Dmitry Lyumkis

Title(s)Assistant Adjunct Professor, Molecular Biology
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    1. Kinetic coevolutionary models predict the temporal emergence of HIV-1 resistance mutations under drug selection pressure. Proc Natl Acad Sci U S A. 2024 Apr 09; 121(15):e2316662121. Biswas A, Choudhuri I, Arnold E, Lyumkis D, Haldane A, Levy RM. PMID: 38557187.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    2. Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding. bioRxiv. 2024 Jan 27. Jing T, Shan Z, Dinh T, Biswas A, Jang S, Greenwood J, Li M, Zhang Z, Gray G, Shin HJ, Zhou B, Passos D, Aiyer S, Li Z, Craigie R, Engelman AN, Kvaratskhelia M, Lyumkis D. PMID: 38328132; PMCID: PMC10849644.
      View in: PubMed   Mentions:
    3. Overcoming resolution attenuation during tilted cryo-EM data collection. Nat Commun. 2024 Jan 09; 15(1):389. Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Ðordevic-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. PMID: 38195598; PMCID: PMC10776679.
      View in: PubMed   Mentions: 1     Fields:    
    4. Elucidating the Molecular Determinants of the Binding Modes of a Third-Generation HIV-1 Integrase Strand Transfer Inhibitor: The Importance of Side Chain and Solvent Reorganization. Viruses. 2024 Jan 02; 16(1). Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. PMID: 38257776.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. A unified Watson-Crick geometry drives transcription of six-letter expanded DNA alphabets by E. coli RNA polymerase. Nat Commun. 2023 Dec 12; 14(1):8219. Oh J, Shan Z, Hoshika S, Xu J, Chong J, Benner SA, Lyumkis D, Wang D. PMID: 38086811; PMCID: PMC10716388.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    6. Structural basis of branching during RNA splicing. Nat Struct Mol Biol. 2024 Jan; 31(1):179-189. Haack DB, Rudolfs B, Zhang C, Lyumkis D, Toor N. PMID: 38057551; PMCID: PMC10968580.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization. bioRxiv. 2023 Dec 01. Sun Q, Biswas A, Lyumkis D, Levy R, Deng N. PMID: 38077045; PMCID: PMC10705364.
      View in: PubMed   Mentions:
    8. Assembly landscape for the bacterial large ribosomal subunit. Nat Commun. 2023 08 26; 14(1):5220. Sheng K, Li N, Rabuck-Gibbons JN, Dong X, Lyumkis D, Williamson JR. PMID: 37633970; PMCID: PMC10460392.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    9. Anisotropy in CryoEM Resolution is Dominated by Preferred Orientations, but not Structure Factors: A Study Using a Highly Symmetric Structure. Microsc Microanal. 2023 Jul 22; 29(29 Suppl 1):1021-1023. Baldwin PR, Aiyer S, Strutzenberg TS, Lyumkis D. PMID: 37613383.
      View in: PubMed   Mentions:    Fields:    
    10. CryoFAST™: Automated Cryo-Electron Microscopy Data Acquisition Using Machine Learning. Microsc Microanal. 2023 Jul 22; 29(29 Suppl 1):1036. Kumar N, Gray E, Lyumkis D, Mehrani A. PMID: 37613294.
      View in: PubMed   Mentions:    Fields:    
    11. Mechanisms of HIV-1 integrase resistance to dolutegravir and potent inhibition of drug-resistant variants. Sci Adv. 2023 07 21; 9(29):eadg5953. Li M, Oliveira Passos D, Shan Z, Smith SJ, Sun Q, Biswas A, Choudhuri I, Strutzenberg TS, Haldane A, Deng N, Li Z, Zhao XZ, Briganti L, Kvaratskhelia M, Burke TR, Levy RM, Hughes SH, Craigie R, Lyumkis D. PMID: 37478179.
