Crossref journal-article
Elsevier BV
Journal of Structural Biology (78)
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Lyumkis, D., Brilot, A. F., Theobald, D. L., & Grigorieff, N. (2013). Likelihood-based classification of cryo-EM images using FREALIGN. Journal of Structural Biology, 183(3), 377–388.

Authors 4
  1. Dmitry Lyumkis (first)
  2. Axel F. Brilot (additional)
  3. Douglas L. Theobald (additional)
  4. Nikolaus Grigorieff (additional)
References 51 Referenced 241
  1. 10.1038/308032a0 / Nature / Cryo-electron microscopy of viruses by Adrian (1984)
  2. 10.7554/eLife.00461 / eLife / Ribosome structures to near-atomic resolution from thirty thousand cryo-EM particles by Bai (2013)
  3. 10.1016/j.jsb.2009.02.012 / J. Struct. Biol. / Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules by Baxter (2009)
  4. 10.1016/j.jsb.2012.02.003 / J. Struct. Biol. / Beam-induced motion of vitrified specimen on holey carbon film by Brilot (2012)
  5. 10.1016/j.str.2012.08.026 / Structure / Movies of ice-embedded particles enhance resolution in electron cryo-microscopy by Campbell (2012)
  6. 10.1073/pnas.0904024106 / Proc. Natl. Acad. Sci. USA / Molecular interactions in rotavirus assembly and uncoating seen by high-resolution cryo-EM by Chen (2009)
  7. 10.1109/18.857786 / IEEE Trans. Inf. Theory / Ab initio reconstruction and experimental design for cryo electron microscopy by Doerschuk (2000)
  8. 10.1016/j.jsb.2007.11.007 / J. Struct. Biol. / Detection and separation of heterogeneity in molecular complexes by statistical analysis of their two-dimensional projections by Elad (2008)
  9. 10.1016/j.str.2010.06.001 / Structure / Ab initio structure determination from electron microscopic images of single molecules coexisting in different functional states by Elmlund (2010)
  10. 10.1038/nature09206 / Nature / Ribosome dynamics and tRNA movement by time-resolved electron cryomicroscopy by Fischer (2010)
  11. 10.1146/annurev-biochem-060408-173330 / Annu. Rev. Biochem. / Structure and dynamics of a processive Brownian motor: the translating ribosome by Frank (2010)
  12. 10.1016/S0076-6879(88)64032-8 / Methods Enzymol. / Studying ribosome structure by electron microscopy and computer-image processing by Frank (1988)
  13. 10.1006/jmbi.1998.1668 / J. Mol. Biol. / Three-dimensional structure of bovine NADH:ubiquinone oxidoreductase (complex I) at 22 A in ice by Grigorieff (1998)
  14. 10.1016/j.jsb.2006.05.004 / J. Struct. Biol. / FREALIGN: high-resolution refinement of single particle structures by Grigorieff (2007)
  15. 10.1016/j.sbi.2011.01.008 / Curr. Opin. Struct. Biol. / Near-atomic resolution reconstructions of icosahedral viruses from electron cryo-microscopy by Grigorieff (2011)
  16. 10.1016/j.jsb.2006.06.006 / J. Struct. Biol. / Bsoft: image processing and molecular modeling for electron microscopy by Heymann (2007)
  17. 10.1016/j.jsb.2009.01.002 / J. Struct. Biol. / Appion: an integrated, database-driven pipeline to facilitate EM image processing by Lander (2009)
  18. 10.1016/S0076-6879(10)83004-6 / Methods Enzymol. / Unified data resource for cryo-EM by Lawson (2010)
  19. 10.1093/nar/gkq880 / Nucleic Acids Res. / EMDataBank.org: unified data resource for CryoEM by Lawson (2011)
  20. {'key': '10.1016/j.jsb.2013.07.005_b0100', 'first-page': '169', 'article-title': 'Classification by Bootstrapping in Single Particle Methods', 'volume': '2010', 'author': 'Liao', 'year': '2010', 'journal-title': 'Proc. IEEE Int. Symp. Biomed. Imaging'} / Proc. IEEE Int. Symp. Biomed. Imaging / Classification by Bootstrapping in Single Particle Methods by Liao (2010)
  21. 10.1006/jsbi.1999.4174 / J. Struct. Biol. / EMAN: semiautomated software for high-resolution single-particle reconstructions by Ludtke (1999)
  22. 10.1016/j.sbi.2009.01.001 / Curr. Opin. Struct. Biol. / Structural mapping of spliceosomes by electron microscopy by Luhrmann (2009)
  23. 10.1016/j.ultramic.2005.02.004 / Ultramicroscopy / ACE: automated CTF estimation by Mallick (2005)
  24. 10.1016/S1047-8477(03)00069-8 / J. Struct. Biol. / Accurate determination of local defocus and specimen tilt in electron microscopy by Mindell (2003)
  25. 10.1126/science.1193220 / Science / Visualizing ribosome biogenesis: parallel assembly pathways for the 30S subunit by Mulder (2010)
  26. 10.1016/j.jsb.2006.01.003 / J. Struct. Biol. / Estimation of variance in single-particle reconstruction using the bootstrap technique by Penczek (2006)
  27. 10.1002/jcc.20084 / J. Comput. Chem. / UCSF Chimera–a visualization system for exploratory research and analysis by Pettersen (2004)
