Project

General

Profile

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