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Dmitry Lyumkis - Publications

Affiliations: 
Salk Institute for Biological Studies, La Jolla, CA, United States 
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33 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Rabuck-Gibbons JN, Lyumkis D, Williamson JR. Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates. Structure (London, England : 1993). PMID 34990602 DOI: 10.1016/j.str.2021.12.005  0.301
2020 Jóźwik IK, Passos DO, Lyumkis D. Structural Biology of HIV Integrase Strand Transfer Inhibitors. Trends in Pharmacological Sciences. 41: 611-626. PMID 32624197 DOI: 10.1016/J.Tips.2020.06.003  0.372
2020 Passos DO, Li M, Jozwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, TRBJ, Craigie R, Lyumkis D. Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science. 367: 810-814. DOI: 10.2210/Pdb6Put/Pdb  0.372
2019 Rabuck-Gibbons JN, Popova AM, Greene EM, Cervantes CF, Lyumkis D, Williamson JR. SrmB Rescues Trapped Ribosome Assembly Intermediates. Journal of Molecular Biology. PMID 31877323 DOI: 10.1016/J.Jmb.2019.12.013  0.357
2019 Baldwin PR, Lyumkis D. Non-Uniformity of Projection Distributions Attenuates Resolution in Cryo-EM. Progress in Biophysics and Molecular Biology. PMID 31525386 DOI: 10.1016/J.Pbiomolbio.2019.09.002  0.317
2019 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. 178: 612-623.e12. PMID 31348888 DOI: 10.1016/J.Cell.2019.06.035  0.316
2019 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. 8. PMID 31120420 DOI: 10.7554/Elife.46344  0.361
2019 Lyumkis D. Challenges and opportunities in cryo-EM single-particle analysis Journal of Biological Chemistry. 294: 5181-5197. PMID 30804214 DOI: 10.1074/Jbc.Rev118.005602  0.388
2018 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. PMID 30528101 DOI: 10.1016/J.Ultramic.2018.11.016  0.433
2018 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. Nature Communications. 9: 3628. PMID 30194371 DOI: 10.1038/S41467-018-06076-6  0.395
2017 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. PMID 28700571 DOI: 10.1038/Nature23010  0.342
2017 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. Nature Methods. PMID 28671674 DOI: 10.1038/Nmeth.4347  0.373
2017 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 (New York, N.Y.). 355: 89-92. PMID 28059769 DOI: 10.1126/Science.Aah5163  0.408
2017 Chesterman C, Tuske S, Zheng J, Jeon Y, Zhang C, Cantara W, Musier-Forsyth K, Griffin PR, Lyumkis D, Arnold E. Structural investigation of the HIV-1 reverse transcriptase initiation complex by HDX, SAXS, CryoEM and X-ray crystallography Acta Crystallographica Section a Foundations and Advances. 73: a286-a286. DOI: 10.1107/S0108767317097185  0.313
2017 Lyumkis D, Tan YZ, Baldwin P. Collecting and processing single-particle cryo-EM data with tilts Protocol Exchange. DOI: 10.1038/Protex.2017.055  0.324
2016 Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell. 167: 1610-1622.e15. PMID 27912064 DOI: 10.1016/J.Cell.2016.11.020  0.357
2016 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. 530: 358-61. PMID 26887496 DOI: 10.1038/Nature16955  0.369
2015 Passos DO, Lyumkis D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. Journal of Structural Biology. 192: 235-44. PMID 26470814 DOI: 10.1016/J.Jsb.2015.10.002  0.387
2015 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 (London, England : 1993). PMID 26388028 DOI: 10.1016/J.Str.2015.07.020  0.396
2014 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. Proceedings of the National Academy of Sciences of the United States of America. 111: 15981-6. PMID 25349383 DOI: 10.1073/Pnas.1413882111  0.357
2014 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. 3. PMID 25313868 DOI: 10.7554/Elife.04491  0.34
2013 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 (New York, N.Y.). 342: 1484-90. PMID 24179160 DOI: 10.1126/Science.1245627  0.376
2013 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 (New York, N.Y.). 342: 1477-83. PMID 24179159 DOI: 10.1126/Science.1245625  0.335
2013 Lyumkis D, Vinterbo S, Potter CS, Carragher B. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. Journal of Structural Biology. 184: 417-26. PMID 24161732 DOI: 10.1016/J.Jsb.2013.10.009  0.334
2013 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 (London, England : 1993). 21: 1848-58. PMID 24055317 DOI: 10.1016/J.Str.2013.08.012  0.332
2013 Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. Likelihood-based classification of cryo-EM images using FREALIGN. Journal of Structural Biology. 183: 377-88. PMID 23872434 DOI: 10.1016/J.Jsb.2013.07.005  0.354
2013 Yoshioka C, Lyumkis D, Carragher B, Potter CS. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. Journal of Structural Biology. 182: 155-63. PMID 23428431 DOI: 10.1016/J.Jsb.2013.02.007  0.404
2013 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. Proceedings of the National Academy of Sciences of the United States of America. 110: 1702-7. PMID 23319619 DOI: 10.1073/Pnas.1210041110  0.381
2012 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 (London, England : 1993). 20: 1823-8. PMID 23022349 DOI: 10.1016/J.Str.2012.08.026  0.327
2011 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. Journal of Structural Biology. 176: 404-8. PMID 21933715 DOI: 10.1016/J.Jsb.2011.09.002  0.339
2010 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 in Enzymology. 483: 291-338. PMID 20888480 DOI: 10.1016/S0076-6879(10)83015-0  0.332
2010 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, et al. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. Journal of Structural Biology. 169: 389-98. PMID 20018246 DOI: 10.1016/J.Jsb.2009.12.005  0.362
2010 Lyumkis D, Nayak S, Milligan R, Potter C, Carragher B. Automation of Angular Reconstitution for Facilitating the Construction of Initial Models in Single-Particle Electron Microscopy Microscopy and Microanalysis. 16: 756-757. DOI: 10.1017/S1431927610061593  0.345
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