Thomas J Deerinck

Thomas J Deerinck

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Thomas J Deerinck

Publications by authors named "Thomas J Deerinck"

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61Publications

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Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells.

J Cell Biol 2019 Feb 14;218(2):433-444. Epub 2018 Dec 14.

Molecular and Cell Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA

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http://dx.doi.org/10.1083/jcb.201809123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6363465PMC
February 2019

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 24;8(2):239-244. Epub 2019 Jan 24.

Synthetic Biology and Bioenergy Group , J. Craig Venter Institute , La Jolla , California 92037 , United States.

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http://dx.doi.org/10.1021/acssynbio.8b00449DOI Listing
February 2019

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 15;505(4):1251-1256. Epub 2018 Oct 15.

Center for iPS Cell Research and Application, Kyoto University, Kyoto, 606-8507, Japan. Electronic address:

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http://dx.doi.org/10.1016/j.bbrc.2018.10.020DOI Listing
November 2018

CDeep3M-Plug-and-Play cloud-based deep learning for image segmentation.

Nat Methods 2018 09 31;15(9):677-680. Epub 2018 Aug 31.

National Center for Microscopy and Imaging Research, School of Medicine, University of California San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1038/s41592-018-0106-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6548193PMC
September 2018

Spines of the porcupine fish: Structure, composition, and mechanical properties.

J Mech Behav Biomed Mater 2017 09 28;73:38-49. Epub 2017 Feb 28.

Materials Science and Engineering Program, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0418, USA; Mechanical and Aerospace Engineering, University of California, San Diego, 9500 Gilman Dr., La Jolla, CA 92093-0411, USA.

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http://dx.doi.org/10.1016/j.jmbbm.2017.02.029DOI Listing
September 2017

Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells.

Nat Protoc 2017 Sep 10;12(9):1792-1816. Epub 2017 Aug 10.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.nature.com/doifinder/10.1038/nprot.2017.065
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http://dx.doi.org/10.1038/nprot.2017.065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851282PMC
September 2017

Activity-dependent trafficking of lysosomes in dendrites and dendritic spines.

J Cell Biol 2017 08 19;216(8):2499-2513. Epub 2017 Jun 19.

Section of Neurobiology, Division of Biological Sciences, University of California, San Diego, La Jolla, CA

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http://dx.doi.org/10.1083/jcb.201704068DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551717PMC
August 2017

ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells.

Science 2017 07;357(6349)

Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1126/science.aag0025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5646685PMC
July 2017

Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells.

Cell Chem Biol 2017 Mar 23;24(3):404-414. Epub 2017 Feb 23.

Departments of Genetics, Biology, and Chemistry, Stanford University, Stanford, CA 94305, USA. Electronic address:

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http://dx.doi.org/10.1016/j.chembiol.2017.02.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5886301PMC
March 2017

Fragility of foot process morphology in kidney podocytes arises from chaotic spatial propagation of cytoskeletal instability.

PLoS Comput Biol 2017 03 16;13(3):e1005433. Epub 2017 Mar 16.

R. D. Berlin Center for Cell Analysis & Modeling, U. Connecticut School of Medicine, Farmington, CT, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1005433DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5373631PMC
March 2017

High resolution three-dimensional reconstruction of fibrotic skeletal muscle extracellular matrix.

J Physiol 2017 02 14;595(4):1159-1171. Epub 2016 Dec 14.

Department of Bioengineering, University of California San Diego, La Jolla, CA, 92093, USA.

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http://dx.doi.org/10.1113/JP273376DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5309386PMC
February 2017

Deceleration of probe beam by stage bias potential improves resolution of serial block-face scanning electron microscopic images.

Adv Struct Chem Imaging 2017 15;2(1):11. Epub 2016 Sep 15.

National Center for Microscopy and Imaging Research, University of California at San Diego, BSB 1000, 9500 Gilman Dr., La Jolla, CA 92093-0608 USA.

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http://ascimaging.springeropen.com/articles/10.1186/s40679-0
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http://dx.doi.org/10.1186/s40679-016-0025-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5025511PMC
September 2016

Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts.

Cell 2016 Aug;166(5):1295-1307.e21

Department of Chemistry, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.07.041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5167540PMC
August 2016

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 21;104:206. Epub 2016 May 21.

Molecular and Cell Biology Laboratory, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.05.005DOI Listing
July 2016

Click-EM for imaging metabolically tagged nonprotein biomolecules.

Nat Chem Biol 2016 06 25;12(6):459-65. Epub 2016 Apr 25.

Department of Pharmacology, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nchembio.2076DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4871776PMC
June 2016

Correlative stochastic optical reconstruction microscopy and electron microscopy.

PLoS One 2015 15;10(4):e0124581. Epub 2015 Apr 15.

