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Downing, Kenneth

TitleBiophysicist Senior Sci/Engr
InstitutionLawrence Berkeley National Lab
DepartmentMolecular Biophys & Integ Bio
Address1 Cyclotron Road
Berkeley CA 94720
Phone510/486-5941
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    Collapse Research 
    Collapse Research Activities and Funding
    In-Focus Phase Contrast for Cryo-EM
    NIH/NIGMS R01GM083039Sep 30, 2007 - Aug 31, 2015
    Role: Co-Principal Investigator
    CCD Camera for Intermediate Voltage Electron Microscopes
    NIH/NIGMS R01GM075519May 1, 2006 - Jul 31, 2011
    Role: Principal Investigator
    Gordon Reseach Conference on 3D EM of Macromolecules
    NIH/NCRR R13RR018366Apr 1, 2003 - Mar 31, 2008
    Role: Co-Principal Investigator
    IMPROVEMENT TO CCD CAMERA PERFORMANCE ON IVEM
    NIH/NCRR R01RR013183Jun 20, 1998 - Jun 19, 2002
    Role: Principal Investigator
    Electron Microscopy of Biological Macromolecules
    NIH/NIGMS P01GM051487Jul 8, 1994 - May 31, 2019
    Role: Co-Principal Investigator
    TUBULIN STRUCTURE BY ELECTRON CRYSTALLOGRAPHY
    NIH/NIGMS R01GM046033Aug 1, 1992 - Aug 31, 2004
    Role: Principal Investigator
    MACROMOLECULAR SURFACES BY SCANNING TUNNELING
    NIH/NCRR R03RR003637Dec 1, 1986 - Nov 30, 1988
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    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. Kellogg EH, Hejab NMA, Poepsel S, Downing K, DiMaio F, Nogales E. Near-atomic model of microtubule-tau interactions. Science. 2018 May 10. PMID: 29748322.
      View in: PubMed
    2. Loo WS, Jiang X, Maslyn JA, Oh HJ, Zhu C, Downing K, Balsara NP. Reentrant phase behavior and coexistence in asymmetric block copolymer electrolytes. Soft Matter. 2018 Apr 18; 14(15):2789-2795. PMID: 29513329.
      View in: PubMed
    3. Downing K, Glaeser RM. Estimating the effect of finite depth of field in single-particle cryo-EM. Ultramicroscopy. 2018 Jan; 184(Pt A):94-99. PMID: 28869854.
      View in: PubMed
    4. Chiu W, Downing K. Editorial overview: Cryo Electron Microscopy: Exciting advances in CryoEM Herald a new era in structural biology. Curr Opin Struct Biol. 2017 Oct; 46:iv-viii. PMID: 28801059.
      View in: PubMed
    5. Killilea AN, Csencsits R, Le EBNT, Patel AM, Kenny SJ, Xu K, Downing K. Cytoskeletal organization in microtentacles. Exp Cell Res. 2017 08 15; 357(2):291-298. PMID: 28551375.
      View in: PubMed
    6. Kellogg EH, Hejab NMA, Howes S, Northcote P, Miller JH, Díaz JF, Downing K, Nogales E. Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures. J Mol Biol. 2017 Mar 10; 429(5):633-646. PMID: 28104363.
      View in: PubMed
    7. Finbloom JA, Han K, Aanei IL, Hartman EC, Finley DT, Dedeo MT, Fishman M, Downing K, Francis MB. Stable Disk Assemblies of a Tobacco Mosaic Virus Mutant as Nanoscale Scaffolds for Applications in Drug Delivery. Bioconjug Chem. 2016 Oct 07. PMID: 27712069.
      View in: PubMed
    8. Han BG, Watson Z, Kang H, Pulk A, Downing K, Cate J, Glaeser RM. Long shelf-life streptavidin support-films suitable for electron microscopy of biological macromolecules. J Struct Biol. 2016 08; 195(2):238-244. PMID: 27320699.