      View in: PubMed   Mentions: 5     Fields:    
    12. Overcoming Resolution Attenuation During Tilted Cryo-EM Data Collection. bioRxiv. 2023 Jul 15. Aiyer S, Baldwin PR, Tan SM, Shan Z, Oh J, Mehrani A, Bowman ME, Louie G, Passos DO, Ðordevic-Marquardt S, Mietzsch M, Hull JA, Hoshika S, Barad BA, Grotjahn DA, McKenna R, Agbandje-McKenna M, Benner SA, Noel JAP, Wang D, Tan YZ, Lyumkis D. PMID: 37503021; PMCID: PMC10369999.
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    13. Near-physiological in vitro assembly of 50S ribosomes involves parallel pathways. Nucleic Acids Res. 2023 04 11; 51(6):2862-2876. Dong X, Doerfel LK, Sheng K, Rabuck-Gibbons JN, Popova AM, Lyumkis D, Williamson JR. PMID: 36864669; PMCID: PMC10085682.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    14. The role of filamentation in activation and DNA sequence specificity of the sequence-specific endonuclease SgrAI. Biochem Soc Trans. 2022 Nov 18. Lyumkis D, Horton NC. PMID: 36398769.
      View in: PubMed   Mentions:    Fields:    
    15. B-to-A transition in target DNA during retroviral integration. Nucleic Acids Res. 2022 Aug 26; 50(15):8898-8918. Józwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman AN, Lyumkis D. PMID: 35947647; PMCID: PMC9410886.
      View in: PubMed   Mentions: 2     Fields:    Translation:AnimalsCells
    16. Cryo-EM structure of the HIV-1 Pol polyprotein provides insights into virion maturation. Sci Adv. 2022 Jul 08; 8(27):eabn9874. Harrison JJEK, Passos DO, Bruhn JF, Bauman JD, Tuberty L, DeStefano JJ, Ruiz FX, Lyumkis D, Arnold E. PMID: 35857464; PMCID: PMC9258950.
      View in: PubMed   Mentions: 4     Fields:    
    17. Single-Particle Cryo-EM Data Collection with Stage Tilt using Leginon. J Vis Exp. 2022 07 01; (185). Aiyer S, Strutzenberg TS, Bowman ME, Noel JP, Lyumkis D. PMID: 35848829; PMCID: PMC9733953.
      View in: PubMed   Mentions: 2     Fields:    
    18. Multivalent interactions essential for lentiviral integrase function. Nat Commun. 2022 05 03; 13(1):2416. Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P. PMID: 35504909; PMCID: PMC9065133.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansAnimalsCells
    19. Pretransition state and apo structures of the filament-forming enzyme SgrAI elucidate mechanisms of activation and substrate specificity. J Biol Chem. 2022 04; 298(4):101760. Shan Z, Ghadirian N, Lyumkis D, Horton NC. PMID: 35202658; PMCID: PMC8960973.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    20. Quantitative mining of compositional heterogeneity in cryo-EM datasets of ribosome assembly intermediates. Structure. 2022 04 07; 30(4):498-509.e4. Rabuck-Gibbons JN, Lyumkis D, Williamson JR. PMID: 34990602; PMCID: PMC9891661.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    21. Retroviral integrase: Structure, mechanism, and inhibition. Enzymes. 2021; 50:249-300. Passos DO, Li M, Craigie R, Lyumkis D. PMID: 34861940; PMCID: PMC8732146.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansCells
    22. HIV-1 Integrase Inhibitors with Modifications That Affect Their Potencies against Drug Resistant Integrase Mutants. ACS Infect Dis. 2021 06 11; 7(6):1469-1482. Smith SJ, Zhao XZ, Passos DO, Pye VE, Cherepanov P, Lyumkis D, Burke TR, Hughes SH. PMID: 33686850; PMCID: PMC8205226.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    23. Integrase Strand Transfer Inhibitors Are Effective Anti-HIV Drugs. Viruses. 2021 01 29; 13(2). Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR, Hughes SH. PMID: 33572956; PMCID: PMC7912079.