  28. 10.1016/0304-3991(88)90016-2 / Ultramicroscopy / Three-dimensional reconstruction from electron micrographs of disordered specimens. I. Method by Provencher (1988)
  29. 10.1038/nature09547 / Nature / Head swivel on the ribosome facilitates translocation by means of intra-subunit tRNA hybrid sites by Ratje (2010)
  30. 10.1016/j.jmb.2003.07.013 / J. Mol. Biol. / Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy by Rosenthal (2003)
  31. 10.1016/S0076-6879(10)82012-9 / Methods Enzymol. / Classification of structural heterogeneity by maximum-likelihood methods by Scheres (2010)
  32. 10.1016/j.jmb.2011.11.010 / J. Mol. Biol. / A Bayesian view on cryo-EM structure determination by Scheres (2012)
  33. 10.1016/j.jsb.2012.09.006 / J. Struct. Biol. / RELION: implementation of a Bayesian approach to cryo-EM structure determination by Scheres (2012)
  34. 10.1093/bioinformatics/bti1140 / Bioinformatics / Fast maximum-likelihood refinement of electron microscopy images by Scheres (2005)
  35. 10.1016/j.jmb.2005.02.031 / J. Mol. Biol. / Maximum-likelihood multi-reference refinement for electron microscopy images by Scheres (2005)
  36. 10.1038/nprot.2008.62 / Nat. Protoc. / Image processing for electron microscopy single-particle analysis using XMIPP by Scheres (2008)
  37. 10.1038/emboj.2009.26 / EMBO J. / GTPase activation of elongation factor EF-Tu by the ribosome during decoding by Schuette (2009)
  38. 10.1016/j.jsb.2010.01.007 / J. Struct. Biol. / Automated multi-model reconstruction from single-particle electron microscopy data by Shatsky (2010)
  39. 10.1006/jsbi.1998.4014 / J. Struct. Biol. / A maximum-likelihood approach to single-particle image refinement by Sigworth (1998)
  40. 10.1016/S0076-6879(10)82011-7 / Methods Enzymol. / An introduction to maximum-likelihood methods in cryo-EM by Sigworth (2010)
  41. 10.1016/j.jsb.2012.05.005 / J. Struct. Biol. / Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter by Sindelar (2012)
  42. 10.1016/j.sbi.2009.08.001 / Curr. Opin. Struct. Biol. / Exploring conformational modes of macromolecular assemblies by multiparticle cryo-EM by Spahn (2009)
  43. 10.1016/j.ultramic.2004.08.008 / Ultramicroscopy / Noise bias in the refinement of structures derived from single particles by Stewart (2004)
  44. 10.1126/science.186.4168.1036 / Science / Electron diffraction of frozen, hydrated protein crystals by Taylor (1974)
  45. 10.1515/zna-1966-0417 / Z. Naturforsch. / Zur Defokussierungsabhängigkeit des Phasenkontrastes bei der elektronenmikroskopischen Abbildung by Thon (1966)
  46. 10.1002/j.1460-2075.1985.tb03944.x / EMBO J. / Characteristic views of E. coli and B. stearothermophilus 30S ribosomal subunits in the electron microscope by van Heel (1985)
  47. 10.1006/jsbi.1996.0004 / J. Struct. Biol. / A new generation of the IMAGIC image processing system by van Heel (1996)
  48. 10.1016/0304-3991(88)90017-4 / Ultramicroscopy / Three-dimensional reconstruction from electron micrographs of disordered specimens. II. Implementation and results by Vogel (1988)
  49. 10.1016/j.jsb.2009.12.005 / J. Struct. Biol. / A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy by Voss (2010)
  50. 10.1016/j.str.2011.12.007 / Structure / Iterative stable alignment and clustering of 2D transmission electron microscope images by Yang (2012)
  51. 10.1016/j.jsb.2007.09.013 / J. Struct. Biol. / A maximum likelihood approach to two-dimensional crystals by Zeng (2007)
Dates
Type When
Created 12 years, 1 month ago (July 17, 2013, 5:15 p.m.)
Deposited 1 year, 3 months ago (May 14, 2024, 6:17 p.m.)
Indexed 2 weeks, 5 days ago (Aug. 2, 2025, 12:56 a.m.)
Issued 11 years, 11 months ago (Sept. 1, 2013)
Published 11 years, 11 months ago (Sept. 1, 2013)
Published Print 11 years, 11 months ago (Sept. 1, 2013)
Funders 1
  1. National Institutes of Health 10.13039/100000002

    Region: Americas

    gov (National government)

    Labels3
    1. Institutos Nacionales de la Salud
    2. US National Institutes of Health
    3. NIH
    Awards3
    1. R01 GM094468
    2. P41 GM103310
    3. P01 GM62580

@article{Lyumkis_2013, title={Likelihood-based classification of cryo-EM images using FREALIGN}, volume={183}, ISSN={1047-8477}, url={http://dx.doi.org/10.1016/j.jsb.2013.07.005}, DOI={10.1016/j.jsb.2013.07.005}, number={3}, journal={Journal of Structural Biology}, publisher={Elsevier BV}, author={Lyumkis, Dmitry and Brilot, Axel F. and Theobald, Douglas L. and Grigorieff, Nikolaus}, year={2013}, month=sep, pages={377–388} }