Crossref journal-article
Elsevier BV
Journal of Structural Biology (78)
Bibliography

Chen, Y., Pfeffer, S., Hrabe, T., Schuller, J. M., & Förster, F. (2013). Fast and accurate reference-free alignment of subtomograms. Journal of Structural Biology, 182(3), 235–245.

Authors 5
  1. Yuxiang Chen (first)
  2. Stefan Pfeffer (additional)
  3. Thomas Hrabe (additional)
  4. Jan Michael Schuller (additional)
  5. Friedrich Förster (additional)
References 52 Referenced 72
  1. 10.1016/j.jsb.2010.05.013 / J. Struct. Biol. / Subtomogram alignment by adaptive Fourier coefficient thresholding by Amat (2010)
  2. 10.1016/j.sbi.2009.06.005 / Curr. Opin. Struct. Biol. / Membrane protein structure determination using cryo-electron tomography and 3D image averaging by Bartesaghi (2009)
  3. 10.1016/j.jsb.2008.02.008 / J. Struct. Biol. / Classification and 3D averaging with missing wedge correction in biological electron tomography by Bartesaghi (2008)
  4. 10.1038/nmeth.1390 / Nat. Methods / Visual proteomics of the human pathogen Leptospira interrogans by Beck (2009)
  5. 10.1073/pnas.0903535106 / Proc. Natl. Acad. Sci. USA / Structure and assembly of immature HIV by Briggs (2009)
  6. 10.1016/S0076-6879(10)70027-6 / Methods Enzymol. / The use of in vitro assays to measure endoplasmic reticulum-associated degradation by Brodsky (2010)
  7. 10.1016/j.jsb.2011.12.017 / J. Struct. Biol. / Dynamo: a flexible, user-friendly development tool for subtomogram averaging of cryo-EM data in high-performance computing environments by Castano-Diez (2012)
  8. Chen, Y., Hrabe, T., Pfeffer, S., Pauly, O., Mateus, D., Navab, N., Förster, F., 2012. Detection and identification of macromolecular complexes in cryo-electron tomograms using support vector machines. In: Biomedical Imaging (ISBI). 2012 9th IEEE International Symposium on IEEE. Barcelona, IEEE, pp. 1373–1376.
  9. 10.1098/rspa.1970.0119 / Proc. Royal Soc. / The reconstruction of a three-dimensional structure from its projections and its applications to electron microscopy by Crowther (1970)
  10. 10.1016/j.jsb.2012.09.008 / J. Struct. Biol. / Unraveling the structure of membrane proteins in situ by transfer function corrected cryo-electron tomography by Eibauer (2012)
  11. 10.1016/j.ultramic.2006.02.004 / Ultramicroscopy / CTF determination and correction in electron cryotomography by Fernandez (2006)
  12. 10.1016/S0091-679X(06)79029-X / Methods Cell Biol. / Structure determination in situ by averaging of tomograms by Förster (2007)
  13. 10.1016/S0076-6879(10)83011-3 / Methods Enzymol. / Visual Proteomics by Förster (2010)
  14. 10.1016/j.jsb.2007.07.006 / J. Struct. Biol. / Classification of cryo-electron sub-tomograms using constrained correlation by Förster (2008)
  15. 10.1073/pnas.0409178102 / Proc. Natl. Acad. Sci. USA / Retrovirus envelope protein complex structure in situ studied by cryo-electron tomography by Förster (2005)
  16. 10.1073/pnas.172520299 / Proc. Natl. Acad. Sci. USA / Identification of macromolecular complexes in cryoelectron tomograms of phantom cells by Frangakis (2002)
  17. {'key': '10.1016/j.jsb.2013.03.002_b0085', 'first-page': '125', 'article-title': 'On the correction of the contrast transfer-function in biological electron-microscopy', 'volume': '98', 'author': 'Frank', 'year': '1995', 'journal-title': 'Optik'} / Optik / On the correction of the contrast transfer-function in biological electron-microscopy by Frank (1995)
  18. 10.1016/j.ultramic.2010.10.010 / Ultramicroscopy / Images of paraffin monolayer crystals with perfect contrast: minimization of beam-induced specimen motion by Glaeser (2011)
  19. 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)
  20. 10.1107/S0907444900009549 / Acta Crystallogr. D Biol. Crystallogr. / Resolution measurement in structures derived from single particles by Grigorieff (2000)
  21. 10.1126/science.1090284 / Science / Three-dimensional structure of herpes simplex virus from cryo-electron tomography by Grünewald (2003)
  22. 10.1088/1748-0221/6/03/C03003 / J Instrum. / A high frame rate, 16 million pixels, radiation hard CMOS sensor by Guerrini (2011)
  23. 10.1007/s00041-003-0018-9 / J. Fourier Anal. Appl. / FFTs for the 2-sphere-improvements and variations by Healy (2003)
  24. 10.1016/j.jsb.2011.05.011 / J. Struct. Biol. / Clustering and variance maps for cryo-electron tomography using wedge-masked differences by Heumann (2011)
  25. 10.1016/j.jsb.2006.06.006 / J. Struct. Biol. / Bsoft: image processing and molecular modeling for electron microscopy by Heymann (2007)