      View in: PubMed   Mentions: 25     Fields:    Translation:HumansCellsPHPublic Health
    24. Evaluating Local and Directional Resolution of Cryo-EM Density Maps. Methods Mol Biol. 2021; 2215:161-187. Aiyer S, Zhang C, Baldwin PR, Lyumkis D. PMID: 33368004; PMCID: PMC8294179.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    25. HIV-1 Integrase Inhibitors That Are Active against Drug-Resistant Integrase Mutants. Antimicrob Agents Chemother. 2020 08 20; 64(9). Smith SJ, Zhao XZ, Passos DO, Lyumkis D, Burke TR, Hughes SH. PMID: 32601157; PMCID: PMC7449158.
      View in: PubMed   Mentions: 13     Fields:    Translation:HumansCells
    26. Molecular determinants for dsDNA translocation by the transcription-repair coupling and evolvability factor Mfd. Nat Commun. 2020 07 27; 11(1):3740. Brugger C, Zhang C, Suhanovsky MM, Kim DD, Sinclair AN, Lyumkis D, Deaconescu AM. PMID: 32719356; PMCID: PMC7385628.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    27. Tools for visualizing and analyzing Fourier space sampling in Cryo-EM. Prog Biophys Mol Biol. 2021 03; 160:53-65. Baldwin PR, Lyumkis D. PMID: 32645314; PMCID: PMC7785567.
      View in: PubMed   Mentions: 9     Fields:    
    28. Structural Biology of HIV Integrase Strand Transfer Inhibitors. Trends Pharmacol Sci. 2020 09; 41(9):611-626. Józwik IK, Passos DO, Lyumkis D. PMID: 32624197; PMCID: PMC7429322.
      View in: PubMed   Mentions: 19     Fields:    Translation:HumansAnimalsCells
    29. Structural basis for strand-transfer inhibitor binding to HIV intasomes. Science. 2020 02 14; 367(6479):810-814. Passos DO, Li M, Józwik IK, Zhao XZ, Santos-Martins D, Yang R, Smith SJ, Jeon Y, Forli S, Hughes SH, Burke TR, Craigie R, Lyumkis D. PMID: 32001521; PMCID: PMC7357238.
      View in: PubMed   Mentions: 42     Fields:    Translation:HumansCells
    30. SrmB Rescues Trapped Ribosome Assembly Intermediates. J Mol Biol. 2020 02 14; 432(4):978-990. Rabuck-Gibbons JN, Popova AM, Greene EM, Cervantes CF, Lyumkis D, Williamson JR. PMID: 31877323; PMCID: PMC7106940.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    31. Non-uniformity of projection distributions attenuates resolution in Cryo-EM. Prog Biophys Mol Biol. 2020 01; 150:160-183. Baldwin PR, Lyumkis D. PMID: 31525386; PMCID: PMC7054125.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    32. Mechanism of Filamentation-Induced Allosteric Activation of the SgrAI Endonuclease. Structure. 2019 10 01; 27(10):1497-1507.e3. Polley S, Lyumkis D, Horton NC. PMID: 31447289; PMCID: PMC6774820.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    33. Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA. Cell. 2019 07 25; 178(3):612-623.e12. Haack DB, Yan X, Zhang C, Hingey J, Lyumkis D, Baker TS, Toor N. PMID: 31348888; PMCID: PMC6662634.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    34. HIV-1 integrase tetramers are the antiviral target of pyridine-based allosteric integrase inhibitors. Elife. 2019 05 23; 8. 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. PMID: 31120420; PMCID: PMC6581505.
      View in: PubMed   Mentions: 31     Fields:    Translation:HumansCells
    35. Challenges and opportunities in cryo-EM single-particle analysis. J Biol Chem. 2019 03 29; 294(13):5181-5197. Lyumkis D. PMID: 30804214; PMCID: PMC6442032.
