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David N Mastronarde

TitleProfessor Adjoint
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction
Phone303/492-4350

    Collapse Research 
    Collapse research activities and funding
    R01GM125074     (MASTRONARDE, DAVID N)Jun 1, 2005 - May 31, 2021
    NIH
    Development and Maintenance of IMOD Software
    Role: Principal Investigator
    R01EB005027     (MASTRONARDE, DAVID N)Jun 1, 2005 - Feb 29, 2016
    NIH
    Development and Maintenance of IMOD Software
    Role: Principal Investigator
    R01EY000998     (MASTRONARDE, DAVID N)Sep 1, 1976 - Nov 30, 1986
    NIH
    RECEPTIVE FIELD ORGANIZATION IN THE VISUAL SYSTEM
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Mastronarde DN. Accurate, automatic determination of astigmatism and phase with Ctfplotter in IMOD. J Struct Biol. 2024 Mar; 216(1):108057. PMID: 38182035.
      View in: PubMed
    2. Schorb M, Haberbosch I, Hagen WJH, Schwab Y, Mastronarde DN. Software tools for automated transmission electron microscopy. Nat Methods. 2019 06; 16(6):471-477. PMID: 31086343.
      View in: PubMed
    3. Patwardhan A, Brandt R, Butcher SJ, Collinson L, Gault D, Gr?newald K, Hecksel C, Huiskonen JT, Iudin A, Jones ML, Korir PK, Koster AJ, Lagerstedt I, Lawson CL, Mastronarde D, McCormick M, Parkinson H, Rosenthal PB, Saalfeld S, Saibil HR, Sarntivijai S, Solanes Valero I, Subramaniam S, Swedlow JR, Tudose I, Winn M, Kleywegt GJ. Building bridges between cellular and molecular structural biology. Elife. 2017 07 06; 6. PMID: 28682240.
      View in: PubMed
    4. Marko M, Hsieh C, Leith E, Mastronarde D, Motoki S. Practical Experience with Hole-Free Phase Plates for Cryo Electron Microscopy. Microsc Microanal. 2016 12; 22(6):1316-1328. PMID: 27881198.
      View in: PubMed
    5. Mastronarde DN, Held SR. Automated tilt series alignment and tomographic reconstruction in IMOD. J Struct Biol. 2017 02; 197(2):102-113. PMID: 27444392.
      View in: PubMed
    6. Cheng A, Henderson R, Mastronarde D, Ludtke SJ, Schoenmakers RH, Short J, Marabini R, Dallakyan S, Agard D, Winn M. MRC2014: Extensions to the MRC format header for electron cryo-microscopy and tomography. J Struct Biol. 2015 Nov; 192(2):146-50. PMID: 25882513.
      View in: PubMed
    7. Briegel A, Pilhofer M, Mastronarde DN, Jensen GJ. The challenge of determining handedness in electron tomography and the use of DNA origami gold nanoparticle helices as molecular standards. J Struct Biol. 2013 Jul; 183(1):95-8. PMID: 23639902.
      View in: PubMed
    8. Patwardhan A, Carazo JM, Carragher B, Henderson R, Heymann JB, Hill E, Jensen GJ, Lagerstedt I, Lawson CL, Ludtke SJ, Mastronarde D, Moore WJ, Roseman A, Rosenthal P, Sorzano CO, Sanz-Garc?a E, Scheres SH, Subramaniam S, Westbrook J, Winn M, Swedlow JR, Kleywegt GJ. Data management challenges in three-dimensional EM. Nat Struct Mol Biol. 2012 Dec; 19(12):1203-7. PMID: 23211764.
      View in: PubMed
    9. Heumann JM, Hoenger A, Mastronarde DN. Clustering and variance maps for cryo-electron tomography using wedge-masked differences. J Struct Biol. 2011 Sep; 175(3):288-99. PMID: 21616153.
