Dmitry Lyumkis

Assistant Professor

Laboratory of Genetics

Hearst Foundation Developmental Chair

Salk Institute for Biological Studies - Publications

all Publications


Jóźwik, I.K., Passos, D.O., Lyumkis, D. Structural Biology of HIV Integrase Strand Transfer Inhibitors. (2020) Trends in Pharmacological Sciences. DOI: 10.1016/j.tips.2020.06.003

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Baldwin, P.R., Lyumkis, D. Tools for visualizing and analyzing Fourier space sampling in Cryo-EM. (2020) Progress in Biophysics and Molecular Biology. DOI: 10.1016/j.pbiomolbio.2020.06.003

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Brugger, C., Zhang, C., Suhanovsky, M.M., Kim, D.D., Sinclair, A.N., Lyumkis, D., Deaconescu, A.M. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. (2020) Nature Communications. 11(1):3740. DOI: 10.1038/s41467-020-17457-1

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Smith, S.J., Zhao, X.Z., Passos, D.O., Lyumkis, D., Burke, T.R., Hughes, S.H. HIV-1 Integrase Inhibitors that are active against Drug-Resistant Integrase Mutants. (2020) Antimicrobial Agents and Chemotherapy. DOI: 10.1128/AAC.00611-20

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Passos, D.O., Li, M., Jóźwik, I.K., Zhao, X.Z., Santos-Martins, D., Yang, R., Smith, S.J., Jeon, Y., Forli, S., Hughes, S.H., Burke, T.R., Craigie, R., Lyumkis, D. Structural basis for strand transfer inhibitor binding to HIV intasomes. (2020) Science. DOI: 10.1126/science.aay8015

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Rabuck-Gibbons, J.N., Popova, A.M., Greene, E.M., Cervantes, C.F., Lyumkis, D., Williamson, J.R. SrmB Rescues Trapped Ribosome Assembly Intermediates. (2019) Journal of Molecular Biology. DOI: 10.1016/j.jmb.2019.12.013

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Baldwin, P.R., Lyumkis, D. Non-Uniformity of Projection Distributions Attenuates Resolution in Cryo-EM. (2019) Prog. Biophys. Mol. Biol. DOI: 10.1016/j.pbiomolbio.2019.09.002

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Polley, S., Lyumkis, D., Horton, N.C. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. (2019) Structure. 27(10):1497-1507. DOI: 10.1016/j.str.2019.08.001

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Haack, D.B., Yan, X., Zhang, C., Hingey, J., Lyumkis, D., Baker, T.S., Toor, N. Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. (2019) Cell. 178(3):612-623.e12. DOI: 10.1016/j.cell.2019.06.035

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Koneru, P.C., Francis, A.C., Deng, N., Rebensburg, S.V., Hoyte, A.C., Lindenberger, J., Adu-Ampratwum, D., Larue, R.C., Wempe, M.F., Engelman, A.N., Lyumkis, D., Fuchs, J.R., Levy, R.M., Melikyan, G.B., Kvaratskhelia, M. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. (2019) Elife. 8. DOI: 10.7554/eLife.46344

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Lyumkis, D. Challenges and Opportunities in Cryo-EM Single-Particle Analysis. (2019) Journal of Biological Chemistry. DOI: 10.1074/jbc.REV118.005602

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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. (2018) Ultramicroscopy. DOI: 10.1016/j.ultramic.2018.11.016

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Tan, Y.Z., Aiyer, S., Mietzsch, M., Hull, J.A., McKenna, R., Grieger, J., Samulski, R.J., Baker, T.S., Agbandje-McKenna, M., Lyumkis, D. Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant. (2018) Nature Communications. 9(1):3628. DOI: 10.1038/s41467-018-06076-6

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Zhang, C., Konermann, S., Brideau, N.J., Lotfy, P., Wu, X., Novick, S.J., Strutzenberg, T., Griffin, P.R., Hsu, P.D., Lyumkis, D. Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d. (2018) Cell. 175(1):212-223.e17. DOI: 10.1016/j.cell.2018.09.001

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Tan, Y.Z., Baldwin, P.R., Davis, J.H., Williamson, J.R., Potter, C.S., Carragher, B., Lyumkis, D. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. (2017) Nature Methods. 14(8):793-796. DOI: 10.1038/nmeth.4347

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Ozorowski, G., Pallesen, J., de Val, N., Lyumkis, D., Cottrell, C.A., Torres, J.L., Copps, J., Stanfield, R.L., Cupo, A., Pugach, P., Moore, J.P., Wilson, I.A., Ward, A.B. Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. (2017) Nature. 547(7663):360-363. DOI: 10.1038/nature23010

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Passos, D.O., Li, M., Yang, R., Rebensburg, S.V., 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. (2017) Science. 355(6320):89-92. DOI: 10.1126/science.aah5163

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Davis, J.H., Tan, Y.Z., Carragher, B., Potter, C.S., Lyumkis, D., Williamson, J.R. Modular Assembly of the Bacterial Large Ribosomal Subunit. (2016) Cell. 167(6):1610-1622.e15. DOI: 10.1016/j.cell.2016.11.020

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Polley, S., Passos, D.O., Huang, D.B., Mulero, M.C., Mazumder, A., Biswas, T., Verma, I.M., Lyumkis, D., Ghosh, G. Structural Basis for the Activation of IKK1/α. (2016) Cell Reports. 17(8):1907-1914. DOI: 10.1016/j.celrep.2016.10.067

