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Derek Toomre, PhD

Professor of Cell Biology; Director of the YALE 'CINEMA' Laboratory (Cellular Imaging using New Microscopy Approaches)

Contact Information

Derek Toomre, PhD

Mailing Address

  • Cell Biology

    PO Box 208002, 333 Cedar Street

    New Haven, CT 06520-8002

    United States

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Research Summary

A long-term goal of my laboratory is to understand how the exo-endocytic cycle is spatially regulated during cellular morphogenesis. Two major focuses are the spatial-temporal regulation of membrane traffic in adipocytes in response to insulin signaling and in fibroblasts during cell migration. To elucidated mechanisms that regulate membrane trafficking, my laboratory uses advanced imaging and analysis coupled with RNAi knockdown of key regulator machinery (e.g. exocyst complex). Innovative live cell TIRFM and spinning-disk confocal imaging at the 'CINEMA' imaging center are used to visualize directly, at the single-vesicle level, where and how membrane traffic is delivered and regulated. As impaired vesicle exocytosis is associated with type 2 diabetes and abnormal cell motility is associated with metastasis and cancer, the knowledge gained with this research will be highly significant in understanding the pathologies of these diseases.

Specialized Terms: Cell Biology; Exocytosis; Endocytosis; Membrane Traffic; Tethering; Microscopy; Live Cell Imaging; TIRFM; Single molecule

Extensive Research Description


Cellular Imaging and Analysis of Polarized Membrane Traffic. A major goal of my laboratory is to develop and apply new and state-of-the-art multidimensional optical methods to better understand the basic mechanisms of polarized membrane trafficking and spatial-temporal control of endo-exocytosis.

One important challenge facing modern biology is to understand how individual biochemical reactions are integrated in space and time. Increasingly, new vital probes and optical methods has begun to provide unique mechanistic insight into how molecules, vesicles, organelles and whole cells are (re)organized in response to internal and external cues. This is especially relevant for the dynamic process of membrane traffic and the cytoskeleton in cell polarity - key areas of our interest. Insight into how cells both establish and lose polarity are also essential for understanding disease processes such as metastasis. In particular we are applying the optical methods of Total Internal Reflections Fluorescence Microscopy (TIRFM) and 4D (3D + time) multicolor spinning-disk confocal imaging to directly address, at the single-vesicle level, where and how polarized membrane traffic is delivered. TIRFM imaging (also called evanescent wave microscopy) can selectively illuminate an extremely thin optical section (

Specifically, using advance optical methods our lab is exploring the following related topics:

1) organization and coordination of exocytosis and cytoskeleton in polarized cells and

2) coupling of exo- and endocytosis and molecular mechanisms that regulate this process. For instance, TIRFM imaging has lead to a number of novel observations including imaging of constitutive exocytosis (and the surprising presence of exocytic ‘hot-spots’ for fusion on the cell surface) and nanometer targeting of microtubule plus ends to the cell surface and focal adhesions. To facilitate these and other studies multicolor TIRFM instruments, a 4D spinning disk confocal and electrophysiology instrumentation has been recently implemented here as part of “The CINEMA Lab” ("Cinema Imaging Using New Microscopy Approaches"), with support from Ludwig Institute for Cancer Research (LICR), various grants, Yale and the private sector. We are also collaborating with other groups at Yale (Dr. Jim Duncan’s group, Dept. of Biomedical Engineering) and overseas (Elena Diaz, Spain) to develop novel software to detect, analyze and make computational cellular models of these processes.

Coauthors

Research Interests

Biology; Biophysics; Biotechnology; Chemistry; Nanotechnology; Optics and Photonics