      View in: PubMed
    9. Sun J, Jiang X, Siegmund A, Connolly MD, Downing K, Balsara NP, Zuckermann RN. Morphology and Proton Transport in Humidified Phosphonated Peptoid Block Copolymers. Macromolecules. 2016 Apr 26; 49(8):3083-3090. PMID: 27134312.
      View in: PubMed
    10. Sun J, Jiang X, Lund R, Downing K, Balsara NP, Zuckermann RN. Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles. Proc Natl Acad Sci U S A. 2016 Apr 12; 113(15):3954-9. PMID: 27035944; PMCID: PMC4839393 [Available on 10/12/16].
    11. Luef B, Frischkorn KR, Wrighton KC, Holman HY, Birarda G, Thomas BC, Singh A, Williams KH, Siegerist CE, Tringe SG, Downing K, Comolli LR, Banfield JF. Diverse uncultivated ultra-small bacterial cells in groundwater. Nat Commun. 2015 Feb 27; 6:6372. PMID: 25721682.
      View in: PubMed
    12. Sarkar P, Bosneaga E, Yap EG, Das J, Tsai WT, Cabal A, Neuhaus E, Maji D, Kumar S, Joo M, Yakovlev S, Csencsits R, Yu Z, Bajaj C, Downing K, Auer M. Electron tomography of cryo-immobilized plant tissue: a novel approach to studying 3D macromolecular architecture of mature plant cell walls in situ. PLoS One. 2014; 9(9):e106928. PMID: 25207917; PMCID: PMC4160213.
    13. Beers KM, Yakovlev S, Jackson A, Wang X, Hexemer A, Downing K, Balsara NP. Absence of Schroeder's paradox in a nanostructured block copolymer electrolyte membrane. J Phys Chem B. 2014 Jun 19; 118(24):6785-91. PMID: 24842682; PMCID: PMC4207082.
    14. Chen XC, Wong DT, Yakovlev S, Beers KM, Downing K, Balsara NP. Effect of morphology of nanoscale hydrated channels on proton conductivity in block copolymer electrolyte membranes. Nano Lett. 2014 Jul 09; 14(7):4058-64. PMID: 24854241; PMCID: PMC4207093.
    15. Yakovlev S, Balsara NP, Downing K. Insights on the study of nafion nanoscale morphology by transmission electron microscopy. Membranes (Basel). 2013 Dec 16; 3(4):424-39. PMID: 24957067; PMCID: PMC4021952.
    16. Glaeser RM, Sassolini S, Cambie R, Jin J, Cabrini S, Schmid AK, Danev R, Buijsse B, Csencsits R, Downing K, Larson DM, Typke D, Han BG. Minimizing electrostatic charging of an aperture used to produce in-focus phase contrast in the TEM. Ultramicroscopy. 2013 Dec; 135:6-15. PMID: 23872037; PMCID: PMC3818313.
    17. Ounjai P, Kim KD, Liu H, Dong M, Tauscher AN, Witkowska HE, Downing K. Architectural insights into a ciliary partition. Curr Biol. 2013 Feb 18; 23(4):339-44. PMID: 23375896; PMCID: PMC3580003.
    18. Yakovlev S, Downing K. Visualization of clusters in polymer electrolyte membranes by electron microscopy. Phys Chem Chem Phys. 2013 Jan 28; 15(4):1052-64. PMID: 23165242; PMCID: PMC4185922.
    19. Downing K. Future developments in instrumentation for electron crystallography. Methods Mol Biol. 2013; 955:353-79. PMID: 23132071.
      View in: PubMed
    20. Luef B, Fakra SC, Csencsits R, Wrighton KC, Williams KH, Wilkins MJ, Downing K, Long PE, Comolli LR, Banfield JF. Iron-reducing bacteria accumulate ferric oxyhydroxide nanoparticle aggregates that may support planktonic growth. ISME J. 2013 Feb; 7(2):338-50. PMID: 23038172; PMCID: PMC3554402.
    21. Ounjai P, Kim KD, Lishko PV, Downing K. Three-dimensional structure of the bovine sperm connecting piece revealed by electron cryotomography. Biol Reprod. 2012 Sep; 87(3):73. PMID: 22767409; PMCID: PMC3464910.
