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Thomas Deerinck

Title(s), Neurosciences
SchoolHealth Sciences
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    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. Kim KY, Rios LC, Le H, Perez AJ, Phan S, Bushong EA, Deerinck TJ, Liu YH, Ellisman MA, Lev-Ram V, Ju S, Panda SA, Yoon S, Hirayama M, Mure LS, Hatori M, Ellisman MH, Panda S. Synaptic Specializations of Melanopsin-Retinal Ganglion Cells in Multiple Brain Regions Revealed by Genetic Label for Light and Electron Microscopy. Cell Rep. 2019 Oct 15; 29(3):628-644.e6. PMID: 31618632.
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    2. E Drigo RA, Jacob S, García-Prieto CF, Zheng X, Fukuda M, Nhu HTT, Stelmashenko O, Peçanha FLM, Rodriguez-Diaz R, Bushong E, Deerinck T, Phan S, Ali Y, Leibiger I, Chua M, Boudier T, Song SH, Graf M, Augustine GJ, Ellisman MH, Berggren PO. Author Correction: Structural basis for delta cell paracrine regulation in pancreatic islets. Nat Commun. 2019 Sep 11; 10(1):4218. PMID: 31511521.
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    3. Arrojo E Drigo R, Jacob S, García-Prieto CF, Zheng X, Fukuda M, Nhu HTT, Stelmashenko O, Peçanha FLM, Rodriguez-Diaz R, Bushong E, Deerinck T, Phan S, Ali Y, Leibiger I, Chua M, Boudier T, Song SH, Graf M, Augustine GJ, Ellisman MH, Berggren PO. Structural basis for delta cell paracrine regulation in pancreatic islets. Nat Commun. 2019 Aug 16; 10(1):3700. PMID: 31420552.
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    4. Arrojo E Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer MW. Age Mosaicism across Multiple Scales in Adult Tissues. Cell Metab. 2019 Aug 06; 30(2):343-351.e3. PMID: 31178361.
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    5. Karas BJ, Moreau NG, Deerinck TJ, Gibson DG, Venter JC, Smith HO, Glass JI. Direct Transfer of a Mycoplasma mycoides Genome to Yeast Is Enhanced by Removal of the Mycoides Glycerol Uptake Factor Gene glpF. ACS Synth Biol. 2019 02 15; 8(2):239-244. PMID: 30645947.
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    6. Toyama BH, Arrojo E Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, Hetzer MW. Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. J Cell Biol. 2019 Feb 04; 218(2):433-444. PMID: 30552100.
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    7. Hatani T, Funakoshi S, Deerinck TJ, Bushong EA, Kimura T, Takeshima H, Ellisman MH, Hoshijima M, Yoshida Y. Nano-structural analysis of engrafted human induced pluripotent stem cell-derived cardiomyocytes in mouse hearts using a genetic-probe APEX2. Biochem Biophys Res Commun. 2018 11 10; 505(4):1251-1256. PMID: 30333092.
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    8. Haberl MG, Churas C, Tindall L, Boassa D, Phan S, Bushong EA, Madany M, Akay R, Deerinck TJ, Peltier ST, Ellisman MH. CDeep3M-Plug-and-Play cloud-based deep learning for image segmentation. Nat Methods. 2018 09; 15(9):677-680. PMID: 30171236.
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    9. McGlynn SE, Chadwick GL, O'Neill A, Mackey M, Thor A, Deerinck TJ, Ellisman MH, Orphan VJ. Subgroup Characteristics of Marine Methane-Oxidizing ANME-2 Archaea and Their Syntrophic Partners as Revealed by Integrated Multimodal Analytical Microscopy. Appl Environ Microbiol. 2018 06 01; 84(11). PMID: 29625978.
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    10. Katchalski T, Case T, Kim KY, Ramachandra R, Bushong EA, Deerinck TJ, Haberl MG, Mackey MR, Peltier S, Castillon GA, Fujikawa N, Lawrence AR, Ellisman MH. Iron-specific Signal Separation from within Heavy Metal Stained Biological Samples Using X-Ray Microtomography with Polychromatic Source and Energy-Integrating Detectors. Sci Rep. 2018 05 15; 8(1):7553. PMID: 29765060.
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    11. Martell JD, Deerinck TJ, Lam SS, Ellisman MH, Ting AY. Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Nat Protoc. 2017 Sep; 12(9):1792-1816. PMID: 28796234.
