Salk Institute

Lyumkis Lab
Lyumkis Lab

Lyumkis Lab - Publications

  • Passos D., Li M., Yang R., Rebensburg S., Ghirlando R., Jeon Y., Shkriabai N., Kvaratskhelia M., Craigie R., Lyumkis D. (2017) CryoEM Structures and Atomic Models of the HIV-1 Strand Transfer Complex Intasome. Science, 355(6320), 89-92.
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  • Davis J, Tan YZ, Potter C, Carragher B, Lyumkis D, Williamson JR. (2016) Modular assembly of the bacterial large ribosomal subunit. Cell, 167(6), 1610-1622.
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  • Polley S, Passos DO, Huang D, Biswath T, Lyumkis D, Ghosh G. (2016) Structural basis for the selective participation of IKK1 in non-canonical NF-kB signaling. Cell Reports, 17(8), 1907-1914.
  • Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, & Engelman AN. (2016). Cryo-EM reveals a novel octameric integrase structure for β-retroviral intasome function. Nature, 530(7590), 358–361
  • Passos DO, & Lyumkis D. (2015). Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. Journal of Structural Biology, 192(2), 235—244.
  • Lee JH, de Val N, Lyumkis D., & Ward AB (2015). Model Building and Refinement of a Natively Glycosylated HIV-1 Env Protein by High-Resolution Cryoelectron Microscopy. Structure, 23(10), 1943—1951. PMC4618500.
  • Lyumkis D, Dos Passos DO, Tahara EB, Webb K, Bennett EJ, Vinterbo S, Potter CS, Carragher B, Joazeiro CAP (2014). Structural basis for translational surveillance by the large ribosomal subunit-associated protein quality control complex. Proc. Natl. Acad. Sci. USA. 111, 15981-15986. PMCID: PMC4234556.
  • Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR (2014). A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. eLife 3:e04491. PMC4371863.
  • Lyumkis D, Julien J-P, 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 Env trimer. Science, 342 (6165) 1484-1490.
  • Julien J-P, Cupo A, Sok D, Stanfield RS, Lyumkis D, Deller M, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA. Crystal structure of a soluble cleaved HIV-1 envelope trimer in complex with a glycan-dependent broadly neutralizing antibody. Science, 342 (6165) 1477-1483.
  • Lyumkis D, Brilot A, Theobald D, Grigorieff N. (2013) Likelihood-based classification in Frealign. Journal of Structural Biology, 183(3) 377-388.
  • Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. (2013) Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure, 21, 1-11.
  • Lyumkis D, Vinterbo S, Carragher B, Potter CS. (2013) Optimod: an automated approach for constructing and optimizing initial models in single-particle electron microscopy. Journal of Structural Biology, 184, 417-426.
  • Yoshioka C, Lyumkis D, Carragher B, Potter CS. (2013) Maskiton: Interactive web-based classification of single-particle electron microscopy images. Journal of Structural Biology, 182(2) 155-163.
  • Lyumkis D, Doamekpor S, Bengtson MH, Lee JW, Toro TB, Petroski MD, Lima CD, Potter CS, Carragher B, Joazeiro CAP. (2013) Single-particle EM reveals extensive conformational variability of the Ltn1 E3 ligase. Proc. Natl. Acad. Sci. 110, 1702-1707.
  • Campbell MG, Cheng A, Brilot AF, Moeller A, Lyumkis D, Veesler D, Pan J, Harrison SC, Potter CS, Carragher B, Grigorieff N. (2012). Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure, 20, 1823-1828.
  • Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. (2011). Initial evaluation of a direct detection device for single-particle cryo-electron microscopy. Journal of Structural Biology 176(3), 404-408.
  • Lyumkis D., Moeller A., Cheng A., Herold A., Hou E., Irving C., Jacovetty E., Lau P.W., Mulder A.M., Pulokas J., Quispe J., Voss N.R., Potter C.S., Carragher B. (2010). Automation in single-particle electron microscopy: connecting the pieces. Methods in Enzymology, 483, 315-362.
  • Voss N.R., Lyumkis D., Cheng A., Lau P.W., Mulder A., Lander G.C., Brignole E.J., Fellman D., Irving C., Jacovetty E., Leung A., Pulokas J., Quispe J., Winkler H., Yoshioka C., Carragher B., Potter, C.S. (2010). A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. Journal of Structural Biology, 169, 389-398.
  • 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 CS., Carragher B. (2009). Appion: an integrated, database-driven pipeline to facilitate EM image processing. Journal of Structural Biology 166, 95-102.

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