    22. Watkins BY, Joshi SA, Ball DA, Leggett H, Park S, Kim J, Austin CD, Paler-Martinez A, Xu M, Downing K, Brown EJ. Mycobacterium marinum SecA2 promotes stable granulomas and induces tumor necrosis factor alpha in vivo. Infect Immun. 2012 Oct; 80(10):3512-20. PMID: 22851747; PMCID: PMC3457566.
    23. Murat D, Falahati V, Bertinetti L, Csencsits R, Körnig A, Downing K, Faivre D, Komeili A. The magnetosome membrane protein, MmsF, is a major regulator of magnetite biomineralization in Magnetospirillum magneticum AMB-1. Mol Microbiol. 2012 Aug; 85(4):684-99. PMID: 22716969; PMCID: PMC3570065.
    24. Dong H, Shu JY, Dube N, Ma Y, Tirrell MV, Downing K, Xu T. 3-Helix micelles stabilized by polymer springs. J Am Chem Soc. 2012 Jul 18; 134(28):11807-14. PMID: 22731391; PMCID: PMC4186246.
    25. Henderson R, Sali A, Baker ML, Carragher B, Devkota B, Downing K, Egelman EH, Feng Z, Frank J, Grigorieff N, Jiang W, Ludtke SJ, Medalia O, Penczek PA, Rosenthal PB, Rossmann MG, Schmid MF, Schröder GF, Steven AC, Stokes DL, Westbrook JD, Wriggers W, Yang H, Young J, Berman HM, Chiu W, Kleywegt GJ, Lawson CL. Outcome of the first electron microscopy validation task force meeting. Structure. 2012 Feb 08; 20(2):205-14. PMID: 22325770; PMCID: PMC3328769.
    26. Comolli LR, Duarte R, Baum D, Luef B, Downing K, Larson DM, Csencsits R, Banfield JF. A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments. Microsc Res Tech. 2012 Jun; 75(6):829-36. PMID: 22213355; PMCID: PMC4677670.
    27. Yakovlev S, Wang X, Ercius P, Balsara NP, Downing K. Direct imaging of nanoscale acidic clusters in a polymer electrolyte membrane. J Am Chem Soc. 2011 Dec 28; 133(51):20700-3. PMID: 22107080; PMCID: PMC4224285.
    28. Larson DM, Downing K, Glaeser RM. The surface of evaporated carbon films is an insulating, high-bandgap material. J Struct Biol. 2011 May; 174(2):420-3. PMID: 21338687; PMCID: PMC3086603.
    29. Downing K. Commentary on "Structure of a conserved retroviral RNA packaging element by NMR spectroscopy and cryo-electron tomography" by Y. Miyazaki et al. J Mol Biol. 2010 Dec 17; 404(5):749-50. PMID: 20965201.
      View in: PubMed
    30. Amat F, Comolli LR, Nomellini JF, Moussavi F, Downing K, Smit J, Horowitz M. Analysis of the intact surface layer of Caulobacter crescentus by cryo-electron tomography. J Bacteriol. 2010 Nov; 192(22):5855-65. PMID: 20833802; PMCID: PMC2976456.
    31. Sui H, Downing K. Structural basis of interprotofilament interaction and lateral deformation of microtubules. Structure. 2010 Aug 11; 18(8):1022-31. PMID: 20696402; PMCID: PMC2976607.
    32. Yeh YC, Comolli LR, Downing K, Shapiro L, McAdams HH. The caulobacter Tol-Pal complex is essential for outer membrane integrity and the positioning of a polar localization factor. J Bacteriol. 2010 Oct; 192(19):4847-58. PMID: 20693330; PMCID: PMC2944545.
    33. Byrne ME, Ball DA, Guerquin-Kern JL, Rouiller I, Wu TD, Downing K, Vali H, Komeili A. Desulfovibrio magneticus RS-1 contains an iron- and phosphorus-rich organelle distinct from its bullet-shaped magnetosomes. Proc Natl Acad Sci U S A. 2010 Jul 06; 107(27):12263-8. PMID: 20566879; PMCID: PMC2901430.
