Project

General

Profile

Edit History

Appion citations » History » Version 25

Amber Herold, 01/12/2011 01:43 PM

1 11 Amber Herold 
h1. Appion Citations
2 1 Amber Herold 





    3
    2
    Amber Herold
    
Appion includes software from the following packages:





    4
    
    
    





    5
    
    
    





    6
    10
    Amber Herold
    
h3. ACE





    7
    2
    Amber Herold
    





    8
    10
    Amber Herold
    
* "ACE: automated CTF estimation." (2005) Mallick SP, Carragher B, Potter CS, Kriegman DJ. Ultramicroscopy. v104(1).  PMID: 15935913 





    9
    1
    Amber Herold
    





    10
    2
    Amber Herold
    
h3. Appion





    11
    1
    Amber Herold
    





    12
    
    
    
* "Appion: an integrated, database-driven pipeline to facilitate EM image processing." (2009) Lander GC, Stagg SM, Voss NR, et al.. J Struct Biol. v166(1).  PMID: 19263523  Free text: PMC2775544  DOI: 10.1016/j.jsb.2009.01.002 





    13
    
    
    
* "A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy." (2010) Voss NR, Lyumkis D, Cheng A, et al.. J Struct Biol. v169(3).  PMID: 20018246





    14
    
    
    





    15
    10
    Amber Herold
    
h3. CAN Reference-free Alignment





    16
    2
    Amber Herold
    





    17
    10
    Amber Herold
    
* "Topology representing network enables highly accurate classification of protein images taken by cryo electron-microscope without masking." (2003) Ogura T, Iwasaki K, Sato C. J Struct Biol. v143(3).  PMID: 14572474  





    18
    2
    Amber Herold
    





    19
    12
    Amber Herold
    





    20
    
    
    
h3. Chimera





    21
    
    
    





    22
    14
    Amber Herold
    
* Molecular graphics images were produced using the UCSF Chimera package from the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIH P41 RR001081). "UCSF Chimera--a visualization system for exploratory research and analysis":http://www.ncbi.nlm.nih.gov/pubmed/15264254. Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE. J Comput Chem. 2004 Oct;25(13):1605-12.





    23
    13
    Amber Herold
    
* "More on Chimera Citations":http://www.cgl.ucsf.edu/chimera/docs/credits.html





    24
    
    
    





    25
    12
    Amber Herold
    





    26
    1
    Amber Herold
    
h3. Clustering by Affinity Propogation





    27
    10
    Amber Herold
    





    28
    
    
    
* "Clustering by Passing Messages Between Data Points." (2007) Brendan J. Frey and Delbert Dueck. Science. v315(5814).  PMID: 17218491  





    29
    1
    Amber Herold
    





    30
    12
    Amber Herold
    
h3. CTFFind





    31
    10
    Amber Herold
    





    32
    1
    Amber Herold
    
* "Accurate determination of local defocus and specimen tilt in electron microscopy." (2003) Mindell, JA, Grigorieff N. J Struct Biol. v142(3).  PMID: 12781660  





    33
    10
    Amber Herold
    





    34
    12
    Amber Herold
    
h3. CTFTilt





    35
    1
    Amber Herold
    





    36
    17
    Amber Herold
    
* Mindell JA, GrigorieV N (2003) Accurate determination of local defocus and specimen tilt in electron microscopy. J Struct Biol 142:334–347. "PMID:12781660":http://www.ncbi.nlm.nih.gov/pubmed/12781660





    37
    12
    Amber Herold
    





    38
    
    
    
h3. DogPicker





    39
    
    
    





    40
    1
    Amber Herold
    
* "DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy." (2009) Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. J Struct Biol. v166(2).  PMID: 19374019  Free text: PMC2768396  





    41
    
    
    





    42
    24
    Amber Herold
    
h3. Ed's Iteration Alignment





    43
    
    
    





    44
    
    
    
* "Conformational flexibility of metazoan fatty acid synthase enables catalysis." (2009) Brignole EJ, Smith S, Asturias FJ., Nat Struct Mol Biol., v.16(2). PMID: 19151726, PMCID: 2653270





    45
    
    
    





    46
    10
    Amber Herold
    
h3. EMAN





    47
    4
    Amber Herold
    





    48
    1
    Amber Herold
    
* "EMAN: semiautomated software for high-resolution single-particle reconstructions." (1999) Ludtke SJ, Baldwin PR, Chiu W. J Struct Biol. v128(1).  PMID: 10600563  





    49
    
    
    





    50
    12
    Amber Herold
    
h3. EM-BFACTOR





    51
    
    
    





    52
    18
    Amber Herold
    
* "Optimal Determination of Particle Orientation":http://dx.doi.org/10.1016/j.jmb.2003.07.013, Absolute Hand and Contrast Loss in Single-particle Electron Cryomicroscopy P.B. Rosenthal and R. Henderson Journal of Molecular Biology 333:721-745, 2003.





