanced Electron Microscopy Techniques and Applications
What are the most cited papers in Advanced Electron Microscopy Techniques and Applications?
The most cited paper in Advanced Electron Microscopy Techniques and Applications is "LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales" (Aidan P. Thompson, Hasan Metin Aktulga, Richard A. Berger et al., 2021), with 12,569 citations. Next come "cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination" (11,217) and "Jalview Version 2—a multiple sequence alignment editor and analysis workbench" (11,179).
Showing 50 of 100 papers. Every paper with more than 1,046 citations is listed.
| # | Paper | ||
|---|---|---|---|
| 1 | LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales Aidan P. Thompson, Hasan Metin Aktulga, Richard A. Berger et al. · Computer Physics Communications | 22 Sep 2021 | 12,569 |
| 2 | cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination Ali Punjani, John L. Rubinstein, David J. Fleet et al. · Nature Methods | 6 Feb 2017 | 11,217 |
| 3 | Jalview Version 2—a multiple sequence alignment editor and analysis workbench Andrew Mark Waterhouse, James B Procter, David M. A. Martin et al. · Bioinformatics | 16 Jan 2009 | 11,179 |
| 4 | UCSF ChimeraX : Structure visualization for researchers, educators, and developers Eric F. Pettersen, Thomas D. Goddard, Conrad C. Huang et al. · Protein Science | 3 Sep 2020 | 10,674 |
| 5 | MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy Shawn Q. Zheng, Eugene J. Palovcak, Jean‐Paul Armache et al. · Nature Methods | 27 Feb 2017 | 9,180 |
| 6 | Imaging Intracellular Fluorescent Proteins at Nanometer Resolution Eric Betzig, George H. Patterson, Rachid Sougrat et al. · Science | 10 Aug 2006 | 9,061 |
| 7 | Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix Dorothee Claudia Liebschner et al. · Acta Crystallographica Section D Structural Biology | Oct 2019 | 7,679 |
| 8 | ImageJ2: ImageJ for the next generation of scientific image data Curtis Rueden, Johannes Schindelin, Mark Hiner et al. · BMC Bioinformatics | 29 Nov 2017 | 6,379 |
| 9 | Computer Visualization of Three-Dimensional Image Data Using IMOD James R. Kremer, David N. Mastronarde, J. Richard McIntosh · Journal of Structural Biology | 1996 | 6,195 |
| 10 | Automated electron microscope tomography using robust prediction of specimen movements David N. Mastronarde · Journal of Structural Biology | 25 Aug 2005 | 6,180 |
| 11 | RELION: Implementation of a Bayesian approach to cryo-EM structure determination Sjors H. W. Scheres · Journal of Structural Biology | 19 Sep 2012 | 6,175 |
| 12 | CTFFIND4: Fast and accurate defocus estimation from electron micrographs Alexis L. Rohou, Nikolaus Grigorieff · Journal of Structural Biology | 13 Aug 2015 | 5,758 |
| 13 | A guided tour into subcellular colocalization analysis in light microscopy Susanne Bolte, Fabrice P. Cordelières · Journal of Microscopy | Dec 2006 | 5,686 |
| 14 | Phase retrieval algorithms: a comparison James R. Fienup · Applied Optics | Aug 1982 | 5,681 |
| 15 | Gwyddion: an open-source software for SPM data analysis David Nečas, Petr Klapetek · Open Physics | 16 Nov 2011 | 4,514 |
| 16 | Gctf: Real-time CTF determination and correction Kai Zhang · Journal of Structural Biology | 20 Nov 2015 | 4,155 |
| 17 | Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy Mats G. Gustafsson · Journal of Microscopy | May 2000 | 3,882 |
| 18 | Real-space refinement in PHENIX for cryo-EM and crystallography Pavel V. Afonine, Billy K. Poon, Randy J. Read et al. · Acta Crystallographica Section D Structural Biology | 30 May 2018 | 3,869 |
| 19 | Ultra-High Resolution Imaging by Fluorescence Photoactivation Localization Microscopy Samuel T. Hess, Thanu Prabha Kalambur Girirajan, Michael D. Mason · Biophysical Journal | 15 Sep 2006 | 3,705 |
| 20 | Electron Energy-Loss Spectroscopy in the Electron Microscope Ray F. Egerton, Dale E. Newbury · Physics Today | Nov 1987 | 3,431 |
| 21 | Embedding in Epoxy Resins for Ultrathin Sectioning in Electron Microscopy Keith C. Richardson, Leonard Jarett, E. H. Finke · Stain Technology | 1960 | 3,318 |
| 22 | EMAN2: An extensible image processing suite for electron microscopy Guang Yi Tang, Liwei Peng, Philip Rupert Baldwin et al. · Journal of Structural Biology | 11 Jun 2006 | 3,274 |
| 23 | Far-Field Optical Nanoscopy Stefan W. Hell · Science | 25 May 2007 | 3,002 |
| 24 | iMOSFLM: a new graphical interface for diffraction-image processing withMOSFLM T. Geoff G. Battye, Luke Kontogiannis, Owen Johnson et al. · Acta Crystallographica Section D Biological Crystallography | 17 Mar 2011 | 2,958 |
| 25 | Algebraic Reconstruction Techniques (ART) for three-dimensional electron microscopy and X-ray photography Richard Gordon, Robert Bender, Gábor T. Herman · Journal of Theoretical Biology | Dec 1970 | 2,796 |