    34. Amat F, Comolli LR, Moussavi F, Smit J, Downing K, Horowitz M. Subtomogram alignment by adaptive Fourier coefficient thresholding. J Struct Biol. 2010 Sep; 171(3):332-44. PMID: 20621702; PMCID: PMC4189811.
    35. Goley ED, Comolli LR, Fero KE, Downing K, Shapiro L. DipM links peptidoglycan remodelling to outer membrane organization in Caulobacter. Mol Microbiol. 2010 Jul 01; 77(1):56-73. PMID: 20497504; PMCID: PMC2915588.
    36. Wang H, Downing K. Specimen preparation for electron diffraction of thin crystals. Micron. 2011 Feb; 42(2):132-40. PMID: 20561794; PMCID: PMC3064510.
    37. Sindelar CV, Downing K. An atomic-level mechanism for activation of the kinesin molecular motors. Proc Natl Acad Sci U S A. 2010 Mar 02; 107(9):4111-6. PMID: 20160108; PMCID: PMC2840164.
    38. Bowman GR, Comolli LR, Gaietta GM, Fero M, Hong SH, Jones Y, Lee JH, Downing K, Ellisman MH, McAdams HH, Shapiro L. Caulobacter PopZ forms a polar subdomain dictating sequential changes in pole composition and function. Mol Microbiol. 2010 Apr; 76(1):173-89. PMID: 20149103; PMCID: PMC2935252.
    39. Downing K, Nogales E. Cryoelectron microscopy applications in the study of tubulin structure, microtubule architecture, dynamics and assemblies, and interaction of microtubules with motors. Methods Enzymol. 2010; 483:121-42. PMID: 20888472; PMCID: PMC4165512.
    40. Han BG, Dong M, Liu H, Camp L, Geller J, Singer M, Hazen TC, Choi M, Witkowska HE, Ball DA, Typke D, Downing K, Shatsky M, Brenner SE, Chandonia JM, Biggin MD, Glaeser RM. Survey of large protein complexes in D. vulgaris reveals great structural diversity. Proc Natl Acad Sci U S A. 2009 Sep 29; 106(39):16580-5. PMID: 19805340; PMCID: PMC2742403.
    41. Holman HY, Wozei E, Lin Z, Comolli LR, Ball DA, Borglin S, Fields MW, Hazen TC, Downing K. Real-time molecular monitoring of chemical environment in obligate anaerobes during oxygen adaptive response. Proc Natl Acad Sci U S A. 2009 Aug 04; 106(31):12599-604. PMID: 19541631.
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    42. Gomez ED, Panday A, Feng EH, Chen V, Stone GM, Minor AM, Kisielowski C, Downing K, Borodin O, Smith GD, Balsara NP. Effect of ion distribution on conductivity of block copolymer electrolytes. Nano Lett. 2009 Mar; 9(3):1212-6. PMID: 19193125.
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    43. Nettles JH, Downing K. The tubulin binding mode of microtubule stabilizing agents studied by electron crystallography. Top Curr Chem. 2009; 286:209-57. PMID: 23563614.
      View in: PubMed
    44. Comolli LR, Baker BJ, Downing K, Siegerist CE, Banfield JF. Three-dimensional analysis of the structure and ecology of a novel, ultra-small archaeon. ISME J. 2009 Feb; 3(2):159-67. PMID: 18946497.
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    45. Bowman GR, Comolli LR, Zhu J, Eckart M, Koenig M, Downing K, Moerner WE, Earnest T, Shapiro L. A polymeric protein anchors the chromosomal origin/ParB complex at a bacterial cell pole. Cell. 2008 Sep 19; 134(6):945-55. PMID: 18805088; PMCID: PMC2745220.
