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Volumn 171, Issue 1, 2010, Pages 18-30

Probabilistic principal component analysis with expectation maximization (PPCA-EM) facilitates volume classification and estimates the missing data

Author keywords

Electron microscopy; Expectation maximization; Image processing; Missing cone missing wedge; Multivariate statistical analysis; Principal component analysis; Single particle reconstruction

Indexed keywords

6 PHOSPHOFRUCTOKINASE;

EID: 77953613557     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.04.002     Document Type: Article
Times cited : (45)

References (57)
  • 1
    • 34249936593 scopus 로고    scopus 로고
    • The structure of the ATP-bound state of S. cerevisiae phosphofructokinase determined by cryo-electron microscopy
    • Barcena M., Radermacher M., Bar J., Kopperschlager G., Ruiz T. The structure of the ATP-bound state of S. cerevisiae phosphofructokinase determined by cryo-electron microscopy. Journal of Structure Biology 2007, 159:135-143.
    • (2007) Journal of Structure Biology , vol.159 , pp. 135-143
    • Barcena, M.1    Radermacher, M.2    Bar, J.3    Kopperschlager, G.4    Ruiz, T.5
  • 4
    • 0022799046 scopus 로고
    • Reconstitution of molecule images analysed by correspondence analysis: a tool for structural interpretation [published erratum appears in J Microsc 1987 May;146(Pt 2):222]
    • Bretaudiere J., Frank J. Reconstitution of molecule images analysed by correspondence analysis: a tool for structural interpretation [published erratum appears in J Microsc 1987 May;146(Pt 2):222]. Journal of Microscopy 1986, 144:1-14.
    • (1986) Journal of Microscopy , vol.144 , pp. 1-14
    • Bretaudiere, J.1    Frank, J.2
  • 5
    • 0019417742 scopus 로고
    • Suitability of control materials. General principles and methods of investigation
    • Bretaudiere J., Dumont G., Rej R., Bailly M. Suitability of control materials. General principles and methods of investigation. Clinical Chemistry 1981, 27:798-805.
    • (1981) Clinical Chemistry , vol.27 , pp. 798-805
    • Bretaudiere, J.1    Dumont, G.2    Rej, R.3    Bailly, M.4
  • 6
    • 0025364361 scopus 로고
    • Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles
    • Carazo J.M., Rivera F.F., Zapata E.L., Radermacher M., Frank J. Fuzzy sets-based classification of electron microscopy images of biological macromolecules with an application to ribosomal particles. Journal of Microscopy 1990, 157:187-204.
    • (1990) Journal of Microscopy , vol.157 , pp. 187-204
    • Carazo, J.M.1    Rivera, F.F.2    Zapata, E.L.3    Radermacher, M.4    Frank, J.5
  • 7
    • 34548361908 scopus 로고    scopus 로고
    • Direct localization of the 51 and 24kDa subunits of mitochondrial complex I by three-dimensional difference imaging
    • Clason T., Zickermann V., Ruiz T., Brandt U., Radermacher M. Direct localization of the 51 and 24kDa subunits of mitochondrial complex I by three-dimensional difference imaging. Journal Structure Biology 2007, 159:433-442.
    • (2007) Journal Structure Biology , vol.159 , pp. 433-442
    • Clason, T.1    Zickermann, V.2    Ruiz, T.3    Brandt, U.4    Radermacher, M.5
  • 8
    • 0017676001 scopus 로고
    • Iterative three-dimensional image reconstruction from tomographic projections
    • Colsher J.G. Iterative three-dimensional image reconstruction from tomographic projections. Computer Graphics and Image Process 1977, 6:513.
    • (1977) Computer Graphics and Image Process , vol.6 , pp. 513
    • Colsher, J.G.1
  • 9
    • 0014894609 scopus 로고
    • The reconstruction of a three-dimensional structure from projections and its application to electron microscopy
    • Crowther R.A., DeRosier D.J., Klug A. The reconstruction of a three-dimensional structure from projections and its application to electron microscopy. Proceedings of the Royal Society London Series A 1970, 317:319-340.
