Appion citations » History » Version 13
Amber Herold, 01/12/2011 12:22 PM
| 1 | 11 | Amber Herold | h1. Appion Citations |
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| 2 | 1 | Amber Herold | |
| 3 | 2 | Amber Herold | Appion includes software from the following packages: |
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| 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 |
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| 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 |
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| 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 |
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| 22 | 13 | 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). |
| 23 | "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. |
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| 24 | * "More on Chimera Citations":http://www.cgl.ucsf.edu/chimera/docs/credits.html |
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| 26 | 12 | Amber Herold | |
| 27 | 1 | Amber Herold | h3. Clustering by Affinity Propogation |
| 28 | 10 | Amber Herold | |
| 29 | * "Clustering by Passing Messages Between Data Points." (2007) Brendan J. Frey and Delbert Dueck. Science. v315(5814). PMID: 17218491 |
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| 30 | 1 | Amber Herold | |
| 31 | 12 | Amber Herold | h3. CTFFind |
| 32 | 10 | Amber Herold | |
| 33 | 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 |
| 34 | 10 | Amber Herold | |
| 35 | 12 | Amber Herold | h3. CTFTilt |
| 36 | 1 | Amber Herold | |
| 37 | 12 | Amber Herold | |
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| 39 | h3. DogPicker |
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| 41 | 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 |
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| 43 | 10 | Amber Herold | h3. EMAN |
| 44 | 4 | Amber Herold | |
| 45 | 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 |
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| 47 | 12 | Amber Herold | h3. EM-BFACTOR |
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| 49 | h3. FindEM |
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| 51 | 10 | Amber Herold | h3. Frealign |
| 52 | 4 | Amber Herold | |
| 53 | 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 |
| 54 | 9 | Amber Herold | |
| 55 | 10 | Amber Herold | h3. IMAGIC |
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| 57 | 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 |
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| 59 | 12 | Amber Herold | h3. IMOD |
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| 62 | h3. ProTomo |
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| 65 | h3. RMeasure |
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| 68 | 10 | Amber Herold | h3. SPIDER |
| 69 | 1 | Amber Herold | |
| 70 | * "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 |
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| 71 | 12 | Amber Herold | |
| 72 | h3. TiltPicker |
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| 74 | 10 | Amber Herold | |
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| 76 | 5 | Amber Herold | h3. XMIPP |
| 77 | 9 | Amber Herold | |
| 78 | 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 |
| 79 | * "Fast maximum-likelihood refinement of electron microscopy images." (2005) Scheres SH, Valle M, Carazo JM. Bioinformatics. v21(Suppl 2). PMID: 16204112 |
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| 80 | * "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 |
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| 81 | 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 |