Derek Toomre, PhD
Research & Publications
Biography
News
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
- 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.
- Acylation – A New Means to Control Traffic Through the GolgiErnst 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.
- Labeling Strategies Matter for Super-Resolution Microscopy: A Comparison between HaloTags and SNAP-tagsErdmann 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.
- Seeing the long tail: A novel green fluorescent protein, SiriusGFP, for ultra long timelapse imagingZhong 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 2018, 313: 68-76. PMID: 30578868, PMCID: PMC9431725, DOI: 10.1016/j.jneumeth.2018.12.008.
- S-Palmitoylation Sorts Membrane Cargo for Anterograde Transport in the GolgiErnst 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.
- Assessing photodamage in live-cell STED microscopyKilian 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.
- The Rab-effector protein RABEP2 regulates endosomal trafficking to mediate vascular endothelial growth factor receptor-2 (VEGFR2)-dependent signalingKofler 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 Journal Of Biological Chemistry 2018, 293: 4805-4817. PMID: 29425100, PMCID: PMC5880142, DOI: 10.1074/jbc.m117.812172.
- Leptin Is Produced by Parathyroid Glands and Stimulates Parathyroid Hormone SecretionHoang 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.
- STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live CellsErdmann RS, Toomre D, Schepartz A. STED Imaging of Golgi Dynamics with Cer-SiR: A Two-Component, Photostable, High-Density Lipid Probe for Live Cells 2017, 1663: 65-78. PMID: 28924659, PMCID: PMC6146391, DOI: 10.1007/978-1-4939-7265-4_6.
- Novel ecto-tagged integrins reveal their trafficking in live cellsHuet-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 cisternaeDunlop 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.
- HIDE Probes: A New Toolkit for Visualizing Organelle Dynamics, Longer and at Super-ResolutionThompson 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‐SiRThompson 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 Edition 2017, 56: 10408-10412. PMID: 28679029, PMCID: PMC5576494, DOI: 10.1002/anie.201704783.
- Long time-lapse nanoscopy with spontaneously blinking membrane probesTakakura 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.
- Excess cholesterol inhibits glucose‐stimulated fusion pore dynamics in insulin exocytosisXu 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.
- A novel physiological role for ARF1 in the formation of bidirectional tubules from the GolgiBottanelli 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.
- Differential requirement for N‐ethylmaleimide‐sensitive factor in endosomal trafficking of transferrin receptor from anterograde trafficking of vesicular stomatitis virus glycoprotein GFan 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.
- Erratum: Endothelial exocytosis of angiopoietin-2 resulting from CCM3 deficiency contributes to cerebral cavernous malformationZhou 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: 1502-1502. PMID: 27923033, DOI: 10.1038/nm1216-1502c.
- Endothelial exocytosis of angiopoietin-2 resulting from CCM3 deficiency contributes to cerebral cavernous malformationZhou 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.
- The IN/OUT assay: a new tool to study ciliogenesisKukic 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.
- Ultra-High Resolution 3D Imaging of Whole CellsHuang 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.
- Sphingomyelin is sorted at the trans Golgi network into a distinct class of secretory vesicleDeng 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: 6677-6682. PMID: 27247384, PMCID: PMC4914164, DOI: 10.1073/pnas.1602875113.
- Two-colour live-cell nanoscale imaging of intracellular targetsBottanelli 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.
- Optogenetic activation reveals distinct roles of PIP3 and Akt in adipocyte insulin actionXu 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: 2085-2095. PMID: 27076519, PMCID: PMC4878990, DOI: 10.1242/jcs.174805.
- Staphylococcus aureus recruits Cdc42GAP through recycling endosomes and the exocyst to invade human endothelial cellsRauch 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: 2937-2949. PMID: 27311480, PMCID: PMC5004874, DOI: 10.1242/jcs.186213.
- The periciliary ring in polarized epithelial cells is a hot spot for delivery of the apical protein gp135Stoops 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 Journal Of Cell Biology 2015, 211: 287-294. PMID: 26504168, PMCID: PMC4621837, DOI: 10.1083/jcb.201502045.
- Super‐Resolution Imaging of the Golgi in Live Cells with a Bioorthogonal Ceramide ProbeErdmann 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 Edition 2014, 53: 10242-10246. PMID: 25081303, PMCID: PMC4593319, DOI: 10.1002/anie.201403349.
- 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.