      View in: PubMed   Mentions: 121     Fields:    Translation:HumansAnimalsCells
    36. Analysis of discrete local variability and structural covariance in macromolecular assemblies using Cryo-EM and focused classification. Ultramicroscopy. 2019 08; 203:170-180. Zhang C, Cantara W, Jeon Y, Musier-Forsyth K, Grigorieff N, Lyumkis D. PMID: 30528101; PMCID: PMC6476647.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    37. Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d. Cell. 2018 Sep 20; 175(1):212-223.e17. Zhang C, Konermann S, Brideau NJ, Lotfy P, Wu X, Novick SJ, Strutzenberg T, Griffin PR, Hsu PD, Lyumkis D. PMID: 30241607; PMCID: PMC6179368.
      View in: PubMed   Mentions: 98     Fields:    Translation:HumansCells
    38. Sub-2 Å Ewald curvature corrected structure of an AAV2 capsid variant. Nat Commun. 2018 09 07; 9(1):3628. Tan YZ, Aiyer S, Mietzsch M, Hull JA, McKenna R, Grieger J, Samulski RJ, Baker TS, Agbandje-McKenna M, Lyumkis D. PMID: 30194371; PMCID: PMC6128836.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    39. Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike. Nature. 2017 07 20; 547(7663):360-363. 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. PMID: 28700571; PMCID: PMC5538736.
      View in: PubMed   Mentions: 144     Fields:    Translation:Cells
    40. Addressing preferred specimen orientation in single-particle cryo-EM through tilting. Nat Methods. 2017 Aug; 14(8):793-796. Tan YZ, Baldwin PR, Davis JH, Williamson JR, Potter CS, Carragher B, Lyumkis D. PMID: 28671674; PMCID: PMC5533649.
      View in: PubMed   Mentions: 396     Fields:    
    41. Cryo-EM structures and atomic model of the HIV-1 strand transfer complex intasome. Science. 2017 01 06; 355(6320):89-92. Passos DO, Li M, Yang R, Rebensburg SV, Ghirlando R, Jeon Y, Shkriabai N, Kvaratskhelia M, Craigie R, Lyumkis D. PMID: 28059769; PMCID: PMC5508583.
      View in: PubMed   Mentions: 106     Fields:    Translation:HumansCells
    42. Modular Assembly of the Bacterial Large Ribosomal Subunit. Cell. 2016 Dec 01; 167(6):1610-1622.e15. Davis JH, Tan YZ, Carragher B, Potter CS, Lyumkis D, Williamson JR. PMID: 27912064; PMCID: PMC5145266.
      View in: PubMed   Mentions: 94     Fields:    Translation:Cells
    43. Structural Basis for the Activation of IKK1/α. Cell Rep. 2016 11 15; 17(8):1907-1914. Polley S, Passos DO, Huang DB, Mulero MC, Mazumder A, Biswas T, Verma IM, Lyumkis D, Ghosh G. PMID: 27851956; PMCID: PMC5508515.
      View in: PubMed   Mentions: 22     Fields:    Translation:HumansCells
    44. Cryo-EM reveals a novel octameric integrase structure for betaretroviral intasome function. Nature. 2016 Feb 18; 530(7590):358-61. Ballandras-Colas A, Brown M, Cook NJ, Dewdney TG, Demeler B, Cherepanov P, Lyumkis D, Engelman AN. PMID: 26887496; PMCID: PMC4908968.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    45. Single-particle cryoEM analysis at near-atomic resolution from several thousand asymmetric subunits. J Struct Biol. 2015 Nov; 192(2):235-44. Passos DO, Lyumkis D. PMID: 26470814.
      View in: PubMed   Mentions: 6     Fields:    Translation:AnimalsCells
    46. 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. Lee JH, de Val N, Lyumkis D, Ward AB. PMID: 26388028; PMCID: PMC4618500.
      View in: PubMed   Mentions: 67     Fields:    Translation:Cells
    47. 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. Lyumkis D, Oliveira dos Passos D, Tahara EB, Webb K, Bennett EJ, Vinterbo S, Potter CS, Carragher B, Joazeiro CA. PMID: 25349383; PMCID: PMC4234556.