Selected Publications

  • Fusion of constitutive membrane traffic with the cell surface observed by evanescent wave microscopy.Toomre D, Steyer JA, Keller P, Almers W, Simons K. Fusion of constitutive membrane traffic with the cell surface observed by evanescent wave microscopy. The Journal Of Cell Biology 2000, 149: 33-40. PMID: 10747085, PMCID: PMC2175107.
  • Lipid rafts and signal transduction.Simons K, Toomre D. Lipid rafts and signal transduction. Nature Reviews. Molecular Cell Biology 2000, 1: 31-9. PMID: 11413487, DOI: 10.1038/35036052.
  • Golgi biogenesis in Toxoplasma gondii.Pelletier L, Stern CA, Pypaert M, Sheff D, Ngô HM, Roper N, He CY, Hu K, Toomre D, Coppens I, Roos DS, Joiner KA, Warren G. Golgi biogenesis in Toxoplasma gondii. Nature 2002, 418: 548-52. PMID: 12152082, DOI: 10.1038/nature00946.
  • Dendritic cell maturation triggers retrograde MHC class II transport from lysosomes to the plasma membrane.Chow A, Toomre D, Garrett W, Mellman I. Dendritic cell maturation triggers retrograde MHC class II transport from lysosomes to the plasma membrane. Nature 2002, 418: 988-94. PMID: 12198549, DOI: 10.1038/nature01006.
  • Selective delivery of secretory cargo in Golgi-derived carriers of nonepithelial cells.Rustom A, Bajohrs M, Kaether C, Keller P, Toomre D, Corbeil D, Gerdes HH. Selective delivery of secretory cargo in Golgi-derived carriers of nonepithelial cells. Traffic (Copenhagen, Denmark) 2002, 3: 279-88. PMID: 11929609, DOI: 10.1034/j.1600-0854.2002.030405.x.
  • Nanometer targeting of microtubules to focal adhesions.Krylyshkina O, Anderson KI, Kaverina I, Upmann I, Manstein DJ, Small JV, Toomre DK. Nanometer targeting of microtubules to focal adhesions. The Journal Of Cell Biology 2003, 161: 853-9. PMID: 12782685, PMCID: PMC2172972, DOI: 10.1083/jcb.200301102.
  • Golgi duplication in Trypanosoma brucei.He CY, Ho HH, Malsam J, Chalouni C, West CM, Ullu E, Toomre D, Warren G. Golgi duplication in Trypanosoma brucei. The Journal Of Cell Biology 2004, 165: 313-21. PMID: 15138289, PMCID: PMC2172185, DOI: 10.1083/jcb.200311076.
  • The Abl/Arg substrate ArgBP2/nArgBP2 coordinates the function of multiple regulatory mechanisms converging on the actin cytoskeleton.Cestra G, Toomre D, Chang S, De Camilli P. The Abl/Arg substrate ArgBP2/nArgBP2 coordinates the function of multiple regulatory mechanisms converging on the actin cytoskeleton. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 1731-6. PMID: 15659545, PMCID: PMC547834, DOI: 10.1073/pnas.0409376102.
  • Phosphatidylinositol phosphate kinase type I gamma regulates dynamics of large dense-core vesicle fusion.Gong LW, Di Paolo G, Diaz E, Cestra G, Diaz ME, Lindau M, De Camilli P, Toomre D. Phosphatidylinositol phosphate kinase type I gamma regulates dynamics of large dense-core vesicle fusion. Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 5204-9. PMID: 15793002, PMCID: PMC555604, DOI: 10.1073/pnas.0501412102.
  • Segmentation and 3D reconstruction of microtubules in total internal reflection fluorescence microscopy (TIRFM).Hadjidemetriou S, Toomre D, Duncan JS. Segmentation and 3D reconstruction of microtubules in total internal reflection fluorescence microscopy (TIRFM). Medical Image Computing And Computer-assisted Intervention : MICCAI ... International Conference On Medical Image Computing And Computer-Assisted Intervention 2005, 8: 761-9. PMID: 16685915, DOI: 10.1007/11566465_94.
  • Spying on IgE receptor signaling: simply complex, or not?Toomre D. Spying on IgE receptor signaling: simply complex, or not? The Journal Of Cell Biology 2005, 171: 415-7. PMID: 16275748, PMCID: PMC2171246, DOI: 10.1083/jcb.200510105.
  • The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotide-exchange factor.Murata T, Delprato A, Ingmundson A, Toomre DK, Lambright DG, Roy CR. The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotide-exchange factor. Nature Cell Biology 2006, 8: 971-7. PMID: 16906144, DOI: 10.1038/ncb1463.
  • Spatio-temporal analysis of constitutive exocytosis in epithelial cells.Sebastian R, Diaz ME, Ayala G, Letinic K, Moncho-Bogani J, Toomre D. Spatio-temporal analysis of constitutive exocytosis in epithelial cells. IEEE/ACM Transactions On Computational Biology And Bioinformatics / IEEE, ACM 2006, 3: 17-32. PMID: 17048390, DOI: 10.1109/TCBB.2006.11.
  • Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stages.Perera RM, Zoncu R, Lucast L, De Camilli P, Toomre D. Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stages. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 19332-7. PMID: 17158794, PMCID: PMC1693868, DOI: 10.1073/pnas.0609795104.
  • Nitric oxide synthase generates nitric oxide locally to regulate compartmentalized protein S-nitrosylation and protein trafficking.Iwakiri Y, Satoh A, Chatterjee S, Toomre DK, Chalouni CM, Fulton D, Groszmann RJ, Shah VH, Sessa WC. Nitric oxide synthase generates nitric oxide locally to regulate compartmentalized protein S-nitrosylation and protein trafficking. Proceedings Of The National Academy Of Sciences Of The United States Of America 2006, 103: 19777-82. PMID: 17170139, PMCID: PMC1750883, DOI: 10.1073/pnas.0605907103.
  • Overlapping events with application to image sequences.Ayala G, Sebastian R, Díaz ME, Díaz E, Zoncu R, Toomre D. Overlapping events with application to image sequences. IEEE Transactions On Pattern Analysis And Machine Intelligence 2006, 28: 1707-12. PMID: 16986551, DOI: 10.1109/TPAMI.2006.199.
  • Vectorial insertion of apical and basolateral membrane proteins in polarized epithelial cells revealed by quantitative 3D live cell imaging.Hua W, Sheff D, Toomre D, Mellman I. Vectorial insertion of apical and basolateral membrane proteins in polarized epithelial cells revealed by quantitative 3D live cell imaging. The Journal Of Cell Biology 2006, 172: 1035-44. PMID: 16567501, PMCID: PMC2063761, DOI: 10.1083/jcb.200512012.
  • Lymphocyte transcellular migration occurs through recruitment of endothelial ICAM-1 to caveola- and F-actin-rich domains.Millán J, Hewlett L, Glyn M, Toomre D, Clark P, Ridley AJ. Lymphocyte transcellular migration occurs through recruitment of endothelial ICAM-1 to caveola- and F-actin-rich domains. Nature Cell Biology 2006, 8: 113-23. PMID: 16429128, DOI: 10.1038/ncb1356.
  • Analysis of spatial dependencies of endocytic proteins based on temporal random sets.Sebastian R, Diaz ME, Ayala G, Zoncu R, Toomre D. Analysis of spatial dependencies of endocytic proteins based on temporal random sets. Conference Proceedings : ... Annual International Conference Of The IEEE Engineering In Medicine And Biology Society. IEEE Engineering In Medicine And Biology Society. Annual Conference 2006, 2006: 4175-8. PMID: 17946228, DOI: 10.1109/IEMBS.2006.260479.
  • Par3 functions in the biogenesis of the primary cilium in polarized epithelial cells.Sfakianos J, Togawa A, Maday S, Hull M, Pypaert M, Cantley L, Toomre D, Mellman I. Par3 functions in the biogenesis of the primary cilium in polarized epithelial cells. The Journal Of Cell Biology 2007, 179: 1133-40. PMID: 18070914, PMCID: PMC2140027, DOI: 10.1083/jcb.200709111.
  • Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate.Zoncu R, Perera RM, Sebastian R, Nakatsu F, Chen H, Balla T, Ayala G, Toomre D, De Camilli PV. Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphate. Proceedings Of The National Academy Of Sciences Of The United States Of America 2007, 104: 3793-8. PMID: 17360432, PMCID: PMC1805489, DOI: 10.1073/pnas.0611733104.
  • A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway.Erdmann KS, Mao Y, McCrea HJ, Zoncu R, Lee S, Paradise S, Modregger J, Biemesderfer D, Toomre D, De Camilli P. A role of the Lowe syndrome protein OCRL in early steps of the endocytic pathway. Developmental Cell 2007, 13: 377-90. PMID: 17765681, PMCID: PMC2025683, DOI: 10.1016/j.devcel.2007.08.004.
  • Internalization, intracellular trafficking, and biodistribution of monoclonal antibody 806: a novel anti-epidermal growth factor receptor antibody.Perera RM, Zoncu R, Johns TG, Pypaert M, Lee FT, Mellman I, Old LJ, Toomre DK, Scott AM. Internalization, intracellular trafficking, and biodistribution of monoclonal antibody 806: a novel anti-epidermal growth factor receptor antibody. Neoplasia (New York, N.Y.) 2007, 9: 1099-110. PMID: 18084617, PMCID: PMC2134906, DOI: 10.1593/neo.07721.
  • Motion tracking of the outer tips of microtubules.Hadjidemetriou S, Toomre D, Duncan J. Motion tracking of the outer tips of microtubules. Medical Image Analysis 2008, 12: 689-702. PMID: 18571462, DOI: 10.1016/j.media.2008.04.004.