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    12. Ou HD, Phan S, Deerinck TJ, Thor A, Ellisman MH, O'Shea CC. ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells. Science. 2017 07 28; 357(6349). PMID: 28751582.
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    13. Goo MS, Sancho L, Slepak N, Boassa D, Deerinck TJ, Ellisman MH, Bloodgood BL, Patrick GN. Activity-dependent trafficking of lysosomes in dendrites and dendritic spines. J Cell Biol. 2017 08 07; 216(8):2499-2513. PMID: 28630145.
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    14. Falkenberg CV, Azeloglu EU, Stothers M, Deerinck TJ, Chen Y, He JC, Ellisman MH, Hone JC, Iyengar R, Loew LM. Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability. PLoS Comput Biol. 2017 03; 13(3):e1005433. PMID: 28301477.
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    15. Su FY, Bushong EA, Deerinck TJ, Seo K, Herrera S, Graeve OA, Kisailus D, Lubarda VA, McKittrick J. Spines of the porcupine fish: Structure, composition, and mechanical properties. J Mech Behav Biomed Mater. 2017 09; 73:38-49. PMID: 28274703.
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    16. Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY. Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. Cell Chem Biol. 2017 Mar 16; 24(3):404-414. PMID: 28238724.
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    17. Gillies AR, Chapman MA, Bushong EA, Deerinck TJ, Ellisman MH, Lieber RL. High resolution three-dimensional reconstruction of fibrotic skeletal muscle extracellular matrix. J Physiol. 2017 02 15; 595(4):1159-1171. PMID: 27859324.
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    18. Bouwer JC, Deerinck TJ, Bushong E, Astakhov V, Ramachandra R, Peltier ST, Ellisman MH. Deceleration of probe beam by stage bias potential improves resolution of serial block-face scanning electron microscopic images. Adv Struct Chem Imaging. 2017; 2(1):11. PMID: 27695667.
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    19. Loh KH, Stawski PS, Draycott AS, Udeshi ND, Lehrman EK, Wilton DK, Svinkina T, Deerinck TJ, Ellisman MH, Stevens B, Carr SA, Ting AY. Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. Cell. 2016 Aug 25; 166(5):1295-1307.e21. PMID: 27565350.
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    20. Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY. A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. Nat Biotechnol. 2016 07; 34(7):774-80. PMID: 27240195.
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    21. Ou HD, Deerinck TJ, Bushong E, Ellisman MH, O'Shea CC. Corrigendum to 'Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy' [Methods 90 (2015) 39-48]. Methods. 2016 Jul 15; 104:206. PMID: 27221672.
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    22. Ngo JT, Adams SR, Deerinck TJ, Boassa D, Rodriguez-Rivera F, Palida SF, Bertozzi CR, Ellisman MH, Tsien RY. Click-EM for imaging metabolically tagged nonprotein biomolecules. Nat Chem Biol. 2016 06; 12(6):459-65. PMID: 27110681.
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    23. van Baren MJ, Bachy C, Reistetter EN, Purvine SO, Grimwood J, Sudek S, Yu H, Poirier C, Deerinck TJ, Kuo A, Grigoriev IV, Wong CH, Smith RD, Callister SJ, Wei CL, Schmutz J, Worden AZ. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants. BMC Genomics. 2016 Mar 31; 17:267. PMID: 27029936.
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    24. Hutchison CA, Chuang RY, Noskov VN, Assad-Garcia N, Deerinck TJ, Ellisman MH, Gill J, Kannan K, Karas BJ, Ma L, Pelletier JF, Qi ZQ, Richter RA, Strychalski EA, Sun L, Suzuki Y, Tsvetanova B, Wise KS, Smith HO, Glass JI, Merryman C, Gibson DG, Venter JC. Design and synthesis of a minimal bacterial genome. Science. 2016 Mar 25; 351(6280):aad6253. PMID: 27013737.
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    25. Ou HD, Deerinck TJ, Bushong E, Ellisman MH, O'Shea CC. Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy. Methods. 2015 Nov 15; 90:39-48. PMID: 26066760.
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    26. Karas BJ, Diner RE, Lefebvre SC, McQuaid J, Phillips AP, Noddings CM, Brunson JK, Valas RE, Deerinck TJ, Jablanovic J, Gillard JT, Beeri K, Ellisman MH, Glass JI, Hutchison CA, Smith HO, Venter JC, Allen AE, Dupont CL, Weyman PD. Designer diatom episomes delivered by bacterial conjugation. Nat Commun. 2015 Apr 21; 6:6925. PMID: 25897682.