      View in: PubMed   Mentions: 63     Fields:    Translation:AnimalsCells
    48. A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. Elife. 2014 Oct 14; 3. Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR. PMID: 25313868; PMCID: PMC4371863.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    49. Cryo-EM structure of a fully glycosylated soluble cleaved HIV-1 envelope trimer. Science. 2013 Dec 20; 342(6165):1484-90. 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. PMID: 24179160; PMCID: PMC3954647.
      View in: PubMed   Mentions: 482     Fields:    Translation:Cells
    50. Crystal structure of a soluble cleaved HIV-1 envelope trimer. Science. 2013 Dec 20; 342(6165):1477-83. Julien JP, Cupo A, Sok D, Stanfield RL, Lyumkis D, Deller MC, Klasse PJ, Burton DR, Sanders RW, Moore JP, Ward AB, Wilson IA. PMID: 24179159; PMCID: PMC3886632.
      View in: PubMed   Mentions: 590     Fields:    Translation:HumansCells
    51. Optimod--an automated approach for constructing and optimizing initial models for single-particle electron microscopy. J Struct Biol. 2013 Dec; 184(3):417-26. Lyumkis D, Vinterbo S, Potter CS, Carragher B. PMID: 24161732; PMCID: PMC3885246.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    52. Allosteric regulation of DNA cleavage and sequence-specificity through run-on oligomerization. Structure. 2013 Oct 08; 21(10):1848-58. Lyumkis D, Talley H, Stewart A, Shah S, Park CK, Tama F, Potter CS, Carragher B, Horton NC. PMID: 24055317; PMCID: PMC3898938.
      View in: PubMed   Mentions: 14     Fields:    Translation:Cells
    53. Likelihood-based classification of cryo-EM images using FREALIGN. J Struct Biol. 2013 Sep; 183(3):377-388. Lyumkis D, Brilot AF, Theobald DL, Grigorieff N. PMID: 23872434; PMCID: PMC3824613.
      View in: PubMed   Mentions: 137     Fields:    Translation:Cells
    54. Maskiton: Interactive, web-based classification of single-particle electron microscopy images. J Struct Biol. 2013 May; 182(2):155-63. Yoshioka C, Lyumkis D, Carragher B, Potter CS. PMID: 23428431; PMCID: PMC3645979.
      View in: PubMed   Mentions: 4     Fields:    Translation:Cells
    55. 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. Lyumkis D, Doamekpor SK, Bengtson MH, Lee JW, Toro TB, Petroski MD, Lima CD, Potter CS, Carragher B, Joazeiro CA. PMID: 23319619; PMCID: PMC3562785.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    56. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy. Structure. 2012 Nov 07; 20(11):1823-8. Campbell MG, Cheng A, Brilot AF, Moeller A, Lyumkis D, Veesler D, Pan J, Harrison SC, Potter CS, Carragher B, Grigorieff N. PMID: 23022349; PMCID: PMC3510009.
      View in: PubMed   Mentions: 137     Fields:    Translation:Cells
    57. Initial evaluation of a direct detection device detector for single particle cryo-electron microscopy. J Struct Biol. 2011 Dec; 176(3):404-8. Milazzo AC, Cheng A, Moeller A, Lyumkis D, Jacovetty E, Polukas J, Ellisman MH, Xuong NH, Carragher B, Potter CS. PMID: 21933715; PMCID: PMC3210420.
      View in: PubMed   Mentions: 45     Fields:    
    58. Automation in single-particle electron microscopy connecting the pieces. Methods Enzymol. 2010; 483:291-338. 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. PMID: 20888480.
      View in: PubMed   Mentions: 13     Fields:    
    59. A toolbox for ab initio 3-D reconstructions in single-particle electron microscopy. J Struct Biol. 2010 Mar; 169(3):389-98. 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. PMID: 20018246; PMCID: PMC2826578.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    60. Appion: an integrated, database-driven pipeline to facilitate EM image processing. J Struct Biol. 2009 Apr; 166(1):95-102. 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. PMID: 19263523; PMCID: PMC2775544.
      View in: PubMed   Mentions: 563     Fields:    
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