  • Both daughter cells traffic and exocytose membrane at the cleavage furrow during mammalian cytokinesis.Goss JW, Toomre DK. Both daughter cells traffic and exocytose membrane at the cleavage furrow during mammalian cytokinesis. The Journal Of Cell Biology 2008, 181: 1047-54. PMID: 18573914, PMCID: PMC2442215, DOI: 10.1083/jcb.200712137.
  • The tyrosine kinase activity of c-Src regulates actin dynamics and organization of podosomes in osteoclasts.Destaing O, Sanjay A, Itzstein C, Horne WC, Toomre D, De Camilli P, Baron R. The tyrosine kinase activity of c-Src regulates actin dynamics and organization of podosomes in osteoclasts. Molecular Biology Of The Cell 2008, 19: 394-404. PMID: 17978100, PMCID: PMC2174183, DOI: 10.1091/mbc.E07-03-0227.
  • Measuring spatiotemporal dependencies in bivariate temporal random sets with applications to cell biology.Díaz E, Sebastian R, Ayala G, Díaz ME, Zoncu R, Toomre D, Gasman S. Measuring spatiotemporal dependencies in bivariate temporal random sets with applications to cell biology. IEEE Transactions On Pattern Analysis And Machine Intelligence 2008, 30: 1659-71. PMID: 18617722, DOI: 10.1109/TPAMI.2007.70821.
  • Repair of injured plasma membrane by rapid Ca2+-dependent endocytosis.Idone V, Tam C, Goss JW, Toomre D, Pypaert M, Andrews NW. Repair of injured plasma membrane by rapid Ca2+-dependent endocytosis. The Journal Of Cell Biology 2008, 180: 905-14. PMID: 18316410, PMCID: PMC2265401, DOI: 10.1083/jcb.200708010.
  • Analyzing protein-protein spatial-temporal dependencies from image sequences using fuzzy temporal random sets.Díaz ME, Ayala G, León T, Zoncu R, Toomre D. Analyzing protein-protein spatial-temporal dependencies from image sequences using fuzzy temporal random sets. Journal Of Computational Biology : A Journal Of Computational Molecular Cell Biology 2008, 15: 1221-36. PMID: 18973437, DOI: 10.1089/cmb.2008.0055.
  • A phosphoinositide switch controls the maturation and signaling properties of APPL endosomes.Zoncu R, Perera RM, Balkin DM, Pirruccello M, Toomre D, De Camilli P. A phosphoinositide switch controls the maturation and signaling properties of APPL endosomes. Cell 2009, 136: 1110-21. PMID: 19303853, PMCID: PMC2705806, DOI: 10.1016/j.cell.2009.01.032.
  • Exocyst is involved in polarized cell migration and cerebral cortical development.Letinic K, Sebastian R, Toomre D, Rakic P. Exocyst is involved in polarized cell migration and cerebral cortical development. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 11342-7. PMID: 19549839, PMCID: PMC2708724, DOI: 10.1073/pnas.0904244106.
  • Spatial control of EGF receptor activation by reversible dimerization on living cells.Chung I, Akita R, Vandlen R, Toomre D, Schlessinger J, Mellman I. Spatial control of EGF receptor activation by reversible dimerization on living cells. Nature 2010, 464: 783-7. PMID: 20208517, DOI: 10.1038/nature08827.
  • A new wave of cellular imaging.Toomre D, Bewersdorf J. A new wave of cellular imaging. Annual Review Of Cell And Developmental Biology 2010, 26: 285-314. PMID: 20929313, DOI: 10.1146/annurev-cellbio-100109-104048.
  • Estimation of 3D geometry of microtubules using multi-angle total internal reflection fluorescence microscopy.Yang Q, Karpikov A, Toomre D, Duncan J. Estimation of 3D geometry of microtubules using multi-angle total internal reflection fluorescence microscopy. Medical Image Computing And Computer-assisted Intervention : MICCAI ... International Conference On Medical Image Computing And Computer-Assisted Intervention 2010, 13: 538-45. PMID: 20879357, DOI: 10.1007/978-3-642-15745-5_66.
  • The inositol 5-phosphatase SHIP2 regulates endocytic clathrin-coated pit dynamics.Nakatsu F, Perera RM, Lucast L, Zoncu R, Domin J, Gertler FB, Toomre D, De Camilli P. The inositol 5-phosphatase SHIP2 regulates endocytic clathrin-coated pit dynamics. The Journal Of Cell Biology 2010, 190: 307-15. PMID: 20679431, PMCID: PMC2922640, DOI: 10.1083/jcb.201005018.
  • Deciphering subcellular processes in live imaging datasets via dynamic probabilistic networks.Letinic K, Sebastian R, Barthel A, Toomre D. Deciphering subcellular processes in live imaging datasets via dynamic probabilistic networks. Bioinformatics (Oxford, England) 2010, 26: 2029-36. PMID: 20581401, PMCID: PMC2916721, DOI: 10.1093/bioinformatics/btq331.