    46. Dietrich KA, Sindelar CV, Brewer PD, Downing K, Cremo CR, Rice SE. The kinesin-1 motor protein is regulated by a direct interaction of its head and tail. Proc Natl Acad Sci U S A. 2008 Jul 01; 105(26):8938-43. PMID: 18579780; PMCID: PMC2449343.
    47. Downing K, Glaeser RM. Restoration of weak phase-contrast images recorded with a high degree of defocus: the "twin image" problem associated with CTF correction. Ultramicroscopy. 2008 Aug; 108(9):921-8. PMID: 18508199; PMCID: PMC2694513.
    48. Downing K, Mooney PE. A charge coupled device camera with electron decelerator for intermediate voltage electron microscopy. Rev Sci Instrum. 2008 Apr; 79(4):043702. PMID: 18447528; PMCID: PMC2678785.
    49. Comolli LR, Spakowitz AJ, Siegerist CE, Jardine PJ, Grimes S, Anderson DL, Bustamante C, Downing K. Three-dimensional architecture of the bacteriophage phi29 packaged genome and elucidation of its packaging process. Virology. 2008 Feb 20; 371(2):267-77. PMID: 18001811.
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    50. Downing K, Sui H, Auer M. Electron tomography: a 3D view of the subcellular world. Anal Chem. 2007 Nov 01; 79(21):7949-57. PMID: 18044021.
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    51. Park MJ, Downing K, Jackson A, Gomez ED, Minor AM, Cookson D, Weber AZ, Balsara NP. Increased water retention in polymer electrolyte membranes at elevated temperatures assisted by capillary condensation. Nano Lett. 2007 Nov; 7(11):3547-52. PMID: 17960948.
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    52. Killilea AN, Downing K, Killilea DW. Zinc deficiency reduces paclitaxel efficacy in LNCaP prostate cancer cells. Cancer Lett. 2007 Dec 08; 258(1):70-9. PMID: 17905512.
      View in: PubMed
    53. Wille H, Govaerts C, Borovinskiy A, Latawiec D, Downing K, Cohen FE, Prusiner SB. Electron crystallography of the scrapie prion protein complexed with heavy metals. Arch Biochem Biophys. 2007 Nov 15; 467(2):239-48. PMID: 17935686; PMCID: PMC3557509.
    54. Amat F, Moussavi F, Comolli LR, Elidan G, Downing K, Horowitz M. Markov random field based automatic image alignment for electron tomography. J Struct Biol. 2008 Mar; 161(3):260-75. PMID: 17855124.
      View in: PubMed
    55. Sindelar CV, Downing K. The beginning of kinesin's force-generating cycle visualized at 9-A resolution. J Cell Biol. 2007 May 07; 177(3):377-85. PMID: 17470637; PMCID: PMC2064809.
    56. Downing K, Sui H. Structural insights into microtubule doublet interactions in axonemes. Curr Opin Struct Biol. 2007 Apr; 17(2):253-9. PMID: 17387011.
      View in: PubMed
    57. Cambie R, Downing K, Typke D, Glaeser RM, Jin J. Design of a microfabricated, two-electrode phase-contrast element suitable for electron microscopy. Ultramicroscopy. 2007 Apr-May; 107(4-5):329-39. PMID: 17079082.
      View in: PubMed
    58. Typke D, Gilpin CJ, Downing K, Glaeser RM. Stroboscopic image capture: reducing the dose per frame by a factor of 30 does not prevent beam-induced specimen movement in paraffin. Ultramicroscopy. 2007 Feb-Mar; 107(2-3):106-15. PMID: 16905258.
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    59. Sui H, Downing K. Molecular architecture of axonemal microtubule doublets revealed by cryo-electron tomography. Nature. 2006 Jul 27; 442(7101):475-8. PMID: 16738547.
      View in: PubMed
    60. Rosenberg OS, Deindl S, Comolli LR, Hoelz A, Downing K, Nairn AC, Kuriyan J. Oligomerization states of the association domain and the holoenyzme of Ca2+/CaM kinase II. FEBS J. 2006 Feb; 273(4):682-94. PMID: 16441656.
