A citation-based method for searching scientific literature

Ellen D Zhong, Tristan Bepler, Bonnie Berger, Joseph H Davis. Nat Methods 2021
Times Cited: 91







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



Times Cited
  Times     Co-cited
Similarity



cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination.
Ali Punjani, John L Rubinstein, David J Fleet, Marcus A Brubaker. Nat Methods 2017
42


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
27

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
27

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION.
Takanori Nakane, Dari Kimanius, Erik Lindahl, Sjors Hw Scheres. Elife 2018
246
26

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
24

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
23

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
23

CTFFIND4: Fast and accurate defocus estimation from electron micrographs.
Alexis Rohou, Nikolaus Grigorieff. J Struct Biol 2015
23


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
18

Real-time cryo-electron microscopy data preprocessing with Warp.
Dimitry Tegunov, Patrick Cramer. Nat Methods 2019
329
18

Atomic-resolution protein structure determination by cryo-EM.
Ka Man Yip, Niels Fischer, Elham Paknia, Ashwin Chari, Holger Stark. Nature 2020
202
17

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
17

Biochemistry. The resolution revolution.
Werner Kühlbrandt. Science 2014
601
16

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs.
Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J Noble, Bonnie Berger. Nat Methods 2019
210
16

Retrieving functional pathways of biomolecules from single-particle snapshots.
Ali Dashti, Ghoncheh Mashayekhi, Mrinal Shekhar, Danya Ben Hail, Salah Salah, Peter Schwander, Amedee des Georges, Abhishek Singharoy, Joachim Frank, Abbas Ourmazd. Nat Commun 2020
36
38

Features and development of Coot.
P Emsley, B Lohkamp, W G Scott, K Cowtan. Acta Crystallogr D Biol Crystallogr 2010
15

Structure and Conformational Dynamics of the Human Spliceosomal Bact Complex.
David Haselbach, Ilya Komarov, Dmitry E Agafonov, Klaus Hartmuth, Benjamin Graf, Olexandr Dybkov, Henning Urlaub, Berthold Kastner, Reinhard Lührmann, Holger Stark. Cell 2018
113
14

Accurate prediction of protein structures and interactions using a three-track neural network.
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer,[...]. Science 2021
772
14




Identifying conformational states of macromolecules by eigen-analysis of resampled cryo-EM images.
Pawel A Penczek, Marek Kimmel, Christian M T Spahn. Structure 2011
68
16

Directly reconstructing principal components of heterogeneous particles from cryo-EM images.
Hemant D Tagare, Alp Kucukelbir, Fred J Sigworth, Hongwei Wang, Murali Rao. J Struct Biol 2015
41
26

Trajectories of the ribosome as a Brownian nanomachine.
Ali Dashti, Peter Schwander, Robert Langlois, Russell Fung, Wen Li, Ahmad Hosseinizadeh, Hstau Y Liao, Jesper Pallesen, Gyanesh Sharma, Vera A Stupina,[...]. Proc Natl Acad Sci U S A 2014
125
12

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
12


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
12

cisTEM, user-friendly software for single-particle image processing.
Timothy Grant, Alexis Rohou, Nikolaus Grigorieff. Elife 2018
453
12

Topaz-Denoise: general deep denoising models for cryoEM and cryoET.
Tristan Bepler, Kotaro Kelley, Alex J Noble, Bonnie Berger. Nat Commun 2020
76
13


Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Dorothee Liebschner, Pavel V Afonine, Matthew L Baker, Gábor Bunkóczi, Vincent B Chen, Tristan I Croll, Bradley Hintze, Li Wei Hung, Swati Jain, Airlie J McCoy,[...]. Acta Crystallogr D Struct Biol 2019
10

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
10



Addressing preferred specimen orientation in single-particle cryo-EM through tilting.
Yong Zi Tan, Philip R Baldwin, Joseph H Davis, James R Williamson, Clinton S Potter, Bridget Carragher, Dmitry Lyumkis. Nat Methods 2017
365
9



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

DeepPicker: A deep learning approach for fully automated particle picking in cryo-EM.
Feng Wang, Huichao Gong, Gaochao Liu, Meijing Li, Chuangye Yan, Tian Xia, Xueming Li, Jianyang Zeng. J Struct Biol 2016
78
10

Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy.
Niels Fischer, Andrey L Konevega, Wolfgang Wintermeyer, Marina V Rodnina, Holger Stark. Nature 2010
269
8


Time-resolved cryo-EM using Spotiton.
Venkata P Dandey, William C Budell, Hui Wei, Daija Bobe, Kashyap Maruthi, Mykhailo Kopylov, Edward T Eng, Peter A Kahn, Jenny E Hinshaw, Nidhi Kundu,[...]. Nat Methods 2020
46
17

A Bayesian approach to extracting free-energy profiles from cryo-electron microscopy experiments.
Julian Giraldo-Barreto, Sebastian Ortiz, Erik H Thiede, Karen Palacio-Rodriguez, Bob Carpenter, Alex H Barnett, Pilar Cossio. Sci Rep 2021
10
80

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.
C O S Sorzano, A Jiménez, J Mota, J L Vilas, D Maluenda, M Martínez, E Ramírez-Aportela, T Majtner, J Segura, R Sánchez-García,[...]. Acta Crystallogr F Struct Biol Commun 2019
29
27

High-Throughput Cryo-EM Enabled by User-Free Preprocessing Routines.
Yilai Li, Jennifer N Cash, John J G Tesmer, Michael A Cianfrocco. Structure 2020
25
32

EMPIAR: a public archive for raw electron microscopy image data.
Andrii Iudin, Paul K Korir, José Salavert-Torres, Gerard J Kleywegt, Ardan Patwardhan. Nat Methods 2016
159
7

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
7


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.