  26. {'year': '1931', 'series-title': 'The Theory of Spherical and Ellipsoidal Harmonics', 'author': 'Hobson', 'key': '10.1016/j.jsb.2013.03.002_b0265'} / The Theory of Spherical and Ellipsoidal Harmonics by Hobson (1931)
  27. 10.1016/j.jsb.2011.12.003 / J. Struct. Biol. / PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis by Hrabe (2012)
  28. Huhle, B., Schairer, T., Straßer, W., 2009. Normalized cross-correlation using SOFT. Local and non-local approximation in image processing, In: Local and Non-Local Approximation in Image Processing (LNLA 2009), International Workshop on IEEE, IEEE, pp. 82–86. (10.1109/LNLA.2009.5278398)
  29. 10.1016/j.jsb.2011.06.003 / J. Struct. Biol. / Computer controlled cryo-electron microscopy–TOM(2) a software package for high-throughput applications by Korinek (2011)
  30. 10.1007/s00041-008-9013-5 / J. Fourier Anal. Appl. / FFTs on the rotation group by Kostelec (2008)
  31. 10.1107/S0907444902009794 / Acta Crystallogr. D Biol. Crystallogr. / Fast rotational matching by Kovacs (2002)
  32. 10.1016/j.sbi.2012.07.006 / Curr. Opin. Struct. Biol. / Go hybrid: EM, crystallography, and beyond by Lander (2012)
  33. 10.1038/nature07159 / Nature / Molecular architecture of native HIV-1 gp120 trimers by Liu (2008)
  34. 10.1146/annurev.biochem.73.011303.074112 / Annu. Rev. Biochem. / Structural studies by electron tomography: from cells to molecules by Lucic (2005)
  35. 10.1109/TPAMI.2006.150 / IEEE Trans. Pattern Anal. Mach. Intell. / Rotation recovery from spherical images without correspondences by Makadia (2006)
  36. 10.1016/j.jsb.2004.10.006 / J. Struct. Biol. / TOM software toolbox: acquisition and analysis for electron tomography by Nickell (2005)
  37. 10.1016/j.str.2012.06.010 / Structure / Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes by Pfeffer (2012)
  38. 10.1016/S0304-3991(02)00333-9 / Ultramicroscopy / Particle finding in electron micrographs using a fast local correlation algorithm by Roseman (2003)
  39. 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)
  40. 10.1038/nmeth.2115 / Nat. Methods / Prevention of overfitting in cryo-EM structure determination by Scheres (2012)
  41. 10.1016/j.str.2009.10.009 / Structure / Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization by Scheres (2009)
  42. 10.1016/j.jsb.2007.09.018 / J. Struct. Biol. / Methods for aligning and for averaging 3D volumes with missing data by Schmid (2008)
  43. 10.1016/j.ultramic.2004.08.008 / Ultramicroscopy / Noise bias in the refinement of structures derived from single particles by Stewart (2004)
  44. 10.1016/j.jsb.2010.08.005 / J. Struct. Biol. / Maximum likelihood based classification of electron tomographic data by Stölken (2010)
  45. 10.1371/journal.ppat.0020091 / PLoS Pathog. / The SIV surface spike imaged by electron tomography: one leg or three? by Subramaniam (2006)
  46. 10.1016/j.jsb.2009.03.019 / J. Struct. Biol. / Fully automated, sequential tilt-series acquisition with Leginon by Suloway (2009)
  47. 10.1006/jsbi.1997.3934 / J. Struct. Biol. / Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification by Walz (1997)
  48. 10.1016/j.jsb.2008.10.004 / J. Struct. Biol. / Tomographic subvolume alignment and subvolume classification applied to myosin V and SIV envelope spikes by Winkler (2009)
  49. 10.1016/j.str.2006.05.019 / Structure / Proteasome assembly triggers a switch required for active-site maturation by Witt (2006)
  50. 10.1016/j.jsb.2012.02.014 / J. Struct. Biol. / High-throughput subtomogram alignment and classification by Fourier space constrained fast volumetric matching by Xu (2012)
  51. 10.1016/j.jsb.2009.08.002 / J. Struct. Biol. / Contrast transfer function correction applied to cryo-electron tomography and sub-tomogram averaging by Zanetti (2009)
  52. 10.1016/S0076-6879(10)81012-2 / Meth. Enzymol. / Automated data collection for electron microscopic tomography by Zheng (2010)
Dates
Type When
Created 12 years, 4 months ago (March 22, 2013, 4:46 a.m.)
Deposited 6 years, 1 month ago (July 11, 2019, 2:48 a.m.)
Indexed 3 weeks, 6 days ago (July 24, 2025, 8:02 a.m.)
Issued 12 years, 2 months ago (June 1, 2013)
Published 12 years, 2 months ago (June 1, 2013)
Published Print 12 years, 2 months ago (June 1, 2013)
Funders 0

None

@article{Chen_2013, title={Fast and accurate reference-free alignment of subtomograms}, volume={182}, ISSN={1047-8477}, url={http://dx.doi.org/10.1016/j.jsb.2013.03.002}, DOI={10.1016/j.jsb.2013.03.002}, number={3}, journal={Journal of Structural Biology}, publisher={Elsevier BV}, author={Chen, Yuxiang and Pfeffer, Stefan and Hrabe, Thomas and Schuller, Jan Michael and Förster, Friedrich}, year={2013}, month=jun, pages={235–245} }