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Dmitry Lyumkis

Title(s)Assistant Adjunct Professor, Molecular Biology
SchoolAcademic Aff
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Polley S, Lyumkis D, Horton NC. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. Structure. 2019 Aug 20. PMID: 31447289.
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    2. Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N. Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. Cell. 2019 Jul 25; 178(3):612-623.e12. PMID: 31348888.
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    3. Koneru PC, Francis AC, Deng N, Rebensburg SV, Hoyte AC, Lindenberger J, Adu-Ampratwum D, Larue RC, Wempe MF, Engelman AN, Lyumkis D, Fuchs JR, Levy RM, Melikyan GB, Kvaratskhelia M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. Elife. 2019 May 23; 8. PMID: 31120420.
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    4. Lyumkis D. Challenges and opportunities in cryo-EM single-particle analysis. J Biol Chem. 2019 Mar 29; 294(13):5181-5197. PMID: 30804214.
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    5. Zhang C, Cantara W, Jeon Y, Musier-Forsyth K, Grigorieff N, Lyumkis D. Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification. Ultramicroscopy. 2019 Aug; 203:170-180. PMID: 30528101.
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    6. Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D. Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d. Cell. 2018 Sep 20; 175(1):212-223.e17. PMID: 30241607.
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    7. Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D. Sub-2?Å Ewald curvature corrected structure of an AAV2 capsid variant. Nat Commun. 2018 09 07; 9(1):3628. PMID: 30194371.
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    8. 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. Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Nature. 2017 07 20; 547(7663):360-363. PMID: 28700571.
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    9. Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods. 2017 Aug; 14(8):793-796. PMID: 28671674.
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    10. Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science. 2017 01 06; 355(6320):89-92. PMID: 28059769.
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    11. Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell. 2016 Dec 01; 167(6):1610-1622.e15. PMID: 27912064.
      View in: PubMed
    12. Polley S, Passos DO, Huang DB, Mulero MC, Mazumder A, Biswas T, Verma IM, Lyumkis D, Ghosh G. Structural Basis for the Activation of IKK1/a. Cell Rep. 2016 11 15; 17(8):1907-1914. PMID: 27851956.
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    13. Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Nature. 2016 Feb 18; 530(7590):358-61. PMID: 26887496.
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    14. Passos DO, Lyumkis D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. J Struct Biol. 2015 Nov; 192(2):235-44. PMID: 26470814.
      View in: PubMed
    15. Lee JH, de Val N, Lyumkis D, Ward AB. Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy. Structure. 2015 Oct 06; 23(10):1943-1951. PMID: 26388028.
      View in: PubMed
    16. Lyumkis D, Oliveira dos Passos D, Tahara EB, Webb K, Bennett EJ, Vinterbo S, Potter CS, Carragher B, Joazeiro CA. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. Proc Natl Acad Sci U S A. 2014 Nov 11; 111(45):15981-6. PMID: 25349383; PMCID: PMC4234556.
    17. Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. Elife. 2014 Oct 14; 3. PMID: 25313868.
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    18. 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. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science. 2013 Dec 20; 342(6165):1484-90. PMID: 24179160.
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    19. Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science. 2013 Dec 20; 342(6165):1477-83. PMID: 24179159.
      View in: PubMed
    20. Lyumkis D, Vinterbo S, Potter CS, Carragher B. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. J Struct Biol. 2013 Dec; 184(3):417-26. PMID: 24161732.
      View in: PubMed
    21. Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure. 2013 Oct 08; 21(10):1848-58. PMID: 24055317.
      View in: PubMed
    22. Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol. 2013 Sep; 183(3):377-388. PMID: 23872434; PMCID: PMC3824613.
    23. Yoshioka C, Lyumkis D, Carragher B, Potter CS. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. J Struct Biol. 2013 May; 182(2):155-63. PMID: 23428431.
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    24. Lyumkis D, Doamekpor SK, Bengtson MH, Lee JW, Toro TB, Petroski MD, Lima CD, Potter CS, Carragher B, Joazeiro CA. Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. Proc Natl Acad Sci U S A. 2013 Jan 29; 110(5):1702-7. PMID: 23319619.
      View in: PubMed
    25. Campbell MG, Cheng A, Brilot AF, Moeller A, Lyumkis D, Veesler D, Pan J, Harrison SC, Potter CS, Carragher B, Grigorieff N. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure. 2012 Nov 07; 20(11):1823-8. PMID: 23022349; PMCID: PMC3510009.
    26. Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. J Struct Biol. 2011 Dec; 176(3):404-8. PMID: 21933715; PMCID: PMC3210420.
    27. 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. Automation in single-particle electron microscopy connecting the pieces. Methods Enzymol. 2010; 483:291-338. PMID: 20888480.
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    28. 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. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. J Struct Biol. 2010 Mar; 169(3):389-98. PMID: 20018246; PMCID: PMC2826578.
    29. 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. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol. 2009 Apr; 166(1):95-102. PMID: 19263523.
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