  • Automatic detection of large dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution.Díaz E, Ayala G, Díaz ME, Gong LW, Toomre D. Automatic detection of large dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution. IEEE/ACM Transactions On Computational Biology And Bioinformatics / IEEE, ACM 2010, 7: 2-11. PMID: 20150664, DOI: 10.1109/TCBB.2008.30.
  • Dual-mode of insulin action controls GLUT4 vesicle exocytosis.Xu Y, Rubin BR, Orme CM, Karpikov A, Yu C, Bogan JS, Toomre DK. Dual-mode of insulin action controls GLUT4 vesicle exocytosis. The Journal Of Cell Biology 2011, 193: 643-53. PMID: 21555461, PMCID: PMC3166865, DOI: 10.1083/jcb.201008135.
  • An expectation maximization based method for subcellular particle tracking using multi-angle TIRF microscopy.Liang L, Shen H, De Camilli P, Toomre DK, Duncan JS. An expectation maximization based method for subcellular particle tracking using multi-angle TIRF microscopy. Medical Image Computing And Computer-assisted Intervention : MICCAI ... International Conference On Medical Image Computing And Computer-Assisted Intervention 2011, 14: 629-36. PMID: 22003671, PMCID: PMC3648983, DOI: 10.1007/978-3-642-23623-5_79.
  • Splice isoform estrogen receptors as integral transmembrane proteins.Kim KH, Toomre D, Bender JR. Splice isoform estrogen receptors as integral transmembrane proteins. Molecular Biology Of The Cell 2011, 22: 4415-23. PMID: 21937726, PMCID: PMC3216666, DOI: 10.1091/mbc.E11-05-0416.
  • 3-D reconstruction of microtubules from multi-angle total internal reflection fluorescence microscopy using Bayesian framework.Yang Q, Karpikov A, Toomre D, Duncan JS. 3-D reconstruction of microtubules from multi-angle total internal reflection fluorescence microscopy using Bayesian framework. IEEE Transactions On Image Processing : A Publication Of The IEEE Signal Processing Society 2011, 20: 2248-59. PMID: 21324778, DOI: 10.1109/TIP.2011.2114359.
  • Exocyst function is regulated by effector phosphorylation.Chen XW, Leto D, Xiao J, Goss J, Wang Q, Shavit JA, Xiong T, Yu G, Ginsburg D, Toomre D, Xu Z, Saltiel AR. Exocyst function is regulated by effector phosphorylation. Nature Cell Biology 2011, 13: 580-8. PMID: 21516108, PMCID: PMC3904505, DOI: 10.1038/ncb2226.
  • Using light to see and control membrane traffic.Xu Y, Melia TJ, Toomre DK. Using light to see and control membrane traffic. Current Opinion In Chemical Biology 2011, 15: 822-30. PMID: 22079055, DOI: 10.1016/j.cbpa.2011.10.016.
  • Optogenetic control of phosphoinositide metabolism.Idevall-Hagren O, Dickson EJ, Hille B, Toomre DK, De Camilli P. Optogenetic control of phosphoinositide metabolism. Proceedings Of The National Academy Of Sciences Of The United States Of America 2012, 109: E2316-23. PMID: 22847441, PMCID: PMC3435206, DOI: 10.1073/pnas.1211305109.
  • The Legionella pneumophila effector DrrA is sufficient to stimulate SNARE-dependent membrane fusion.Arasaki K, Toomre DK, Roy CR. The Legionella pneumophila effector DrrA is sufficient to stimulate SNARE-dependent membrane fusion. Cell Host & Microbe 2012, 11: 46-57. PMID: 22264512, PMCID: PMC3266541, DOI: 10.1016/j.chom.2011.11.009.
  • Caveolae, fenestrae and transendothelial channels retain PV1 on the surface of endothelial cells.Tkachenko E, Tse D, Sideleva O, Deharvengt SJ, Luciano MR, Xu Y, McGarry CL, Chidlow J, Pilch PF, Sessa WC, Toomre DK, Stan RV. Caveolae, fenestrae and transendothelial channels retain PV1 on the surface of endothelial cells. PloS One 2012, 7: e32655. PMID: 22403691, PMCID: PMC3293851, DOI: 10.1371/journal.pone.0032655.
  • Cellular imaging using total internal reflection fluorescence microscopy: theory and instrumentation.Toomre D. Cellular imaging using total internal reflection fluorescence microscopy: theory and instrumentation. Cold Spring Harbor Protocols 2012, 2012: 414-24. PMID: 22474668, DOI: 10.1101/pdb.top068650.
  • Alignment and calibration of total internal reflection fluorescence microscopy systems.Toomre D. Alignment and calibration of total internal reflection fluorescence microscopy systems. Cold Spring Harbor Protocols 2012, 2012: 504-9. PMID: 22474669, DOI: 10.1101/pdb.prot068668.