      View in: PubMed
    10. Anderson JR, Jones BW, Watt CB, Shaw MV, Yang JH, Demill D, Lauritzen JS, Lin Y, Rapp KD, Mastronarde D, Koshevoy P, Grimm B, Tasdizen T, Whitaker R, Marc RE. Exploring the retinal connectome. Mol Vis. 2011 Feb 03; 17:355-79. PMID: 21311605.
      View in: PubMed
    11. Kang BH, Nielsen E, Preuss ML, Mastronarde D, Staehelin LA. Electron tomography of RabA4b- and PI-4K?1-labeled trans Golgi network compartments in Arabidopsis. Traffic. 2011 Mar; 12(3):313-29. PMID: 21134079.
      View in: PubMed
    12. Friedman JR, Webster BM, Mastronarde DN, Verhey KJ, Voeltz GK. ER sliding dynamics and ER-mitochondrial contacts occur on acetylated microtubules. J Cell Biol. 2010 Aug 09; 190(3):363-75. PMID: 20696706.
      View in: PubMed
    13. Cope J, Gilbert S, Rayment I, Mastronarde D, Hoenger A. Cryo-electron tomography of microtubule-kinesin motor complexes. J Struct Biol. 2010 May; 170(2):257-65. PMID: 20025975.
      View in: PubMed
    14. Xiong Q, Morphew MK, Schwartz CL, Hoenger AH, Mastronarde DN. CTF determination and correction for low dose tomographic tilt series. J Struct Biol. 2009 Dec; 168(3):378-87. PMID: 19732834.
      View in: PubMed
    15. Anderson JR, Jones BW, Yang JH, Shaw MV, Watt CB, Koshevoy P, Spaltenstein J, Jurrus E, U V K, Whitaker RT, Mastronarde D, Tasdizen T, Marc RE. A computational framework for ultrastructural mapping of neural circuitry. PLoS Biol. 2009 Mar; 7(3):e1000074. PMID: 19855814.
      View in: PubMed
    16. McIntosh JR, Grishchuk EL, Morphew MK, Efremov AK, Zhudenkov K, Volkov VA, Cheeseman IM, Desai A, Mastronarde DN, Ataullakhanov FI. Fibrils connect microtubule tips with kinetochores: a mechanism to couple tubulin dynamics to chromosome motion. Cell. 2008 Oct 17; 135(2):322-33. PMID: 18957206.
      View in: PubMed
    17. Mastronarde DN. Correction for non-perpendicularity of beam and tilt axis in tomographic reconstructions with the IMOD package. J Microsc. 2008 May; 230(Pt 2):212-7. PMID: 18445149.
      View in: PubMed
    18. H??g JL, Schwartz C, Noon AT, O'Toole ET, Mastronarde DN, McIntosh JR, Antony C. Organization of interphase microtubules in fission yeast analyzed by electron tomography. Dev Cell. 2007 Mar; 12(3):349-61. PMID: 17336902.
      View in: PubMed
    19. Mastronarde DN. Automated electron microscope tomography using robust prediction of specimen movements. J Struct Biol. 2005 Oct; 152(1):36-51. PMID: 16182563.
      View in: PubMed
    20. Caldwell JP, Mastronarde DN, Woods JL, Bryson WG. The three-dimensional arrangement of intermediate filaments in Romney wool cortical cells. J Struct Biol. 2005 Sep; 151(3):298-305. PMID: 16125413.
      View in: PubMed
    21. Winey M, Morgan GP, Straight PD, Giddings TH, Mastronarde DN. Three-dimensional ultrastructure of Saccharomyces cerevisiae meiotic spindles. Mol Biol Cell. 2005 Mar; 16(3):1178-88. PMID: 15635095.
      View in: PubMed
    22. McIntosh R, Nicastro D, Mastronarde D. New views of cells in 3D: an introduction to electron tomography. Trends Cell Biol. 2005 Jan; 15(1):43-51. PMID: 15653077.