- Reticulon 4 Is Necessary for Endoplasmic Reticulum Tubulation, STIM1-Orai1 Coupling, and Store-operated Calcium EntryJozsef 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 Journal Of Biological Chemistry 2014, 289: 9380-9395. PMID: 24558039, PMCID: PMC3969502, DOI: 10.1074/jbc.m114.548602.
- A Network of Interactions Enables CCM3 and STK24 to Coordinate UNC13D-Driven Vesicle Exocytosis in NeutrophilsZhang 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.
- Video-rate nanoscopy using sCMOS camera–specific single-molecule localization algorithmsHuang 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: 653-658. PMID: 23708387, PMCID: PMC3696415, DOI: 10.1038/nmeth.2488.
- Live-cell imaging of exocyst links its spatiotemporal dynamics to various stages of vesicle fusionRivera-Molina F, Toomre D. Live-cell imaging of exocyst links its spatiotemporal dynamics to various stages of vesicle fusion Journal Of Cell Biology 2013, 201: 673-680. PMID: 23690179, PMCID: PMC3664709, DOI: 10.1083/jcb.201212103.
- The Neuropilin 1 Cytoplasmic Domain Is Required for VEGF-A-Dependent ArteriogenesisLanahan 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: 156-168. PMID: 23639442, PMCID: PMC3774154, DOI: 10.1016/j.devcel.2013.03.019.
- Optogenetic control of phosphoinositide metabolismIdevall-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-e2323. PMID: 22847441, PMCID: PMC3435206, DOI: 10.1073/pnas.1211305109.
- 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 SystemsToomre D. Alignment and Calibration of Total Internal Reflection Fluorescence Microscopy Systems Cold Spring Harbor Protocols 2012, 2012: pdb.prot068668. 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.
- Caveolae, Fenestrae and Transendothelial Channels Retain PV1 on the Surface of Endothelial CellsTkachenko 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.
- The Legionella pneumophila Effector DrrA Is Sufficient to Stimulate SNARE-Dependent Membrane FusionArasaki 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.
- Using light to see and control membrane trafficXu Y, Melia TJ, Toomre DK. Using light to see and control membrane traffic Current Opinion In Chemical Biology 2011, 15: 822-830. PMID: 22079055, DOI: 10.1016/j.cbpa.2011.10.016.
- Splice isoform estrogen receptors as integral transmembrane proteinsKim KH, Toomre D, Bender JR. Splice isoform estrogen receptors as integral transmembrane proteins Molecular Biology Of The Cell 2011, 22: 4415-4423. PMID: 21937726, PMCID: PMC3216666, DOI: 10.1091/mbc.e11-05-0416.
- Dual-mode of insulin action controls GLUT4 vesicle exocytosisXu Y, Rubin BR, Orme CM, Karpikov A, Yu C, Bogan JS, Toomre DK. Dual-mode of insulin action controls GLUT4 vesicle exocytosis Journal Of Cell Biology 2011, 193: 643-653. PMID: 21555461, PMCID: PMC3166865, DOI: 10.1083/jcb.201008135.
- Exocyst function regulated by effector phosphorylationChen 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 regulated by effector phosphorylation Nature Cell Biology 2011, 13: 580-588. PMID: 21516108, PMCID: PMC3904505, DOI: 10.1038/ncb2226.
- 3-D Reconstruction of Microtubules from Multi-Angle Total Internal Reflection Fluorescence Microscopy Using Bayesian FrameworkYang 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 2011, 20: 2248-2259. PMID: 21324778, DOI: 10.1109/tip.2011.2114359.
- An Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF MicroscopyLiang L, Shen H, De Camilli P, Toomre DK, Duncan JS. An Expectation Maximization Based Method for Subcellular Particle Tracking Using Multi-angle TIRF Microscopy 2011, 14: 629-636. PMID: 22003671, PMCID: PMC3648983, DOI: 10.1007/978-3-642-23623-5_79.
- A New Wave of Cellular ImagingToomre 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.
- The inositol 5-phosphatase SHIP2 regulates endocytic clathrin-coated pit dynamicsNakatsu 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 Journal Of Cell Biology 2010, 190: 307-315. PMID: 20679431, PMCID: PMC2922640, DOI: 10.1083/jcb.201005018.
- Deciphering subcellular processes in live imaging datasets via dynamic probabilistic networksLetinic K, Sebastian R, Barthel A, Toomre D. Deciphering subcellular processes in live imaging datasets via dynamic probabilistic networks Bioinformatics 2010, 26: 2029-2036. PMID: 20581401, PMCID: PMC2916721, DOI: 10.1093/bioinformatics/btq331.
