Bibliography

BMR+19

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.

BRL+15

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.

CMF+13

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.

FLS17

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.

HS17

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

JBH05

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.

KFSL16

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.

KST14

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.

MG03

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.

PRFB17

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.

RG15

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.

RH03

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.

Sch10

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.

Sch12a

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.

Sch12b

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.

SC12

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.

SNRS+08

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.

Smi99

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.

TPB+07

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.

Zha16

Kai Zhang. Gctf: Real-time CTF determination and correction. Journal of Structural Biology, 193(1):1–12, January 2016. doi:10.1016/j.jsb.2015.11.003.

ZPA+17

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.

ZNS20

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.