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    27. Kim D, Deerinck TJ, Sigal YM, Babcock HP, Ellisman MH, Zhuang X. Correlative stochastic optical reconstruction microscopy and electron microscopy. PLoS One. 2015; 10(4):e0124581. PMID: 25874453.
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    28. Lam SS, Martell JD, Kamer KJ, Deerinck TJ, Ellisman MH, Mootha VK, Ting AY. Directed evolution of APEX2 for electron microscopy and proximity labeling. Nat Methods. 2015 Jan; 12(1):51-4. PMID: 25419960.
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    29. Perez AJ, Seyedhosseini M, Deerinck TJ, Bushong EA, Panda S, Tasdizen T, Ellisman MH. A workflow for the automatic segmentation of organelles in electron microscopy image stacks. Front Neuroanat. 2014; 8:126. PMID: 25426032.
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    30. Liu DS, Nivón LG, Richter F, Goldman PJ, Deerinck TJ, Yao JZ, Richardson D, Phipps WS, Ye AZ, Ellisman MH, Drennan CL, Baker D, Ting AY. Computational design of a red fluorophore ligase for site-specific protein labeling in living cells. Proc Natl Acad Sci U S A. 2014 Oct 28; 111(43):E4551-9. PMID: 25313043.
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    31. Gillies AR, Bushong EA, Deerinck TJ, Ellisman MH, Lieber RL. Three-dimensional reconstruction of skeletal muscle extracellular matrix ultrastructure. Microsc Microanal. 2014 Dec; 20(6):1835-40. PMID: 25275291.
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    32. Ludwig A, Howard G, Mendoza-Topaz C, Deerinck T, Mackey M, Sandin S, Ellisman MH, Nichols BJ. Molecular composition and ultrastructure of the caveolar coat complex. PLoS Biol. 2013; 11(8):e1001640. PMID: 24013648.
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    33. Holcomb PS, Hoffpauir BK, Hoyson MC, Jackson DR, Deerinck TJ, Marrs GS, Dehoff M, Wu J, Ellisman MH, Spirou GA. Synaptic inputs compete during rapid formation of the calyx of Held: a new model system for neural development. J Neurosci. 2013 Aug 07; 33(32):12954-69. PMID: 23926251.
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    34. Hatch EM, Fischer AH, Deerinck TJ, Hetzer MW. Catastrophic nuclear envelope collapse in cancer cell micronuclei. Cell. 2013 Jul 03; 154(1):47-60. PMID: 23827674.
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    35. Li N, Wu X, Holzer RG, Lee JH, Todoric J, Park EJ, Ogata H, Gukovskaya AS, Gukovsky I, Pizzo DP, VandenBerg S, Tarin D, Atay C, Arkan MC, Deerinck TJ, Moscat J, Diaz-Meco M, Dawson D, Erkan M, Kleeff J, Karin M. Loss of acinar cell IKKa triggers spontaneous pancreatitis in mice. J Clin Invest. 2013 May; 123(5):2231-43. PMID: 23563314.
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    36. Holcomb PS, Deerinck TJ, Ellisman MH, Spirou GA. Construction of a polarized neuron. J Physiol. 2013 Jul 01; 591(13):3145-50. PMID: 23339176.
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    37. Martell JD, Deerinck TJ, Sancak Y, Poulos TL, Mootha VK, Sosinsky GE, Ellisman MH, Ting AY. Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy. Nat Biotechnol. 2012 Nov; 30(11):1143-8. PMID: 23086203.
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    38. Ou HD, Kwiatkowski W, Deerinck TJ, Noske A, Blain KY, Land HS, Soria C, Powers CJ, May AP, Shu X, Tsien RY, Fitzpatrick JA, Long JA, Ellisman MH, Choe S, O'Shea CC. A structural basis for the assembly and functions of a viral polymer that inactivates multiple tumor suppressors. Cell. 2012 Oct 12; 151(2):304-19. PMID: 23063122.
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    39. Davalos D, Ryu JK, Merlini M, Baeten KM, Le Moan N, Petersen MA, Deerinck TJ, Smirnoff DS, Bedard C, Hakozaki H, Gonias Murray S, Ling JB, Lassmann H, Degen JL, Ellisman MH, Akassoglou K. Fibrinogen-induced perivascular microglial clustering is required for the development of axonal damage in neuroinflammation. Nat Commun. 2012; 3:1227. PMID: 23187627.