- Spatial control of EGF receptor activation by reversible dimerization on living cellsChung 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: 783-787. PMID: 20208517, DOI: 10.1038/nature08827.
- Estimation of 3D Geometry of Microtubules Using Multi-angle Total Internal Reflection Fluorescence MicroscopyYang Q, Karpikov A, Toomre D, Duncan J. Estimation of 3D Geometry of Microtubules Using Multi-angle Total Internal Reflection Fluorescence Microscopy 2010, 13: 538-545. PMID: 20879357, DOI: 10.1007/978-3-642-15745-5_66.
- Exocyst is involved in polarized cell migration and cerebral cortical developmentLetinic 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: 11342-11347. PMID: 19549839, PMCID: PMC2708724, DOI: 10.1073/pnas.0904244106.
- A Phosphoinositide Switch Controls the Maturation and Signaling Properties of APPL EndosomesZoncu 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: 1110-1121. PMID: 19303853, PMCID: PMC2705806, DOI: 10.1016/j.cell.2009.01.032.
- Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random SetsDaz M, Ayala G, Len T, Zoncu R, Toomre D. Analyzing Protein-Protein Spatial-Temporal Dependencies from Image Sequences Using Fuzzy Temporal Random Sets Journal Of Computational Biology 2008, 15: 1221-1236. PMID: 18973437, DOI: 10.1089/cmb.2008.0055.
- Measuring Spatiotemporal Dependencies in Bivariate Temporal Random Sets with Applications to Cell BiologyDiaz E, Sebastian R, Ayala G, Diaz M, 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: 1659-1671. PMID: 18617722, DOI: 10.1109/tpami.2007.70821.
- Both daughter cells traffic and exocytose membrane at the cleavage furrow during mammalian cytokinesisGoss JW, Toomre DK. Both daughter cells traffic and exocytose membrane at the cleavage furrow during mammalian cytokinesis Journal Of Cell Biology 2008, 181: 1047-1054. PMID: 18573914, PMCID: PMC2442215, DOI: 10.1083/jcb.200712137.
- Motion tracking of the outer tips of microtubulesHadjidemetriou 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.
- Repair of injured plasma membrane by rapid Ca2+-dependent endocytosisIdone V, Tam C, Goss JW, Toomre D, Pypaert M, Andrews NW. Repair of injured plasma membrane by rapid Ca2+-dependent endocytosis Journal Of Cell Biology 2008, 180: 905-914. PMID: 18316410, PMCID: PMC2265401, DOI: 10.1083/jcb.200708010.
- Automatic Detection of Large Dense-Core Vesicles in Secretory Cells and Statistical Analysis of Their Intracellular DistributionDíaz 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 2008, 7: 2-11. PMID: 20150664, DOI: 10.1109/tcbb.2008.30.
- Par3 functions in the biogenesis of the primary cilium in polarized epithelial cellsSfakianos 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 Journal Of Cell Biology 2007, 179: 1133-1140. PMID: 18070914, PMCID: PMC2140027, DOI: 10.1083/jcb.200709111.
- Internalization, Intracellular Trafficking, Biodistribution of Monoclonal Antibody 806: A Novel Anti-Epidermal Growth Factor Receptor AntibodyPerera RM, Zoncu R, Johns TG, Pypaert M, Lee FT, Mellman I, Old LJ, Toomre DK, Scott AM. Internalization, Intracellular Trafficking, Biodistribution of Monoclonal Antibody 806: A Novel Anti-Epidermal Growth Factor Receptor Antibody Neoplasia 2007, 9: 1099-1110. PMID: 18084617, PMCID: PMC2134906, DOI: 10.1593/neo.07721.
- The Tyrosine Kinase Activity of c-Src Regulates Actin Dynamics and Organization of Podosomes in OsteoclastsDestaing 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 2007, 19: 394-404. PMID: 17978100, PMCID: PMC2174183, DOI: 10.1091/mbc.e07-03-0227.
- A Role of the Lowe Syndrome Protein OCRL in Early Steps of the Endocytic PathwayErdmann 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: 377-390. PMID: 17765681, PMCID: PMC2025683, DOI: 10.1016/j.devcel.2007.08.004.
- Loss of endocytic clathrin-coated pits upon acute depletion of phosphatidylinositol 4,5-bisphosphateZoncu 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: 3793-3798. PMID: 17360432, PMCID: PMC1805489, DOI: 10.1073/pnas.0611733104.
- Nitric oxide synthase generates nitric oxide locally to regulate compartmentalized protein S-nitrosylation and protein traffickingIwakiri 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: 19777-19782. PMID: 17170139, PMCID: PMC1750883, DOI: 10.1073/pnas.0605907103.