  • Generating live cell data using total internal reflection fluorescence microscopy.Toomre D. Generating live cell data using total internal reflection fluorescence microscopy. Cold Spring Harbor Protocols 2012, 2012: 439-46. PMID: 22474670, DOI: 10.1101/pdb.ip068676.
  • The neuropilin 1 cytoplasmic domain is required for VEGF-A-dependent arteriogenesis.Lanahan A, Zhang X, Fantin A, Zhuang Z, Rivera-Molina F, Speichinger K, Prahst C, Zhang J, Wang Y, Davis G, Toomre D, Ruhrberg C, Simons M. The neuropilin 1 cytoplasmic domain is required for VEGF-A-dependent arteriogenesis. Developmental Cell 2013, 25: 156-68. PMID: 23639442, PMCID: PMC3774154, DOI: 10.1016/j.devcel.2013.03.019.
  • Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms.Huang F, Hartwich TM, Rivera-Molina FE, Lin Y, Duim WC, Long JJ, Uchil PD, Myers JR, Baird MA, Mothes W, Davidson MW, Toomre D, Bewersdorf J. Video-rate nanoscopy using sCMOS camera-specific single-molecule localization algorithms. Nature Methods 2013, 10: 653-8. PMID: 23708387, PMCID: PMC3696415, DOI: 10.1038/nmeth.2488.
  • Live-cell imaging of exocyst links its spatiotemporal dynamics to various stages of vesicle fusion.Rivera-Molina F, Toomre D. Live-cell imaging of exocyst links its spatiotemporal dynamics to various stages of vesicle fusion. The Journal Of Cell Biology 2013, 201: 673-80. PMID: 23690179, PMCID: PMC3664709, DOI: 10.1083/jcb.201212103.
  • A network of interactions enables CCM3 and STK24 to coordinate UNC13D-driven vesicle exocytosis in neutrophils.Zhang Y, Tang W, Zhang H, Niu X, Xu Y, Zhang J, Gao K, Pan W, Boggon TJ, Toomre D, Min W, Wu D. A network of interactions enables CCM3 and STK24 to coordinate UNC13D-driven vesicle exocytosis in neutrophils. Developmental Cell 2013, 27: 215-226. PMID: 24176643, PMCID: PMC3834565, DOI: 10.1016/j.devcel.2013.09.021.
  • Super-resolution imaging of the Golgi in live cells with a bioorthogonal ceramide probe.Erdmann RS, Takakura H, Thompson AD, Rivera-Molina F, Allgeyer ES, Bewersdorf J, Toomre D, Schepartz A. Super-resolution imaging of the Golgi in live cells with a bioorthogonal ceramide probe. Angewandte Chemie (International Ed. In English) 2014, 53: 10242-6. PMID: 25081303, PMCID: PMC4593319, DOI: 10.1002/anie.201403349.
  • Reticulon 4 is necessary for endoplasmic reticulum tubulation, STIM1-Orai1 coupling, and store-operated calcium entry.Jozsef L, Tashiro K, Kuo A, Park EJ, Skoura A, Albinsson S, Rivera-Molina F, Harrison KD, Iwakiri Y, Toomre D, Sessa WC. Reticulon 4 is necessary for endoplasmic reticulum tubulation, STIM1-Orai1 coupling, and store-operated calcium entry. The Journal Of Biological Chemistry 2014, 289: 9380-95. PMID: 24558039, PMCID: PMC3969502, DOI: 10.1074/jbc.M114.548602.
  • Pushing the boundaries: the development of super-resolution microscopy at yale and beyond: an interview with Derek Toomre, PhD.Toomre D. Pushing the boundaries: the development of super-resolution microscopy at yale and beyond: an interview with Derek Toomre, PhD. The Yale Journal Of Biology And Medicine 2014, 87: 55-62. PMID: 24600336, PMCID: PMC3941448.
  • The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135.Stoops EH, Hull M, Olesen C, Mistry K, Harder JL, Rivera-Molina F, Toomre D, Caplan MJ. The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135. The Journal Of Cell Biology 2015, 211: 287-94. PMID: 26504168, PMCID: PMC4621837, DOI: 10.1083/jcb.201502045.
  • Optogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin action.Xu Y, Nan D, Fan J, Bogan JS, Toomre D. Optogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin action. Journal Of Cell Science 2016, 129: 2085-95. PMID: 27076519, PMCID: PMC4878990, DOI: 10.1242/jcs.174805.
  • Erratum: Endothelial exocytosis of angiopoietin-2 resulting from CCM3 deficiency contributes to cerebral cavernous malformation.Zhou HJ, Qin L, Zhang H, Tang W, Ji W, He Y, Liang X, Wang Z, Yuan Q, Vortmeyer A, Toomre D, Fuh G, Yan M, Kluger MS, Wu D, Min W. Erratum: Endothelial exocytosis of angiopoietin-2 resulting from CCM3 deficiency contributes to cerebral cavernous malformation. Nature Medicine 2016, 22: 1502. PMID: 27923033, DOI: 10.1038/nm1216-1502c.