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Ballandras-Colas, A., Brown, M., Cook, N.J., Dewdney, T.G., Demeler, B., Cherepanov, P., Lyumkis, D., Engelman, A.N. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. (2016) Nature. 530(7590):358-61. DOI: 10.1038/nature16955

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Passos, D.O., Lyumkis, D. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. (2015) Journal of Structural Biology. 192(2):235-44. DOI: 10.1016/j.jsb.2015.10.002

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Lee, J.H., de Val, N., Lyumkis, D., Ward, A.B. Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy. (2015) Structure. 23(10):1943-51. DOI: 10.1016/j.str.2015.07.020

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Lyumkis, D., Oliveira dos Passos, D., Tahara, E.B., Webb, K., Bennett, E.J., Vinterbo, S., Potter, C.S., Carragher, B., Joazeiro, C.A. Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. (2014) Proceedings of the National Academy of Sciences of the United States of America. 111(45):15981-6. DOI: 10.1073/pnas.1413882111

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Sashital, D.G., Greeman, C.A., Lyumkis, D., Potter, C.S., Carragher, B., Williamson, J.R. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. (2014) Elife. 3. DOI: 10.7554/eLife.04491

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Lyumkis, D., Julien, J.P., de Val, N., Cupo, A., Potter, C.S., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Carragher, B., Wilson, I.A., Ward, A.B. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. (2013) Science. 342(6165):1484-90. DOI: 10.1126/science.1245627

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Julien, J.P., Cupo, A., Sok, D., Stanfield, R.L., Lyumkis, D., Deller, M.C., Klasse, P.J., Burton, D.R., Sanders, R.W., Moore, J.P., Ward, A.B., Wilson, I.A. Crystal structure of a soluble cleaved HIV-1 envelope trimer. (2013) Science. 342(6165):1477-83. DOI: 10.1126/science.1245625

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Lyumkis, D., Vinterbo, S., Potter, C.S., Carragher, B. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. (2013) Journal of Structural Biology. 184(3):417-26. DOI: 10.1016/j.jsb.2013.10.009

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Lyumkis, D., Talley, H., Stewart, A., Shah, S., Park, C.K., Tama, F., Potter, C.S., Carragher, B., Horton, N.C. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. (2013) Structure. 21(10):1848-58. DOI: 10.1016/j.str.2013.08.012

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Lyumkis, D., Brilot, A.F., Theobald, D.L., Grigorieff, N. Likelihood-based classification of cryo-EM images using FREALIGN. (2013) Journal of Structural Biology. 183(3):377-388. DOI: 10.1016/j.jsb.2013.07.005

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Yoshioka, C., Lyumkis, D., Carragher, B., Potter, C.S. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. (2013) Journal of Structural Biology. 182(2):155-63. DOI: 10.1016/j.jsb.2013.02.007

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Lyumkis, D., Doamekpor, S.K., Bengtson, M.H., Lee, J.W., Toro, T.B., Petroski, M.D., Lima, C.D., Potter, C.S., Carragher, B., Joazeiro, C.A. Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. (2013) Proceedings of the National Academy of Sciences of the United States of America. 110(5):1702-7. DOI: 10.1073/pnas.1210041110

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Campbell, M.G., Cheng, A., Brilot, A.F., Moeller, A., Lyumkis, D., Veesler, D., Pan, J., Harrison, S.C., Potter, C.S., Carragher, B., Grigorieff, N. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. (2012) Structure. 20(11):1823-8. DOI: 10.1016/j.str.2012.08.026

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Milazzo, A.C., Cheng, A., Moeller, A., Lyumkis, D., Jacovetty, E., Polukas, J., Ellisman, M.H., Xuong, N.H., Carragher, B., Potter, C.S. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. (2011) Journal of Structural Biology. 176(3):404-8. DOI: 10.1016/j.jsb.2011.09.002

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Voss, N.R., Lyumkis, D., Cheng, A., Lau, P.W., Mulder, A., Lander, G.C., Brignole, E.J., Fellmann, D., Irving, C., Jacovetty, E.L., Leung, A., Pulokas, J., Quispe, J.D., Winkler, H., Yoshioka, C., Carragher, B., Potter, C.S. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. (2010) Journal of Structural Biology. 169(3):389-98. DOI: 10.1016/j.jsb.2009.12.005

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Lyumkis, D., Moeller, A., Cheng, A., Herold, A., Hou, E., Irving, C., Jacovetty, E.L., Lau, P.W., Mulder, A.M., Pulokas, J., Quispe, J.D., Voss, N.R., Potter, C.S., Carragher, B. Automation in single-particle electron microscopy connecting the pieces. (2010) Meth. Enzymol. 483:291-338. DOI: 10.1016/S0076-6879(10)83015-0

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Lander, G.C., Stagg, S.M., Voss, N.R., Cheng, A., Fellmann, D., Pulokas, J., Yoshioka, C., Irving, C., Mulder, A., Lau, P.W., Lyumkis, D., Potter, C.S., Carragher, B. Appion: an integrated, database-driven pipeline to facilitate EM image processing. (2009) Journal of Structural Biology. 166(1):95-102. DOI: 10.1016/j.jsb.2009.01.002

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Education

BS, University of California San Diego
PhD, The Scripps Research Institute


Awards & Honors

  • Helmsley-Salk Fellow, 2014-2017
  • National Institute of Health Director’s Early Independence Award, 2015
  • George Palade Award, 2016