Tristan Bepler, Andrew Morin, Micah Rapp, Julia Brasch, Lawrence Shapiro, Alex J. Noble, and Bonnie Berger. Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs. Nature Methods, 2019. doi:10.1038/s41592-019-0575-8.


Tanmay A. M. Bharat, Christopher J. Russo, Jan Löwe, Lori A. Passmore, and Sjors H. W. Scheres. Advances in Single-Particle Electron Cryomicroscopy Structure Determination applied to Sub-tomogram Averaging. Structure (London, England: 1993), 23(9):1743–1753, September 2015. doi:10.1016/j.str.2015.06.026.


Tim-Oliver Buchholz, Mareike Jordan, Gaia Pigino, and Florian Jug. Cryo-CARE: Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data. 2019 IEEE 16th International Symposium on Biomedical Imaging (ISBI 2019), pages 502–506, April 2019. doi:10.1109/ISBI.2019.8759519.


Shaoxia Chen, Greg McMullan, Abdul R. Faruqi, Garib N. Murshudov, Judith M. Short, Sjors H. W. Scheres, and Richard Henderson. High-resolution noise substitution to measure overfitting and validate resolution in 3d structure determination by single particle electron cryomicroscopy. Ultramicroscopy, 135:24–35, December 2013. doi:10.1016/j.ultramic.2013.06.004.


Paul Emsley, Bernhard Lohkamp, William G. Scott, and Kevin Cowtan. Features and development of coot. Acta Crystallographica Section D - Biological Crystallography, 66:486–501, 2010. doi:10.1107/S0907444910007493.


Rafael Fernandez-Leiro and Sjors H. W. Scheres. A pipeline approach to single-particle processing in RELION. Acta Crystallographica. Section D, Structural Biology, 73(Pt 6):496–502, June 2017. doi:10.1107/S2059798316019276.


Shaoda He and Sjors H. W. Scheres. Helical reconstruction in RELION. Journal of Structural Biology, 2017. doi:10.1016/j.jsb.2017.02.003.


David M Belnap J Bernard Heymann, Mónica Chagoyen. Common conventions for interchange and archiving of three-dimensional electron microscopy information in structural biology. Journal of Structural Biology, 151(2):196–207, 2005.


Kiarash Jamali, Lukas Käll, Rui Zhang, Alan Brown, Dari Kimanius, and Sjors H. W. Scheres. Automated model building and protein identification in cryo-EM maps. Nature, 628(8007):450–457, April 2024. doi:10.1038/s41586-024-07215-4.


Dari Kimanius, Björn O Forsberg, Sjors HW Scheres, and Erik Lindahl. Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2. eLife, November 2016. doi:10.7554/eLife.18722.


Alp Kucukelbir, Fred J Sigworth, and Hemant D Tagare. Quantifying the local resolution of cryo-EM density maps. Nature methods, 11(1):63–65, January 2014. doi:10.1038/nmeth.2727.


Joseph A Mindell and Nikolaus Grigorieff. Accurate determination of local defocus and specimen tilt in electron microscopy. Journal of Structural Biology, 142(3):334–347, 2003.


Ali Punjani, John L. Rubinstein, David J. Fleet, and Marcus A. Brubaker. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods, 14(3):290–296, March 2017. doi:10.1038/nmeth.4169.


Alexis Rohou and Nikolaus Grigorieff. CTFFIND4: Fast and accurate defocus estimation from electron micrographs. Journal of Structural Biology, 192(2):216–221, November 2015. doi:10.1016/j.jsb.2015.08.008.


Peter B Rosenthal and Richard Henderson. Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology, 333(4):721–745, October 2003.


Sjors H W Scheres. Classification of Structural Heterogeneity by Maximum-Likelihood Methods. In Cryo-EM, Part B: 3-D Reconstruction, volume 482 of Methods in Enzymology, pages 295–320. Academic Press, 2010.


Sjors H W Scheres. A Bayesian view on cryo-EM structure determination. Journal of Molecular Biology, 415(2):406–418, January 2012. doi:10.1016/j.jmb.2011.11.010.


Sjors H W Scheres. RELION: Implementation of a Bayesian approach to cryo-EM structure determination. Journal of Structural Biology, 180(3):519–530, December 2012. doi:10.1016/j.jsb.2012.09.006.


Sjors H W Scheres and Shaoxia Chen. Prevention of overfitting in cryo-EM structure determination. Nature methods, 9(9):853–854, September 2012. doi:10.1038/nmeth.2115.


Sjors H W Scheres, R. Nunez-Ramirez, C. O. S Sorzano, J. M Carazo, and R. Marabini. Image processing for electron microscopy single-particle analysis using XMIPP. Nature Protocols, 3(6):977–90, 2008.


Johannes Schwab, Dari Kimanius, Alister Burt, Tom Dendooven, and Sjors Scheres. Dynamight: estimating molecular motions with improved reconstruction from cryo-em images. bioRxiv, 2023. doi:10.1101/2023.10.18.562877.


J M Smith. Ximdisp–A visualization tool to aid structure determination from electron microscope images. Journal of structural biology, 125(2-3):223–228, May 1999. doi:10.1006/jsbi.1998.4073.


Guang Tang, Liwei Peng, Philip R Baldwin, Deepinder S Mann, Wen Jiang, Ian Rees, and Steven J Ludtke. EMAN2: an extensible image processing suite for electron microscopy. Journal of Structural Biology, 157(1):38–46, January 2007. doi:10.1016/j.jsb.2006.05.009.


Thorsten Wagner, Felipe Merino, Markus Stabrin, Toshio Moriya, Claudia Antoni, Amir Apelbaum, Philine Hagel, Oleg Sitsel, Tobias Raisch, Daniel Prumbaum, Dennis Quentin, Daniel Roderer, Sebastian Tacke, Birte Siebolds, Evelyn Schubert, Tanvir R. Shaikh, Pascal Lill, Christos Gatsogiannis, and Stefan Raunser. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Communications Biology, 2(1):1–13, June 2019. doi:10.1038/s42003-019-0437-z.


Keitaro Yamashita, Colin M. Palmer, Tom Burnley, and Garib N. Murshudov. Cryo-EM single-particle structure refinement and map calculation using \it Servalcat. Acta Crystallographica Section D, 77(10):1282–1291, Oct 2021. doi:10.1107/S2059798321009475.


Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Kliment A. Verba, Yifan Cheng, and David A. Agard. MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy. Nature Methods, 14(4):331–332, April 2017. doi:10.1038/nmeth.4193.


Jasenko Zivanov, Takanori Nakane, and Sjors Scheres. Estimation of high-order aberrations and anisotropic magnification from cryo-em datasets in relion-3.1. IUCrJ, 2020. doi:10.1107/S2052252520000081.