    • (1970) Proceedings of the Royal Society London Series A , vol.317 , pp. 319-340
    • Crowther, R.A.1    DeRosier, D.J.2    Klug, A.3
  • 12
    • 0002579892 scopus 로고
    • La méthode de nuées dynamiques
    • Diday E. La méthode de nuées dynamiques. Revue Statistique Appliquée 1971, 19:19-34.
    • (1971) Revue Statistique Appliquée , vol.19 , pp. 19-34
    • Diday, E.1
  • 13
    • 0015644825 scopus 로고
    • A fuzzy relative of the ISODATA process and its use in detecting compact well-separated clusters
    • Dunn J. A fuzzy relative of the ISODATA process and its use in detecting compact well-separated clusters. Journal of Cybernetics 1973, 3:32-57.
    • (1973) Journal of Cybernetics , vol.3 , pp. 32-57
    • Dunn, J.1
  • 14
    • 33847232164 scopus 로고    scopus 로고
    • Structure determination in situ by averaging of tomograms
    • Förster F., Hegerl R. Structure determination in situ by averaging of tomograms. Methods in Cell Biology Volume 2007, 79:741-767.
    • (2007) Methods in Cell Biology Volume , vol.79 , pp. 741-767
    • Förster, F.1    Hegerl, R.2
  • 16
    • 0020484108 scopus 로고
    • Correspondence analysis of aligned images of biological particles
    • Frank J., van Heel M. Correspondence analysis of aligned images of biological particles. Journal of Molecular Biology 1982, 161:134-137.
    • (1982) Journal of Molecular Biology , vol.161 , pp. 134-137
    • Frank, J.1    van Heel, M.2
  • 17
    • 0018243812 scopus 로고
    • Reconstruction of glutamine synthetase using computer averaging
    • Frank J., Goldfarb W., Eisenberg D., Baker T.S. Reconstruction of glutamine synthetase using computer averaging. Ultramicroscopy 1978, 3:283.
    • (1978) Ultramicroscopy , vol.3 , pp. 283
    • Frank, J.1    Goldfarb, W.2    Eisenberg, D.3    Baker, T.S.4
  • 19
    • 0037438344 scopus 로고    scopus 로고
    • Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding
    • Grünewald K., Medalia O., Gross A., Steven A.C., Baumeister W. Prospects of electron cryotomography to visualize macromolecular complexes inside cellular compartments: implications of crowding. Biophysical Chemistry 2003, 100:577-591.
    • (2003) Biophysical Chemistry , vol.100 , pp. 577-591
    • Grünewald, K.1    Medalia, O.2    Gross, A.3    Steven, A.C.4    Baumeister, W.5
  • 20
    • 0015759316 scopus 로고
    • ART: mathematics and applications (a report on the mathematical foundations and on the applicability to real data of the algebraic reconstruction techniques)
    • Herman G., Lent A., Rowland S. ART: mathematics and applications (a report on the mathematical foundations and on the applicability to real data of the algebraic reconstruction techniques). Journal of Theoretical Biology 1973, 42:1-32.
    • (1973) Journal of Theoretical Biology , vol.42 , pp. 1-32
    • Herman, G.1    Lent, A.2    Rowland, S.3
  • 23
    • 84944296850 scopus 로고
    • Three-dimensional electron microscopy of individual biological objects. II. Test calculations
    • a
    • Hoppe W., Schramm H.J., Sturm M., Hunsmann N., Gaßmann J. Three-dimensional electron microscopy of individual biological objects. II. Test calculations. Zeitschrift fuer Naturforschung 1976, 31a:1370-1379.