  • Ultra-High Resolution 3D Imaging of Whole Cells.Huang F, Sirinakis G, Allgeyer ES, Schroeder LK, Duim WC, Kromann EB, Phan T, Rivera-Molina FE, Myers JR, Irnov I, Lessard M, Zhang Y, Handel MA, Jacobs-Wagner C, Lusk CP, Rothman JE, Toomre D, Booth MJ, Bewersdorf J. Ultra-High Resolution 3D Imaging of Whole Cells. Cell 2016, 166: 1028-1040. PMID: 27397506, PMCID: PMC5005454, DOI: 10.1016/j.cell.2016.06.016.
  • The IN/OUT assay: a new tool to study ciliogenesis.Kukic I, Rivera-Molina F, Toomre D. The IN/OUT assay: a new tool to study ciliogenesis. Cilia 2016, 5: 23. PMID: 27493724, PMCID: PMC4972980, DOI: 10.1186/s13630-016-0044-2.
  • Endothelial exocytosis of angiopoietin-2 resulting from CCM3 deficiency contributes to cerebral cavernous malformation.Zhou HJ, Qin L, Zhang H, Tang W, Ji W, He Y, Liang X, Wang Z, Yuan Q, Vortmeyer A, Toomre D, Fuh G, Yan M, Kluger MS, Wu D, Min W. Endothelial exocytosis of angiopoietin-2 resulting from CCM3 deficiency contributes to cerebral cavernous malformation. Nature Medicine 2016, 22: 1033-1042. PMID: 27548575, PMCID: PMC5014607, DOI: 10.1038/nm.4169.
  • Two-colour live-cell nanoscale imaging of intracellular targets.Bottanelli F, Kromann EB, Allgeyer ES, Erdmann RS, Wood Baguley S, Sirinakis G, Schepartz A, Baddeley D, Toomre DK, Rothman JE, Bewersdorf J. Two-colour live-cell nanoscale imaging of intracellular targets. Nature Communications 2016, 7: 10778. PMID: 26940217, PMCID: PMC4785223, DOI: 10.1038/ncomms10778.
  • Staphylococcus aureus recruits Cdc42GAP through recycling endosomes and the exocyst to invade human endothelial cells.Rauch L, Hennings K, Trasak C, Röder A, Schröder B, Koch-Nolte F, Rivera-Molina F, Toomre D, Aepfelbacher M. Staphylococcus aureus recruits Cdc42GAP through recycling endosomes and the exocyst to invade human endothelial cells. Journal Of Cell Science 2016, 129: 2937-49. PMID: 27311480, PMCID: PMC5004874, DOI: 10.1242/jcs.186213.
  • Sphingomyelin is sorted at the trans Golgi network into a distinct class of secretory vesicle.Deng Y, Rivera-Molina FE, Toomre DK, Burd CG. Sphingomyelin is sorted at the trans Golgi network into a distinct class of secretory vesicle. Proceedings Of The National Academy Of Sciences Of The United States Of America 2016, 113: 6677-82. PMID: 27247384, PMCID: PMC4914164, DOI: 10.1073/pnas.1602875113.
  • Excess cholesterol inhibits glucose-stimulated fusion pore dynamics in insulin exocytosis.Xu Y, Toomre DK, Bogan JS, Hao M. Excess cholesterol inhibits glucose-stimulated fusion pore dynamics in insulin exocytosis. Journal Of Cellular And Molecular Medicine 2017, 21: 2950-2962. PMID: 28544529, PMCID: PMC5661106, DOI: 10.1111/jcmm.13207.
  • STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells.Erdmann RS, Toomre D, Schepartz A. STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells. Methods In Molecular Biology (Clifton, N.J.) 2017, 1663: 65-78. PMID: 28924659, PMCID: PMC6146391, DOI: 10.1007/978-1-4939-7265-4_6.
  • Differential requirement for N-ethylmaleimide-sensitive factor in endosomal trafficking of transferrin receptor from anterograde trafficking of vesicular stomatitis virus glycoprotein G.Fan J, Zhou X, Wang Y, Kuang C, Sun Y, Liu X, Toomre D, Xu Y. Differential requirement for N-ethylmaleimide-sensitive factor in endosomal trafficking of transferrin receptor from anterograde trafficking of vesicular stomatitis virus glycoprotein G. FEBS Letters 2017, 591: 273-281. PMID: 27995606, DOI: 10.1002/1873-3468.12532.
  • Leptin Is Produced by Parathyroid Glands and Stimulates Parathyroid Hormone Secretion.Hoang D, Broer N, Sosa JA, Abitbol N, Yao X, Li F, Rivera-Molina F, Toomre DK, Roman SA, Sue G, Kim S, Li AY, Callender GG, Simpson C, Narayan D. Leptin Is Produced by Parathyroid Glands and Stimulates Parathyroid Hormone Secretion. Annals Of Surgery 2017, 266: 1075-1083. PMID: 27611607, DOI: 10.1097/SLA.0000000000002004.
  • Novel ecto-tagged integrins reveal their trafficking in live cells.Huet-Calderwood C, Rivera-Molina F, Iwamoto DV, Kromann EB, Toomre D, Calderwood DA. Novel ecto-tagged integrins reveal their trafficking in live cells. Nature Communications 2017, 8: 570. PMID: 28924207, PMCID: PMC5603536, DOI: 10.1038/s41467-017-00646-w.
  • Land-locked mammalian Golgi reveals cargo transport between stable cisternae.Dunlop MH, Ernst AM, Schroeder LK, Toomre DK, Lavieu G, Rothman JE. Land-locked mammalian Golgi reveals cargo transport between stable cisternae. Nature Communications 2017, 8: 432. PMID: 28874656, PMCID: PMC5585379, DOI: 10.1038/s41467-017-00570-z.