| 26 | Optimal Determination of Particle Orientation, Absolute Hand, and Contrast Loss in Single-particle Electron Cryomicroscopy Peter B. Rosenthal, Richard A. Henderson · Journal of Molecular Biology | Oct 2003 | 2,705 |
| 27 | Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification Ignacio Arganda‐Carreras, Verena Kaynig, Curtis Rueden et al. · Bioinformatics | 28 Mar 2017 | 2,553 |
| 28 | Ultrafast Spin Dynamics in Ferromagnetic Nickel Emmanuel Beaurepaire, J.‐C. Merle, A. Daunois et al. · Physical Review Letters | 27 May 1996 | 2,463 |
| 29 | EMAN: Semiautomated Software for High-Resolution Single-Particle Reconstructions Steven J. Ludtke, Philip Rupert Baldwin, Wah Keung Chiu · Journal of Structural Biology | Dec 1999 | 2,442 |
| 30 | Cryo-electron microscopy of vitrified specimens Jacques Dubochet, Marc Adrian, Jiin-Ju Chang et al. · Quarterly Reviews of Biophysics | May 1988 | 2,424 |
| 31 | Automated protein model building combined with iterative structure refinement. Anastassis Perrakis, Richard James Morris, Victor S. Lamzin · Nature Structural Biology | May 1999 | 2,424 |
| 32 | Maximally localized Wannier functions for entangled energy bands Ivo Souza, Nicola Marzari, David Vanderbilt · Physical review. B, Condensed matter | 19 Dec 2001 | 2,272 |
| 33 | A collaborative framework for 3D alignment and classification of heterogeneous subvolumes in cryo-electron tomography Oleg Kuybeda, Gabriel A. Frank, Alberto Bartesaghi et al. · Journal of Structural Biology | 27 Oct 2012 | 2,247 |
| 34 | Advanced methods of microscope control using μManager software Arthur Edelstein, Mark A. Tsuchida, Nenad Amodaj et al. · Journal of Biological Methods | 7 Nov 2014 | 2,234 |
| 35 | Attosecond science P. B. Corkum, Ferenc Krausz · Nature Physics | Jun 2007 | 2,150 |
| 36 | Femtosecond X-ray protein nanocrystallography Henry N. Chapman et al. · Nature | Feb 2011 | 2,130 |
| 37 | Accurate and efficient algorithm for Bader charge integration Min Yu, Dallas R. Trinkle · The Journal of Chemical Physics | 10 Feb 2011 | 2,108 |
| 38 | Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution Bi‐Chang Chen et al. · Science | 23 Oct 2014 | 2,103 |
| 39 | XtalView/Xfit—A Versatile Program for Manipulating Atomic Coordinates and Electron Density Duncan E. McRee · Journal of Structural Biology | Apr 1999 | 2,102 |
| 40 | Simultaneous phase and amplitude extraction from a single defocused image of a homogeneous object David M. Paganin, Sheridan C. Mayo, Timur E. Gureyev et al. · Journal of Microscopy | Apr 2002 | 2,083 |
| 41 | SPIDER and WEB: Processing and Visualization of Images in 3D Electron Microscopy and Related Fields Joachim Frank, Michael Radermacher, Pawel A. Penczek et al. · Journal of Structural Biology | 1996 | 2,077 |
| 42 | Quantifying the local resolution of cryo-EM density maps Alp Kucukelbir, Fred J. Sigworth, Hemant D. Tagare · Nature Methods | 10 Nov 2013 | 2,053 |
| 43 | Automated molecular microscopy: The new Leginon system Christian J. M. Suloway, James Pulokas, Denis Fellmann et al. · Journal of Structural Biology | 21 Apr 2005 | 2,048 |
| 44 | Extending the methodology of X-ray crystallography to allow imaging of micrometre-sized non-crystalline specimens Jianwei Miao, Pambos S. Charalambous, Janos Kirz et al. · Nature | Jul 1999 | 1,983 |
| 45 | Electron counting and beam-induced motion correction enable near-atomic-resolution single-particle cryo-EM Xueming Li, Paul E. Mooney, Shawn Q. Zheng et al. · Nature Methods | 3 May 2013 | 1,968 |
| 46 | Non-uniform refinement: adaptive regularization improves single-particle cryo-EM reconstruction Ali Punjani, Haowei Zhang, David J. Fleet · Nature Methods | 30 Nov 2020 | 1,940 |
| 47 | 7 × 7 Reconstruction on Si(111) Resolved in Real Space Gerd K. Binnig, Heinrich Rohrer, Ch. Gerber et al. · Physical Review Letters | 10 Jan 1983 | 1,904 |
| 48 | Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs Tristan Bepler, Andrew Morin, Micah Rapp et al. · Nature Methods | 7 Oct 2019 | 1,871 |
| 49 | Serial Block-Face Scanning Electron Microscopy to Reconstruct Three-Dimensional Tissue Nanostructure Winfried T. Denk, Heinz Horstmann · PLoS Biology | 14 Oct 2004 | 1,735 |
| 50 | ThunderSTORM: a comprehensive ImageJ plug-in for PALM and STORM data analysis and super-resolution imaging Martin Ovesný, Pavel Křížek, Josef Borkovec et al. · Bioinformatics | 26 Apr 2014 | 1,704 |
Citations are OpenAlex's own counts, from its 2026-09-23 snapshot, so the ranking can differ from Google Scholar or Web of Science. A paper is listed for a field when OpenAlex files it under one of the field's topics; retracted papers and papers whose citation count cannot be traced to citing works are left out, and a preprint and the article it became are shown once. Release dates are OpenAlex's: where a source gave only a month or a year, that is what is shown. How the lists are chosen.