    • (1976) Zeitschrift fuer Naturforschung , vol.31 , pp. 1370-1379
    • Hoppe, W.1    Schramm, H.J.2    Sturm, M.3    Hunsmann, N.4    Gaßmann, J.5
  • 24
    • 84944295787 scopus 로고
    • Three-dimensional electron microscopy of individual biological objects. III. Experimental results on yeast fatty acid synthetase
    • a
    • Hoppe W., Schramm H.J., Sturm M., Hunsmann N., Gaßmann J. Three-dimensional electron microscopy of individual biological objects. III. Experimental results on yeast fatty acid synthetase. Zeitschrift fuer Naturforschung 1976, 31a:1380-1390.
    • (1976) Zeitschrift fuer Naturforschung , vol.31 , pp. 1380-1390
    • Hoppe, W.1    Schramm, H.J.2    Sturm, M.3    Hunsmann, N.4    Gaßmann, J.5
  • 25
    • 0014129195 scopus 로고
    • Hierarchical clustering schemes
    • Johnson S. Hierarchical clustering schemes. Psychometrika 1967, 2:241-254.
    • (1967) Psychometrika , vol.2 , pp. 241-254
    • Johnson, S.1
  • 26
    • 0020633272 scopus 로고
    • Three-dimensional reconstruction and averaging of 30S ribosomal subunits of Escherichia coli from electron micrographs
    • Knauer V., Hegerl R., Hoppe W. Three-dimensional reconstruction and averaging of 30S ribosomal subunits of Escherichia coli from electron micrographs. Journal of Molecular Biology 1983, 163:409-430.
    • (1983) Journal of Molecular Biology , vol.163 , pp. 409-430
    • Knauer, V.1    Hegerl, R.2    Hoppe, W.3
  • 28
    • 32544460568 scopus 로고    scopus 로고
    • The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles
    • Leschziner A.E., Nogales E. The orthogonal tilt reconstruction method: an approach to generating single-class volumes with no missing cone for ab initio reconstruction of asymmetric particles. Journal of Structural Biology 2006, 153:284-299.
    • (2006) Journal of Structural Biology , vol.153 , pp. 284-299
    • Leschziner, A.E.1    Nogales, E.2
  • 31
    • 0002512329 scopus 로고
    • Methods for the enhancement of image detail and accentuation of structure in electron microscopy
    • Markham R., Frey S., Hills G. Methods for the enhancement of image detail and accentuation of structure in electron microscopy. Virology 1963, 20:88-102.
    • (1963) Virology , vol.20 , pp. 88-102
    • Markham, R.1    Frey, S.2    Hills, G.3
  • 32
  • 33
    • 84868684804 scopus 로고    scopus 로고
    • Numpy,. NumPy Reference. Available from
    • Numpy, 2009. NumPy Reference. Available from: http://numpy.org.
    • (2009)
  • 34
    • 0020536972 scopus 로고
    • Three-dimensional reconstruction and averaging of 50S ribosomal subunits of Escherichia coli from electron micrographs
    • Oettl H., Hegerl R., Hoppe W. Three-dimensional reconstruction and averaging of 50S ribosomal subunits of Escherichia coli from electron micrographs. Journal of Molecular Biology 1983, 163:431-450.
    • (1983) Journal of Molecular Biology , vol.163 , pp. 431-450
    • Oettl, H.1    Hegerl, R.2    Hoppe, W.3
  • 36
    • 0000325341 scopus 로고
    • On lines and planes of closest fit to systems of points in space
    • Pearson K. On lines and planes of closest fit to systems of points in space. Philosophical Magazine 1901, 2(572):559.
    • (1901) Philosophical Magazine , vol.2 , Issue.572 , pp. 559
    • Pearson, K.1
  • 37
    • 84868673618 scopus 로고
    • Dreidimensionale Rekonstruktion bei kegelfrörmiger Kippung im Elektronenmikroskop. Ph.D. Thesis, Technische Universität München.