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    61. Judd EM, Comolli LR, Chen JC, Downing K, Moerner WE, McAdams HH. Distinct constrictive processes, separated in time and space, divide caulobacter inner and outer membranes. J Bacteriol. 2005 Oct; 187(20):6874-82. PMID: 16199556; PMCID: PMC1251605.
    62. Comolli LR, Downing K. Dose tolerance at helium and nitrogen temperatures for whole cell electron tomography. J Struct Biol. 2005 Dec; 152(3):149-56. PMID: 16198601.
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    63. Typke D, Nordmeyer RA, Jones A, Lee J, Avila-Sakar A, Downing K, Glaeser RM. High-throughput film-densitometry: an efficient approach to generate large data sets. J Struct Biol. 2005 Jan; 149(1):17-29. PMID: 15629654.
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    64. Glaeser RM, Downing K. Specimen charging on thin films with one conducting layer: discussion of physical principles. Microsc Microanal. 2004 Dec; 10(6):790-6. PMID: 19780321.
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    65. Downing K, McCartney MR, Glaeser RM. Experimental characterization and mitigation of specimen charging on thin films with one conducting layer. Microsc Microanal. 2004 Dec; 10(6):783-9. PMID: 19780320.
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    66. Nettles JH, Li H, Cornett B, Krahn JM, Snyder JP, Downing K. The binding mode of epothilone A on alpha,beta-tubulin by electron crystallography. Science. 2004 Aug 06; 305(5685):866-9. PMID: 15297674.
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    67. Typke D, Downing K, Glaeser RM. Electron microscopy of biological macromolecules: bridging the gap between what physics allows and what we currently can get. Microsc Microanal. 2004 Feb; 10(1):21-7. PMID: 15306063.
      View in: PubMed
    68. Paluh JL, Killilea AN, Detrich HW, Downing K. Meiosis-specific failure of cell cycle progression in fission yeast by mutation of a conserved beta-tubulin residue. Mol Biol Cell. 2004 Mar; 15(3):1160-71. PMID: 14657251; PMCID: PMC363098.
    69. Li H, DeRosier DJ, Nicholson WV, Nogales E, Downing K. Microtubule structure at 8 A resolution. Structure. 2002 Oct; 10(10):1317-28. PMID: 12377118.
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    70. Zhong S, Dadarlat VM, Glaeser RM, Head-Gordon T, Downing K. Modeling chemical bonding effects for protein electron crystallography: the transferable fragmental electrostatic potential (TFESP) method. Acta Crystallogr A. 2002 Mar; 58(Pt 2):162-70. PMID: 11832586.
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    71. Downing K, Li H. Accurate Recording and Measurement of Electron Diffraction Data in Structural and Difference Fourier Studies of Proteins. Microsc Microanal. 2001 Sep; 7(5):407-417. PMID: 12597803.
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    72. Downing K. Structural basis for the interaction of tubulin with proteins and drugs that affect microtubule dynamics. Annu Rev Cell Dev Biol. 2000; 16:89-111. PMID: 11031231.
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    73. Downing K, Nogales E. Crystallographic structure of tubulin: implications for dynamics and drug binding. Cell Struct Funct. 1999 Oct; 24(5):269-75. PMID: 15216882.
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    74. Downing K, Hendrickson FM. Performance of a 2k CCD camera designed for electron crystallography at 400 kV. Ultramicroscopy. 1999 Jan; 75(4):215-33. PMID: 9919710.
      View in: PubMed
    75. Downing K, Nogales E. Tubulin structure: insights into microtubule properties and functions. Curr Opin Struct Biol. 1998 Dec; 8(6):785-91. PMID: 9914260.
      View in: PubMed
    76. Downing K, Nogales E. Tubulin and microtubule structure. Curr Opin Cell Biol. 1998 Feb; 10(1):16-22. PMID: 9484591.
      View in: PubMed
    77. Downing K, Nogales E. New insights into microtubule structure and function from the atomic model of tubulin. Eur Biophys J. 1998; 27(5):431-6. PMID: 9760724.
      View in: PubMed
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