Appion

Appion citations » History » Revision 6

Revision 5 (Amber Herold, 11/10/2010 11:16 AM) → Revision 6/29 (Amber Herold, 11/10/2010 11:32 AM)

h1. Appion citations 

 Appion includes software from the following packages: 

 $title, $year, $authorlist, $journal, $volume=false, $issue=false, $pmid=false, $pmcid=false, $doi=false, $logo=false 

 h3. EMAN 

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

 h3. SPIDER 

 "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  

 h3. IMAGIC 

 "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   

 h3. Appion 

 "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  
 "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 

  

 h3. Frealign 

 FREALIGN: high-resolution refinement of single particle structures.", 2007, "Grigorieff, N.", "J Struct Biol.", 157, 1, 16828314, false, "10.1016/j.jsb.2006.05.004", "img/grigorieff_lab.png"); 

 h3. Initial Model 

 A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.", 2010, "Voss NR, Lyumkis D, Cheng A, <i>et&nbsp;al.</i>", "J Struct Biol.", 169, 3, 20018246, false, false, "img/topbarbackgrnd.jpg"); 

 h3. Dog Picking 

 "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   

 h3. ACE 

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

 h3. CTFfind 

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

 h3. XMIPP 

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

 

 h3. CAN Reference-free Alignment 

 "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   

 h3. Clustering by Affinity Propogation 

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