- Two synaptojanin 1 isoforms are recruited to clathrin-coated pits at different stagesPerera 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: 19332-19337. PMID: 17158794, PMCID: PMC1693868, DOI: 10.1073/pnas.0609795104.
- The Legionella pneumophila effector protein DrrA is a Rab1 guanine nucleotide-exchange factorMurata 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: 971-977. PMID: 16906144, DOI: 10.1038/ncb1463.
- Analysis of Spatially and Temporally Overlapping Events with Application to Image SequencesAyala G, Sebastian R, Díaz ME, Díaz E, Zoncu R, Toomre D. Analysis of Spatially and Temporally Overlapping Events with Application to Image Sequences IEEE Transactions On Pattern Analysis And Machine Intelligence 2006, 28: 1707-1712. 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 imagingHua 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 Journal Of Cell Biology 2006, 172: 1035-1044. PMID: 16567501, PMCID: PMC2063761, DOI: 10.1083/jcb.200512012.
- Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial CellsSebastian 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 2006, 3: 17-32. PMID: 17048390, DOI: 10.1109/tcbb.2006.11.
- Lymphocyte transcellular migration occurs through recruitment of endothelial ICAM-1 to caveola- and F-actin-rich domainsMillán 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: 113-123. PMID: 16429128, DOI: 10.1038/ncb1356.
- Analysis of spatial dependencies of endocytic proteins based on temporal random setsSebastian R, Diaz M, Ayala G, Zoncu R, Toomre D. Analysis of spatial dependencies of endocytic proteins based on temporal random sets Annual International Conference Of The IEEE Engineering In Medicine And Biology Society (EMBC) 2006, 2006: 4175-4178. PMID: 17946228, DOI: 10.1109/iembs.2006.260479.
- Spying on IgE receptor signalingToomre D. Spying on IgE receptor signaling Journal Of Cell Biology 2005, 171: 415-417. PMID: 16275748, PMCID: PMC2171246, DOI: 10.1083/jcb.200510105.
- Phosphatidylinositol phosphate kinase type Iγ regulates dynamics of large dense-core vesicle fusionGong LW, Di Paolo G, Diaz E, Cestra G, Diaz ME, Lindau M, De Camilli P, Toomre D. Phosphatidylinositol phosphate kinase type Iγ regulates dynamics of large dense-core vesicle fusion Proceedings Of The National Academy Of Sciences Of The United States Of America 2005, 102: 5204-5209. PMID: 15793002, PMCID: PMC555604, DOI: 10.1073/pnas.0501412102.
- The Abl/Arg substrate ArgBP2/nArgBP2 coordinates the function of multiple regulatory mechanisms converging on the actin cytoskeletonCestra 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: 1731-1736. PMID: 15659545, PMCID: PMC547834, DOI: 10.1073/pnas.0409376102.
- 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) 2005, 8: 761-769. PMID: 16685915, DOI: 10.1007/11566465_94.
- Golgi duplication in Trypanosoma bruceiHe CY, Ho HH, Malsam J, Chalouni C, West CM, Ullu E, Toomre D, Warren G. Golgi duplication in Trypanosoma brucei Journal Of Cell Biology 2004, 165: 313-321. PMID: 15138289, PMCID: PMC2172185, DOI: 10.1083/jcb.200311076.
- Nanometer targeting of microtubules to focal adhesionsKrylyshkina O, Anderson KI, Kaverina I, Upmann I, Manstein DJ, Small JV, Toomre DK. Nanometer targeting of microtubules to focal adhesions Journal Of Cell Biology 2003, 161: 853-859. PMID: 12782685, PMCID: PMC2172972, DOI: 10.1083/jcb.200301102.
- Golgi biogenesis in Toxoplasma gondiiPelletier 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: 548-552. PMID: 12152082, DOI: 10.1038/nature00946.
- Dendritic cell maturation triggers retrograde MHC class II transport from lysosomes to the plasma membraneChow 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: 988-994. PMID: 12198549, DOI: 10.1038/nature01006.
- Selective Delivery of Secretory Cargo in Golgi‐Derived Carriers of Nonepithelial CellsRustom A, Bajohrs M, Kaether C, Keller P, Toomre D, Corbeil D, Gerdes H. Selective Delivery of Secretory Cargo in Golgi‐Derived Carriers of Nonepithelial Cells Traffic 2002, 3: 279-288. PMID: 11929609, DOI: 10.1034/j.1600-0854.2002.030405.x.