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Appion: an integrated, database-driven pipeline to facilitate EM image processing.
Lander GC, Stagg SM, Voss NR, Cheng A, Fellmann D, Pulokas J, Yoshioka C, Irving C, Mulder A, Lau PW, Lyumkis D, Potter CS, Carragher B. Lander GC, et al. J Struct Biol. 2009 Apr;166(1):95-102. doi: 10.1016/j.jsb.2009.01.002. J Struct Biol. 2009. PMID: 19263523 Free PMC article.
A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy.
Voss NR, Lyumkis D, Cheng A, Lau PW, Mulder A, Lander GC, Brignole EJ, Fellmann D, Irving C, Jacovetty EL, Leung A, Pulokas J, Quispe JD, Winkler H, Yoshioka C, Carragher B, Potter CS. Voss NR, et al. J Struct Biol. 2010 Mar;169(3):389-98. doi: 10.1016/j.jsb.2009.12.005. Epub 2009 Dec 16. J Struct Biol. 2010. PMID: 20018246 Free PMC article.
Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of establishing a reliable 3-D reconstruction using only 2-D images. ...We have developed a "toolbox" of ab initio reconstruction …
Structure determination of a novel macromolecular complex via single-particle electron microscopy depends upon overcoming the challenge of e …
Automation in single-particle electron microscopy connecting the pieces.
Lyumkis D, Moeller A, Cheng A, Herold A, Hou E, Irving C, Jacovetty EL, Lau PW, Mulder AM, Pulokas J, Quispe JD, Voss NR, Potter CS, Carragher B. Lyumkis D, et al. Methods Enzymol. 2010;483:291-338. doi: 10.1016/S0076-6879(10)83015-0. Methods Enzymol. 2010. PMID: 20888480
Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy.
Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. Milazzo AC, et al. J Struct Biol. 2011 Dec;176(3):404-8. doi: 10.1016/j.jsb.2011.09.002. Epub 2011 Sep 10. J Struct Biol. 2011. PMID: 21933715 Free PMC article.
Movies of ice-embedded particles enhance resolution in electron cryo-microscopy.
Campbell MG, Cheng A, Brilot AF, Moeller A, Lyumkis D, Veesler D, Pan J, Harrison SC, Potter CS, Carragher B, Grigorieff N. Campbell MG, et al. Structure. 2012 Nov 7;20(11):1823-8. doi: 10.1016/j.str.2012.08.026. Epub 2012 Sep 27. Structure. 2012. PMID: 23022349 Free PMC article.
Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase.
Lyumkis D, Doamekpor SK, Bengtson MH, Lee JW, Toro TB, Petroski MD, Lima CD, Potter CS, Carragher B, Joazeiro CA. Lyumkis D, et al. Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1702-7. doi: 10.1073/pnas.1210041110. Epub 2013 Jan 14. Proc Natl Acad Sci U S A. 2013. PMID: 23319619 Free PMC article.
Likelihood-based classification of cryo-EM images using FREALIGN.
Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. Lyumkis D, et al. J Struct Biol. 2013 Sep;183(3):377-388. doi: 10.1016/j.jsb.2013.07.005. Epub 2013 Jul 17. J Struct Biol. 2013. PMID: 23872434 Free PMC article.
Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.
Lyumkis D, Vinterbo S, Potter CS, Carragher B. Lyumkis D, et al. J Struct Biol. 2013 Dec;184(3):417-26. doi: 10.1016/j.jsb.2013.10.009. Epub 2013 Oct 24. J Struct Biol. 2013. PMID: 24161732 Free PMC article.
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