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    40. Ellisman MH, Deerinck TJ, Shu X, Sosinsky GE. Picking faces out of a crowd: genetic labels for identification of proteins in correlated light and electron microscopy imaging. Methods Cell Biol. 2012; 111:139-55. PMID: 22857927.
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    41. Deerinck T. Advancing the state of the art. Interview by Kristie Nybo. Biotechniques. 2011 Nov; 51(5):311. PMID: 22054543.
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    42. Shu X, Lev-Ram V, Deerinck TJ, Qi Y, Ramko EB, Davidson MW, Jin Y, Ellisman MH, Tsien RY. A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms. PLoS Biol. 2011 Apr; 9(4):e1001041. PMID: 21483721.
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    43. Kim JE, O'Sullivan ML, Sanchez CA, Hwang M, Israel MA, Brennand K, Deerinck TJ, Goldstein LS, Gage FH, Ellisman MH, Ghosh A. Investigating synapse formation and function using human pluripotent stem cell-derived neurons. Proc Natl Acad Sci U S A. 2011 Feb 15; 108(7):3005-10. PMID: 21278334.
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    44. Gaietta GM, Deerinck TJ, Ellisman MH. Labeling tetracysteine-tagged proteins with biarsenical dyes for live cell imaging. Cold Spring Harb Protoc. 2011 Jan 01; 2011(1):pdb.prot5547. PMID: 21205847.
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    45. Gaietta GM, Deerinck TJ, Ellisman MH. Fluorescence photoconversion of biarsenical-labeled cells for correlated electron microscopy (EM). Cold Spring Harb Protoc. 2011 Jan 01; 2011(1):pdb.prot5548. PMID: 21205848.
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    46. Gaietta GM, Deerinck TJ, Ellisman MH. Correlated live cell light and electron microscopy using tetracysteine tags and biarsenicals. Cold Spring Harb Protoc. 2011 Jan 01; 2011(1):pdb.top94. PMID: 21205860.
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    47. Fitzpatrick K, Skasko M, Deerinck TJ, Crum J, Ellisman MH, Guatelli J. Direct restriction of virus release and incorporation of the interferon-induced protein BST-2 into HIV-1 particles. PLoS Pathog. 2010 Mar 05; 6(3):e1000701. PMID: 20221443.
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    48. West JB, Fu Z, Deerinck TJ, Mackey MR, Obayashi JT, Ellisman MH. Structure-function studies of blood and air capillaries in chicken lung using 3D electron microscopy. Respir Physiol Neurobiol. 2010 Feb 28; 170(2):202-9. PMID: 20038456.
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    49. Lichtenstein A, Gaietta GM, Deerinck TJ, Crum J, Sosinsky GE, Beyer EC, Berthoud VM. The cytoplasmic accumulations of the cataract-associated mutant, Connexin50P88S, are long-lived and form in the endoplasmic reticulum. Exp Eye Res. 2009 Mar; 88(3):600-9. PMID: 19073179.
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    50. Sen D, Deerinck TJ, Ellisman MH, Parker I, Cahalan MD. Quantum dots for tracking dendritic cells and priming an immune response in vitro and in vivo. PLoS One. 2008 Sep 29; 3(9):e3290. PMID: 18820727.
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    51. Deerinck TJ. The application of fluorescent quantum dots to confocal, multiphoton, and electron microscopic imaging. Toxicol Pathol. 2008 Jan; 36(1):112-6. PMID: 18337229.
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    52. Ultanir SK, Kim JE, Hall BJ, Deerinck T, Ellisman M, Ghosh A. Regulation of spine morphology and spine density by NMDA receptor signaling in vivo. Proc Natl Acad Sci U S A. 2007 Dec 04; 104(49):19553-8. PMID: 18048342.
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    53. Lanman J, Crum J, Deerinck TJ, Gaietta GM, Schneemann A, Sosinsky GE, Ellisman MH, Johnson JE. Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy. J Struct Biol. 2008 Mar; 161(3):439-46. PMID: 17998167.
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    54. Sosinsky GE, Crum J, Jones YZ, Lanman J, Smarr B, Terada M, Martone ME, Deerinck TJ, Johnson JE, Ellisman MH. The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications. J Struct Biol. 2008 Mar; 161(3):359-71. PMID: 17962040.