    • Radermacher, M., 1980. Dreidimensionale Rekonstruktion bei kegelfrörmiger Kippung im Elektronenmikroskop. Ph.D. Thesis, Technische Universität München.
    • (1980)
    • Radermacher, M.1
  • 38
    • 0001339881 scopus 로고
    • Three-dimensional reconstruction of single particles from random and nonrandom tilt series
    • Radermacher M. Three-dimensional reconstruction of single particles from random and nonrandom tilt series. Journal of Electron Microscopy Technique 1988, 9:359-394.
    • (1988) Journal of Electron Microscopy Technique , vol.9 , pp. 359-394
    • Radermacher, M.1
  • 39
    • 0028375920 scopus 로고
    • Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms
    • Radermacher M. Three-dimensional reconstruction from random projections: orientational alignment via Radon transforms. Ultramicroscopy 1994, 53:121-136.
    • (1994) Ultramicroscopy , vol.53 , pp. 121-136
    • Radermacher, M.1
  • 40
    • 0001090508 scopus 로고    scopus 로고
    • Radon transform techniques for alignment and 3D reconstruction from random projections
    • Radermacher M. Radon transform techniques for alignment and 3D reconstruction from random projections. Scanning Microscopy 1997, 11:171-177.
    • (1997) Scanning Microscopy , vol.11 , pp. 171-177
    • Radermacher, M.1
  • 41
    • 0011869573 scopus 로고
    • Properties of 3-D reconstruction from projections by conical tilting compared to single axis tilting compared to single axis tilting. In: Proceedings of seventh European Congress on Electron Microscopy,.
    • Radermacher, M., Hoppe, W., 1980. Properties of 3-D reconstruction from projections by conical tilting compared to single axis tilting compared to single axis tilting. In: Proceedings of seventh European Congress on Electron Microscopy, vol. 1. pp. 132-133.
    • (1980) , vol.1 , pp. 132-133
    • Radermacher, M.1    Hoppe, W.2
  • 42
    • 0022605670 scopus 로고
    • A New 3-dimensional reconstruction scheme applied to the 50S ribosomal subunit of E. coli
    • Radermacher M., Wagenknecht T., Verschoor A., Frank J. A New 3-dimensional reconstruction scheme applied to the 50S ribosomal subunit of E. coli. Journal of Microscopy 1986, 141:Rp1-Rp2.
    • (1986) Journal of Microscopy , vol.141
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 43
    • 84985231782 scopus 로고
    • Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli
    • Radermacher M., Wagenknecht T., Verschoor A., Frank J. Three-dimensional reconstruction from a single-exposure, random conical tilt series applied to the 50S ribosomal subunit of Escherichia coli. Journal of Microscopy 1987, 146:113-136.
    • (1987) Journal of Microscopy , vol.146 , pp. 113-136
    • Radermacher, M.1    Wagenknecht, T.2    Verschoor, A.3    Frank, J.4
  • 46
    • 0035782688 scopus 로고    scopus 로고
    • The first three-dimensional structure of phosphofructokinase from Saccharomyces cerevisiae determined by electron microscopy of single particles
    • Ruiz T., Kopperschläger G., Radermacher M. The first three-dimensional structure of phosphofructokinase from Saccharomyces cerevisiae determined by electron microscopy of single particles. Journal of Structural Biology 2001, 136:167-180.
    • (2001) Journal of Structural Biology , vol.136 , pp. 167-180
    • Ruiz, T.1    Kopperschläger, G.2    Radermacher, M.3
  • 47
    • 0041334007 scopus 로고    scopus 로고
    • The 10.8-Å structure of Saccharomyces cerevisiae phosphofructokinase determined by cryoelectron microscopy: localization of the putative fructose 6-phosphate binding sites
    • Ruiz T., Mechin I., Bar J., Rypniewski W., Kopperschlager G., Radermacher M. The 10.8-Å structure of Saccharomyces cerevisiae phosphofructokinase determined by cryoelectron microscopy: localization of the putative fructose 6-phosphate binding sites. Journal of Structural Biology 2003, 143:124-134.