    53
    19
    Amber Herold
    
* "Sharpening high resolution information in single particle electron cryomicroscopy":http://dx.doi.org/10.1016/j.jsb.2008.05.010 J.J. Fernandez, D. Luque, J.R. Caston, J.L. Carrascosa Journal of Structural Biology 164:170-175, 2008. PMID:18614378





    54
    18
    Amber Herold
    





    55
    12
    Amber Herold
    
h3. FindEM





    56
    
    
    





    57
    20
    Amber Herold
    
* "FindEM--a fast, efficient program for automatic selection of particles from electron micrographs." (2004) Roseman AM., J Struct Biol., Volume 145, Issues 1-2. PMID: 15065677





    58
    
    
    
* Roseman, 2003. A.M. Roseman, Particle finding in electron micrographs using a fast local correlation algorithm. Ultramicroscopy 94 (2003), pp. 225–236.





    59
    
    
    





    60
    10
    Amber Herold
    
h3. Frealign





    61
    4
    Amber Herold
    





    62
    10
    Amber Herold
    
* "FREALIGN: high-resolution refinement of single particle structures." (2007) Grigorieff, N. J Struct Biol. v157(1).  PMID: 16828314  DOI: 10.1016/j.jsb.2006.05.004  





    63
    9
    Amber Herold
    





    64
    10
    Amber Herold
    
h3. IMAGIC





    65
    
    
    





    66
    1
    Amber Herold
    
* "A New Generation of the IMAGIC Image Processing System." (1996) van Heel M., Harauz G., Orlova E. V., Schmidt R. & Schatz M. J Struct Biol. v116(1).  PMID: 8742718  





    67
    
    
    





    68
    12
    Amber Herold
    
h3. IMOD





    69
    
    
    





    70
    21
    Amber Herold
    
* Kremer J.R., D.N. Mastronarde and J.R. McIntosh (1996) Computer visualization of three-dimensional image data using IMOD. J. Struct. Biol. 116:71-76. PMID: 8742726





    71
    12
    Amber Herold
    





    72
    
    
    
h3. ProTomo





    73
    21
    Amber Herold
    





    74
    
    
    
* "The Use of Electron Tomography for Structural Analysis of Disordered Protein Arrays" K. A. Taylor, J. Tang, Y. Cheng and H. Winkler, J. Struct. Biol. 120, 372-386, 1997.





    75
    
    
    
* "Focus gradient correction applied to tilt series image data used in electron tomography" H. Winkler, K. A. Taylor, J. Struct. Biol. 143, 24-32, 2003.





    76
    
    
    
* "Accurate marker-free alignment with simultaneous geometry determination and reconstruction of tilt series in electron tomography" H. Winkler and K. A. Taylor, Ultramicroscopy 106, 240-254, 2006.





    77
    
    
    
* "3D reconstruction and processing of volumetric data in cryo-electron tomography" H. Winkler, J. Struct. Biol. 157, 126-137, 2007.





    78
    12
    Amber Herold
    





    79
    
    
    





    80
    
    
    
h3. RMeasure





    81
    
    
    





    82
    22
    Amber Herold
    
* Sousa, D, Grigorieff N.  2007.  Ab initio resolution measurement for single particle structures. J Struct Biol. 157:201-10.





    83
    12
    Amber Herold
    





    84
    25
    Amber Herold
    
h3. SIGNATURE





    85
    
    
    





    86
    
    
    
* "SIGNATURE: a single-particle selection system for molecular electron microscopy." (2007) Chen JZ, Grigorieff N., J Struct Biol. v.157(1) PMID: 16870473





    87
    
    
    





    88
    10
    Amber Herold
    
h3. SPIDER





    89
    1
    Amber Herold
    





    90
    
    
    
* "SPIDER and WEB: processing and visualization of images in 3D electron microscopy and related fields." (1996) Frank J, Radermacher M, Penczek P, Zhu J, Li Y, Ladjadj M, Leith A. J Struct Biol. v116(1).  PMID: 8742743 





    91
    12
    Amber Herold
    





    92
    
    
    
h3. TiltPicker





    93
    
    
    





    94
    23
    Amber Herold
    
* Voss NR, Yoshioka CK, Radermacher M, Potter CS, Carragher B. (2009) "DoG Picker and TiltPicker: software tools to facilitate particle selection in single particle electron microscopy":http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2768396/. J Struct Biol. v166(2): pp. 205-13.





    95
    10
    Amber Herold
    





    96
    5
    Amber Herold
    
h3. XMIPP





    97
    9
    Amber Herold
    





    98
    6
    Amber Herold
    
* "Maximum-likelihood multi-reference refinement for electron microscopy images." (2005) Scheres SH, Valle M, Nuñez R, Sorzano CO, Marabini R, Herman GT, Carazo JM. J Mol Biol. v348(1).  PMID: 15808859  





    99
    
    
    
* "Fast maximum-likelihood refinement of electron microscopy images." (2005) Scheres SH, Valle M, Carazo JM. Bioinformatics. v21(Suppl 2).  PMID: 16204112





    100
    
    
    
* "A Novel Neural Network Technique for Analysis and Classification of EM Single-Particle Images." (2001) A. Pascual-Montano, L. E. Donate, M. Valle, M. Bárcena, R. D. Pascual-Marqui, J. M. Carazo. J Struct Biol. v133(2/3).  PMID: 11472094  





    101
    9
    Amber Herold
    
* "XMIPP: a new generation of an open-source image processing package for electron microscopy." (2004) Sorzano CO, Marabini R, Velázquez-Muriel J, Bilbao-Castro JR, Scheres SH, Carazo JM, Pascual-Montano A. J Struct Biol. v148(2).  PMID: 15477099  DOI: 10.1016/j.jsb.2004.06.006