      View in: PubMed
    23. Sandberg K, Mastronarde DN, Beylkin G. A fast reconstruction algorithm for electron microscope tomography. J Struct Biol. 2003 Oct-Nov; 144(1-2):61-72. PMID: 14643209.
      View in: PubMed
    24. Otegui MS, Mastronarde DN, Kang BH, Bednarek SY, Staehelin LA. Three-dimensional analysis of syncytial-type cell plates during endosperm cellularization visualized by high resolution electron tomography. Plant Cell. 2001 Sep; 13(9):2033-51. PMID: 11549762.
      View in: PubMed
    25. Marsh BJ, Mastronarde DN, Buttle KF, Howell KE, McIntosh JR. Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography. Proc Natl Acad Sci U S A. 2001 Feb 27; 98(5):2399-406. PMID: 11226251.
      View in: PubMed
    26. Giddings TH, O'Toole ET, Morphew M, Mastronarde DN, McIntosh JR, Winey M. Using rapid freeze and freeze-substitution for the preparation of yeast cells for electron microscopy and three-dimensional analysis. Methods Cell Biol. 2001; 67:27-42. PMID: 11550475.
      View in: PubMed
    27. Ladinsky MS, Mastronarde DN, McIntosh JR, Howell KE, Staehelin LA. Golgi structure in three dimensions: functional insights from the normal rat kidney cell. J Cell Biol. 1999 Mar 22; 144(6):1135-49. PMID: 10087259.
      View in: PubMed
    28. Mastronarde DN. Dual-axis tomography: an approach with alignment methods that preserve resolution. J Struct Biol. 1997 Dec; 120(3):343-52. PMID: 9441937.
      View in: PubMed
    29. Winey M, Yarar D, Giddings TH, Mastronarde DN. Nuclear pore complex number and distribution throughout the Saccharomyces cerevisiae cell cycle by three-dimensional reconstruction from electron micrographs of nuclear envelopes. Mol Biol Cell. 1997 Nov; 8(11):2119-32. PMID: 9362057.
      View in: PubMed
    30. O'Toole ET, Mastronarde DN, Giddings TH, Winey M, Burke DJ, McIntosh JR. Three-dimensional analysis and ultrastructural design of mitotic spindles from the cdc20 mutant of Saccharomyces cerevisiae. Mol Biol Cell. 1997 Jan; 8(1):1-11. PMID: 9017591.
      View in: PubMed
    31. Schneider TD, Mastronarde DN. Fast multiple alignment of ungapped DNA sequences using information theory and a relaxation method. Discrete Appl Math. 1996 Dec 01; 71(1-3):259-268. PMID: 19953199.
      View in: PubMed
    32. McDonald K, O'Toole ET, Mastronarde DN, Winey M, Richard McIntosh J. Mapping the three-dimensional organization of microtubules in mitotic spindles of yeast. Trends Cell Biol. 1996 Jun; 6(6):235-9. PMID: 15157462.
      View in: PubMed
    33. Marr KM, Mastronarde DN, Lyon MK. Two-dimensional crystals of photosystem II: biochemical characterization, cryoelectron microscopy and localization of the D1 and cytochrome b559 polypeptides. J Cell Biol. 1996 Mar; 132(5):823-33. PMID: 8603915.
      View in: PubMed
    34. Kremer JR, Mastronarde DN, McIntosh JR. Computer visualization of three-dimensional image data using IMOD. J Struct Biol. 1996 Jan-Feb; 116(1):71-6. PMID: 8742726.
      View in: PubMed
    35. Winey M, Mamay CL, O'Toole ET, Mastronarde DN, Giddings TH, McDonald KL, McIntosh JR. Three-dimensional ultrastructural analysis of the Saccharomyces cerevisiae mitotic spindle. J Cell Biol. 1995 Jun; 129(6):1601-15. PMID: 7790357.
      View in: PubMed
    36. O'Toole E, Mastronarde D, McIntosh JR, Porter ME. Computer-assisted analysis of flagellar structure. Methods Cell Biol. 1995; 47:183-91. PMID: 7476486.