  • A novel physiological role for ARF1 in the formation of bidirectional tubules from the Golgi.Bottanelli F, Kilian N, Ernst AM, Rivera-Molina F, Schroeder LK, Kromann EB, Lessard MD, Erdmann RS, Schepartz A, Baddeley D, Bewersdorf J, Toomre D, Rothman JE. A novel physiological role for ARF1 in the formation of bidirectional tubules from the Golgi. Molecular Biology Of The Cell 2017, 28: 1676-1687. PMID: 28428254, PMCID: PMC5469610, DOI: 10.1091/mbc.E16-12-0863.
  • HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution.Thompson AD, Bewersdorf J, Toomre D, Schepartz A. HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-Resolution. Biochemistry 2017, 56: 5194-5201. PMID: 28792749, PMCID: PMC5854879, DOI: 10.1021/acs.biochem.7b00545.
  • Long-Term Live-Cell STED Nanoscopy of Primary and Cultured Cells with the Plasma Membrane HIDE Probe DiI-SiR.Thompson AD, Omar MH, Rivera-Molina F, Xi Z, Koleske AJ, Toomre DK, Schepartz A. Long-Term Live-Cell STED Nanoscopy of Primary and Cultured Cells with the Plasma Membrane HIDE Probe DiI-SiR. Angewandte Chemie (International Ed. In English) 2017, 56: 10408-10412. PMID: 28679029, PMCID: PMC5576494, DOI: 10.1002/anie.201704783.
  • Long time-lapse nanoscopy with spontaneously blinking membrane probes.Takakura H, Zhang Y, Erdmann RS, Thompson AD, Lin Y, McNellis B, Rivera-Molina F, Uno SN, Kamiya M, Urano Y, Rothman JE, Bewersdorf J, Schepartz A, Toomre D. Long time-lapse nanoscopy with spontaneously blinking membrane probes. Nature Biotechnology 2017, 35: 773-780. PMID: 28671662, PMCID: PMC5609855, DOI: 10.1038/nbt.3876.
  • The Rab-effector protein RABEP2 regulates endosomal trafficking to mediate vascular endothelial growth factor receptor-2 (VEGFR2)-dependent signaling.Kofler N, Corti F, Rivera-Molina F, Deng Y, Toomre D, Simons M. The Rab-effector protein RABEP2 regulates endosomal trafficking to mediate vascular endothelial growth factor receptor-2 (VEGFR2)-dependent signaling. The Journal Of Biological Chemistry 2018, 293: 4805-4817. PMID: 29425100, PMCID: PMC5880142, DOI: 10.1074/jbc.M117.812172.
  • Assessing photodamage in live-cell STED microscopy.Kilian N, Goryaynov A, Lessard MD, Hooker G, Toomre D, Rothman JE, Bewersdorf J. Assessing photodamage in live-cell STED microscopy. Nature Methods 2018, 15: 755-756. PMID: 30275592, PMCID: PMC6915835, DOI: 10.1038/s41592-018-0145-5.
  • S-Palmitoylation Sorts Membrane Cargo for Anterograde Transport in the Golgi.Ernst AM, Syed SA, Zaki O, Bottanelli F, Zheng H, Hacke M, Xi Z, Rivera-Molina F, Graham M, Rebane AA, Björkholm P, Baddeley D, Toomre D, Pincet F, Rothman JE. S-Palmitoylation Sorts Membrane Cargo for Anterograde Transport in the Golgi. Developmental Cell 2018, 47: 479-493.e7. PMID: 30458139, PMCID: PMC6251505, DOI: 10.1016/j.devcel.2018.10.024.
  • Seeing the long tail: A novel green fluorescent protein, SiriusGFP, for ultra long timelapse imaging.Zhong S, Rivera-Molina F, Rivetta A, Toomre D, Santos-Sacchi J, Navaratnam D. Seeing the long tail: A novel green fluorescent protein, SiriusGFP, for ultra long timelapse imaging. Journal Of Neuroscience Methods 2019, 313: 68-76. PMID: 30578868, DOI: 10.1016/j.jneumeth.2018.12.008.
  • Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags.Erdmann RS, Baguley SW, Richens JH, Wissner RF, Xi Z, Allgeyer ES, Zhong S, Thompson AD, Lowe N, Butler R, Bewersdorf J, Rothman JE, St Johnston D, Schepartz A, Toomre D. Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tags. Cell Chemical Biology 2019, 26: 584-592.e6. PMID: 30745239, PMCID: PMC6474801, DOI: 10.1016/j.chembiol.2019.01.003.
  • Acylation - A New Means to Control Traffic Through the Golgi.Ernst AM, Toomre D, Bogan JS. Acylation - A New Means to Control Traffic Through the Golgi. Frontiers In Cell And Developmental Biology 2019, 7: 109. PMID: 31245373, PMCID: PMC6582194, DOI: 10.3389/fcell.2019.00109.
  • New software for automated cilia detection in cells (ACDC).Lauring MC, Zhu T, Luo W, Wu W, Yu F, Toomre D. New software for automated cilia detection in cells (ACDC). Cilia 2019, 8: 1. PMID: 31388414, PMCID: PMC6670212, DOI: 10.1186/s13630-019-0061-z.
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