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Items: 26


Challenges and Opportunities in Cryo-EM Single-Particle Analysis.

Lyumkis D.

J Biol Chem. 2019 Feb 25. pii: jbc.REV118.005602. doi: 10.1074/jbc.REV118.005602. [Epub ahead of print]


Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification.

Zhang C, Cantara W, Jeon Y, Musier-Forsyth K, Grigorieff N, Lyumkis D.

Ultramicroscopy. 2018 Nov 29. pii: S0304-3991(18)30266-3. doi: 10.1016/j.ultramic.2018.11.016. [Epub ahead of print]


Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d.

Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D.

Cell. 2018 Sep 20;175(1):212-223.e17. doi: 10.1016/j.cell.2018.09.001.


Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant.

Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D.

Nat Commun. 2018 Sep 7;9(1):3628. doi: 10.1038/s41467-018-06076-6.


Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike.

Ozorowski G, Pallesen J, de Val N, Lyumkis D, Cottrell CA, Torres JL, Copps J, Stanfield RL, Cupo A, Pugach P, Moore JP, Wilson IA, Ward AB.

Nature. 2017 Jul 20;547(7663):360-363. doi: 10.1038/nature23010. Epub 2017 Jul 12.


Addressing preferred specimen orientation in single-particle cryo-EM through tilting.

Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D.

Nat Methods. 2017 Aug;14(8):793-796. doi: 10.1038/nmeth.4347. Epub 2017 Jul 3.


Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome.

Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D.

Science. 2017 Jan 6;355(6320):89-92. doi: 10.1126/science.aah5163.


Modular Assembly of the Bacterial Large Ribosomal Subunit.

Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR.

Cell. 2016 Dec 1;167(6):1610-1622.e15. doi: 10.1016/j.cell.2016.11.020.


Structural Basis for the Activation of IKK1/α.

Polley S, Passos DO, Huang DB, Mulero MC, Mazumder A, Biswas T, Verma IM, Lyumkis D, Ghosh G.

Cell Rep. 2016 Nov 15;17(8):1907-1914. doi: 10.1016/j.celrep.2016.10.067.


Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function.

Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN.

Nature. 2016 Feb 18;530(7590):358-61. doi: 10.1038/nature16955.


Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits.

Passos DO, Lyumkis D.

J Struct Biol. 2015 Nov;192(2):235-44. doi: 10.1016/j.jsb.2015.10.002. Epub 2015 Oct 22.


Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy.

Lee JH, de Val N, Lyumkis D, Ward AB.

Structure. 2015 Oct 6;23(10):1943-1951. doi: 10.1016/j.str.2015.07.020. Epub 2015 Sep 17.


Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex.

Lyumkis D, Oliveira dos Passos D, Tahara EB, Webb K, Bennett EJ, Vinterbo S, Potter CS, Carragher B, Joazeiro CA.

Proc Natl Acad Sci U S A. 2014 Nov 11;111(45):15981-6. doi: 10.1073/pnas.1413882111. Epub 2014 Oct 27.


A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli.

Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR.

Elife. 2014 Oct 14;3. doi: 10.7554/eLife.04491.


Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer.

Lyumkis D, Julien JP, de Val N, Cupo A, Potter CS, Klasse PJ, Burton DR, Sanders RW, Moore JP, Carragher B, Wilson IA, Ward AB.

Science. 2013 Dec 20;342(6165):1484-90. doi: 10.1126/science.1245627. Epub 2013 Oct 31.


Crystal structure of a soluble cleaved HIV-1 envelope trimer.

Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA.

Science. 2013 Dec 20;342(6165):1477-83. doi: 10.1126/science.1245625. Epub 2013 Oct 31.


Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy.

Lyumkis D, Vinterbo S, Potter CS, Carragher B.

J Struct Biol. 2013 Dec;184(3):417-26. doi: 10.1016/j.jsb.2013.10.009. Epub 2013 Oct 24.


Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization.

Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC.

Structure. 2013 Oct 8;21(10):1848-58. doi: 10.1016/j.str.2013.08.012. Epub 2013 Sep 19.


Likelihood-based classification of cryo-EM images using FREALIGN.

Lyumkis D, Brilot AF, Theobald DL, Grigorieff N.

J Struct Biol. 2013 Sep;183(3):377-388. doi: 10.1016/j.jsb.2013.07.005. Epub 2013 Jul 17.


Maskiton: Interactive, web-based classification of single-particle electron microscopy images.

Yoshioka C, Lyumkis D, Carragher B, Potter CS.

J Struct Biol. 2013 May;182(2):155-63. doi: 10.1016/j.jsb.2013.02.007. Epub 2013 Feb 18.


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.

Proc Natl Acad Sci U S A. 2013 Jan 29;110(5):1702-7. doi: 10.1073/pnas.1210041110. Epub 2013 Jan 14.


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.

Structure. 2012 Nov 7;20(11):1823-8. doi: 10.1016/j.str.2012.08.026. Epub 2012 Sep 27.


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.

J Struct Biol. 2011 Dec;176(3):404-8. doi: 10.1016/j.jsb.2011.09.002. Epub 2011 Sep 10.


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.

Methods Enzymol. 2010;483:291-338. doi: 10.1016/S0076-6879(10)83015-0.


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.

J Struct Biol. 2010 Mar;169(3):389-98. doi: 10.1016/j.jsb.2009.12.005. Epub 2009 Dec 16.


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.

J Struct Biol. 2009 Apr;166(1):95-102.

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