      View in: PubMed
    37. Mastronarde DN, McDonald KL, Ding R, McIntosh JR. Interpolar spindle microtubules in PTK cells. J Cell Biol. 1993 Dec; 123(6 Pt 1):1475-89. PMID: 8253845.
      View in: PubMed
    38. Mastronarde DN, O'Toole ET, McDonald KL, McIntosh JR, Porter ME. Arrangement of inner dynein arms in wild-type and mutant flagella of Chlamydomonas. J Cell Biol. 1992 Sep; 118(5):1145-62. PMID: 1387403.
      View in: PubMed
    39. Wilson CJ, Mastronarde DN, McEwen B, Frank J. Measurement of neuronal surface area using high-voltage electron microscope tomography. Neuroimage. 1992 Aug; 1(1):11-22. PMID: 9343554.
      View in: PubMed
    40. McDonald KL, O'Toole ET, Mastronarde DN, McIntosh JR. Kinetochore microtubules in PTK cells. J Cell Biol. 1992 Jul; 118(2):369-83. PMID: 1629239.
      View in: PubMed
    41. Mastronarde DN. Nonlagged relay cells and interneurons in the cat lateral geniculate nucleus: receptive-field properties and retinal inputs. Vis Neurosci. 1992 May; 8(5):407-41. PMID: 1586644.
      View in: PubMed
    42. Mastronarde DN, Humphrey AL, Saul AB. Lagged Y cells in the cat lateral geniculate nucleus. Vis Neurosci. 1991 Sep; 7(3):191-200. PMID: 1751414.
      View in: PubMed
    43. Mastronarde DN. Correlated firing of retinal ganglion cells. Trends Neurosci. 1989 Feb; 12(2):75-80. PMID: 2469215.
      View in: PubMed
    44. Mastronarde DN. Two classes of single-input X-cells in cat lateral geniculate nucleus. II. Retinal inputs and the generation of receptive-field properties. J Neurophysiol. 1987 Feb; 57(2):381-413. PMID: 3559685.
      View in: PubMed
    45. Mastronarde DN. Two classes of single-input X-cells in cat lateral geniculate nucleus. I. Receptive-field properties and classification of cells. J Neurophysiol. 1987 Feb; 57(2):357-80. PMID: 3559684.
      View in: PubMed
    46. Mastronarde DN. Two types of cat retinal ganglion cells that are suppressed by contrast. Vision Res. 1985; 25(9):1195-6. PMID: 4071998.
      View in: PubMed
    47. Mastronarde DN, Thibeault MA, Dubin MW. Non-uniform postnatal growth of the cat retina. J Comp Neurol. 1984 Oct 01; 228(4):598-608. PMID: 6490971.
      View in: PubMed
    48. Mastronarde DN. Organization of the cat's optic tract as assessed by single-axon recordings. J Comp Neurol. 1984 Jul 20; 227(1):14-22. PMID: 6470207.
      View in: PubMed
    49. George SA, Mastronarde DN, Dubin MW. Prior activity influences the velocity of impulses in frog and cat optic nerve fibers. Brain Res. 1984 Jun 18; 304(1):121-6. PMID: 6331576.
      View in: PubMed
    50. Mastronarde DN. Interactions between ganglion cells in cat retina. J Neurophysiol. 1983 Feb; 49(2):350-65. PMID: 6300342.
      View in: PubMed
    51. Mastronarde DN. Correlated firing of cat retinal ganglion cells. II. Responses of X- and Y-cells to single quantal events. J Neurophysiol. 1983 Feb; 49(2):325-49. PMID: 6300341.
      View in: PubMed
    52. Mastronarde DN. Correlated firing of cat retinal ganglion cells. I. Spontaneously active inputs to X- and Y-cells. J Neurophysiol. 1983 Feb; 49(2):303-24. PMID: 6300340.
      View in: PubMed
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