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    55. Martin BR, Deerinck TJ, Ellisman MH, Taylor SS, Tsien RY. Isoform-specific PKA dynamics revealed by dye-triggered aggregation and DAKAP1alpha-mediated localization in living cells. Chem Biol. 2007 Sep; 14(9):1031-42. PMID: 17884635.
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    56. Bielas SL, Serneo FF, Chechlacz M, Deerinck TJ, Perkins GA, Allen PB, Ellisman MH, Gleeson JG. Spinophilin facilitates dephosphorylation of doublecortin by PP1 to mediate microtubule bundling at the axonal wrist. Cell. 2007 May 04; 129(3):579-91. PMID: 17482550.
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    57. Sosinsky GE, Giepmans BN, Deerinck TJ, Gaietta GM, Ellisman MH. Markers for correlated light and electron microscopy. Methods Cell Biol. 2007; 79:575-91. PMID: 17327175.
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    58. Deerinck TJ, Giepmans BN, Smarr BL, Martone ME, Ellisman MH. Light and electron microscopic localization of multiple proteins using quantum dots. Methods Mol Biol. 2007; 374:43-53. PMID: 17237528.
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    59. Gaietta GM, Giepmans BN, Deerinck TJ, Smith WB, Ngan L, Llopis J, Adams SR, Tsien RY, Ellisman MH. Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopy. Proc Natl Acad Sci U S A. 2006 Nov 21; 103(47):17777-82. PMID: 17101980.
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    60. Zhang SL, Yu Y, Roos J, Kozak JA, Deerinck TJ, Ellisman MH, Stauderman KA, Cahalan MD. STIM1 is a Ca2+ sensor that activates CRAC channels and migrates from the Ca2+ store to the plasma membrane. Nature. 2005 Oct 06; 437(7060):902-5. PMID: 16208375.
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    61. Giepmans BN, Deerinck TJ, Smarr BL, Jones YZ, Ellisman MH. Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dots. Nat Methods. 2005 Oct; 2(10):743-9. PMID: 16179920.
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    62. Sosinsky GE, Deerinck TJ, Greco R, Buitenhuys CH, Bartol TM, Ellisman MH. Development of a model for microphysiological simulations: small nodes of ranvier from peripheral nerves of mice reconstructed by electron tomography. Neuroinformatics. 2005; 3(2):133-62. PMID: 15988042.
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    63. Bubulya PA, Prasanth KV, Deerinck TJ, Gerlich D, Beaudouin J, Ellisman MH, Ellenberg J, Spector DL. Hypophosphorylated SR splicing factors transiently localize around active nucleolar organizing regions in telophase daughter nuclei. J Cell Biol. 2004 Oct 11; 167(1):51-63. PMID: 15479736.
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    64. Ju W, Morishita W, Tsui J, Gaietta G, Deerinck TJ, Adams SR, Garner CC, Tsien RY, Ellisman MH, Malenka RC. Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptors. Nat Neurosci. 2004 Mar; 7(3):244-53. PMID: 14770185.
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    65. Fomina AF, Deerinck TJ, Ellisman MH, Cahalan MD. Regulation of membrane trafficking and subcellular organization of endocytic compartments revealed with FM1-43 in resting and activated human T cells. Exp Cell Res. 2003 Nov 15; 291(1):150-66. PMID: 14597416.
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    66. Mironov AA, Mironov AA, Beznoussenko GV, Trucco A, Lupetti P, Smith JD, Geerts WJ, Koster AJ, Burger KN, Martone ME, Deerinck TJ, Ellisman MH, Luini A. ER-to-Golgi carriers arise through direct en bloc protrusion and multistage maturation of specialized ER exit domains. Dev Cell. 2003 Oct; 5(4):583-94. PMID: 14536060.
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    67. Sosinsky GE, Gaietta GM, Hand G, Deerinck TJ, Han A, Mackey M, Adams SR, Bouwer J, Tsien RY, Ellisman MH. Tetracysteine genetic tags complexed with biarsenical ligands as a tool for investigating gap junction structure and dynamics. Cell Commun Adhes. 2003 Jul-Dec; 10(4-6):181-6. PMID: 14681013.
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    68. Gaietta G, Deerinck TJ, Adams SR, Bouwer J, Tour O, Laird DW, Sosinsky GE, Tsien RY, Ellisman MH. Multicolor and electron microscopic imaging of connexin trafficking. Science. 2002 Apr 19; 296(5567):503-7. PMID: 11964472.
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