    • (2003) Journal of Structural Biology , vol.143 , pp. 124-134
    • Ruiz, T.1    Mechin, I.2    Bar, J.3    Rypniewski, W.4    Kopperschlager, G.5    Radermacher, M.6
  • 48
    • 0017477892 scopus 로고
    • Motif detection in quantum noise-limited electron micrographs by cross-correlation
    • Saxton W.O., Frank J. Motif detection in quantum noise-limited electron micrographs by cross-correlation. Ultramicroscopy 1977, 2:219-227.
    • (1977) Ultramicroscopy , vol.2 , pp. 219-227
    • Saxton, W.O.1    Frank, J.2
  • 49
    • 71049139404 scopus 로고    scopus 로고
    • Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization
    • Scheres S.H., Melero R., Valle M., Carazo J. Averaging of electron subtomograms and random conical tilt reconstructions through likelihood optimization. Structure 2009, 17:1563-1572.
    • (2009) Structure , vol.17 , pp. 1563-1572
    • Scheres, S.H.1    Melero, R.2    Valle, M.3    Carazo, J.4
  • 52
    • 0023102907 scopus 로고
    • Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction
    • van Heel M. Angular reconstitution: a posteriori assignment of projection directions for 3D reconstruction. Ultramicroscopy 1987, 21:111.
    • (1987) Ultramicroscopy , vol.21 , pp. 111
    • van Heel, M.1
  • 53
    • 0019728717 scopus 로고
    • Use of multivariate statistics in analysing the images of biological macromolecules
    • van Heel M., Frank J. Use of multivariate statistics in analysing the images of biological macromolecules. Ultramicroscopy 1981, 6:187-194.
    • (1981) Ultramicroscopy , vol.6 , pp. 187-194
    • van Heel, M.1    Frank, J.2
  • 54
    • 0031423486 scopus 로고    scopus 로고
    • Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification
    • Walz J., Typke D., Nitsch M., Koster A.J., Hegerl R., Baumeister W. Electron tomography of single ice-embedded macromolecules: three-dimensional alignment and classification. Journal of Structural Biology 1997, 120:387-395.
    • (1997) Journal of Structural Biology , vol.120 , pp. 387-395
    • Walz, J.1    Typke, D.2    Nitsch, M.3    Koster, A.J.4    Hegerl, R.5    Baumeister, W.6
  • 55
    • 33845310367 scopus 로고    scopus 로고
    • 3D reconstruction and processing of volumetric data in cryo-electron tomography
    • Winkler H. 3D reconstruction and processing of volumetric data in cryo-electron tomography. Journal of Structural Biology 2007, 157:126-137.
    • (2007) Journal of Structural Biology , vol.157 , pp. 126-137
    • Winkler, H.1
  • 56
    • 0033166855 scopus 로고    scopus 로고
    • Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle
    • Winkler H., Taylor K.A. Multivariate statistical analysis of three-dimensional cross-bridge motifs in insect flight muscle. Ultramicroscopy 1999, 77:141-152.
    • (1999) Ultramicroscopy , vol.77 , pp. 141-152
    • Winkler, H.1    Taylor, K.A.2
  • 57
    • 77953612028 scopus 로고    scopus 로고
    • Multivariate statistical analysis of volumes with missing data. In: Proceedings of 35th Annual Meeting of the Microscopy Society of Canada, Montreal, 20-23 May.
    • Yu, L., Snapp, R., Radermacher, M., 2008. Multivariate statistical analysis of volumes with missing data. In: Proceedings of 35th Annual Meeting of the Microscopy Society of Canada, Montreal, 20-23 May.
    • (2008)
    • Yu, L.1    Snapp, R.2    Radermacher, M.3


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