Howard Hughes Medical Institute, Cambridge, Massachusetts, United States of America; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America; Center for Brain Science, Harvard University, Cambridge, Massachusetts, United States of America; Department of Physics, Harvard University, Cambridge, Massachusetts, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124581PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4398493PMC
January 2016

Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy.

Methods 2015 Nov 9;90:39-48. Epub 2015 Jun 9.

Molecular and Cell Biology Laboratory, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA; Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2015.06.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4655137PMC
November 2015

Directed evolution of APEX2 for electron microscopy and proximity labeling.

Nat Methods 2015 Jan 24;12(1):51-4. Epub 2014 Nov 24.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.3179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296904PMC
January 2015

Three-dimensional reconstruction of skeletal muscle extracellular matrix ultrastructure.

Microsc Microanal 2014 Dec 2;20(6):1835-40. Epub 2014 Oct 2.

1Department of Bioengineering,University of California San Diego,9500 Gilman Drive,La Jolla,CA,92093-0863,USA.

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http://dx.doi.org/10.1017/S1431927614013300DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267978PMC
December 2014

A workflow for the automatic segmentation of organelles in electron microscopy image stacks.

Front Neuroanat 2014 7;8:126. Epub 2014 Nov 7.

Center for Research in Biological Systems, National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA, USA ; Department of Bioengineering, University of California San Diego, La Jolla, CA, USA ; Department of Neurosciences, University of California San Diego, La Jolla, CA, USA.

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http://journal.frontiersin.org/article/10.3389/fnana.2014.00
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http://dx.doi.org/10.3389/fnana.2014.00126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4224098PMC
November 2014

Construction of a polarized neuron.

J Physiol 2013 Jul 21;591(13):3145-50. Epub 2013 Jan 21.

Center for Neuroscience, West Virginia University School of Medicine, One Medical Center Drive, Morgantown, WV 26506-9303, USA.

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http://doi.wiley.com/10.1113/jphysiol.2012.248542
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http://dx.doi.org/10.1113/jphysiol.2012.248542DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3717217PMC
July 2013

Catastrophic nuclear envelope collapse in cancer cell micronuclei.

Cell 2013 Jul;154(1):47-60

Molecular and Cell Biology Laboratory, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.cell.2013.06.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3749778PMC
July 2013

Loss of acinar cell IKKα triggers spontaneous pancreatitis in mice.

J Clin Invest 2013 May 8;123(5):2231-43. Epub 2013 Apr 8.

Laboratory of Gene Regulation and Signal Transduction, Departments of Pharmacology and Pathology, School of Medicine, UCSD, La Jolla, California 92093-0723, USA.

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http://dx.doi.org/10.1172/JCI64498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3635720PMC
May 2013

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

National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, CA 92093-0608, USA.

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https://linkinghub.elsevier.com/retrieve/pii/B97801241602620
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http://dx.doi.org/10.1016/B978-0-12-416026-2.00008-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3532940PMC
December 2012

Engineered ascorbate peroxidase as a genetically encoded reporter for electron microscopy.

Nat Biotechnol 2012 Nov 21;30(11):1143-8. Epub 2012 Oct 21.

Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3699407PMC
http://dx.doi.org/10.1038/nbt.2375DOI Listing
November 2012

A genetically encoded tag for correlated light and electron microscopy of intact cells, tissues, and organisms.

PLoS Biol 2011 Apr 5;9(4):e1001041. Epub 2011 Apr 5.

Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California, United States of America.

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https://dx.plos.org/10.1371/journal.pbio.1001041
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http://dx.doi.org/10.1371/journal.pbio.1001041DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3071375PMC
April 2011

Investigating synapse formation and function using human pluripotent stem cell-derived neurons.

Proc Natl Acad Sci U S A 2011 Feb 28;108(7):3005-10. Epub 2011 Jan 28.

Neurobiology Section, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.1007753108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041068PMC
February 2011

Labeling tetracysteine-tagged proteins with biarsenical dyes for live cell imaging.

Cold Spring Harb Protoc 2011 Jan 1;2011(1):pdb.prot5547. Epub 2011 Jan 1.

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http://dx.doi.org/10.1101/pdb.prot5547DOI Listing
January 2011

Fluorescence photoconversion of biarsenical-labeled cells for correlated electron microscopy (EM).

Cold Spring Harb Protoc 2011 Jan 1;2011(1):pdb.prot5548. Epub 2011 Jan 1.

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http://dx.doi.org/10.1101/pdb.prot5548DOI Listing
January 2011

Correlated live cell light and electron microscopy using tetracysteine tags and biarsenicals.

Cold Spring Harb Protoc 2011 Jan 1;2011(1):pdb.top94. Epub 2011 Jan 1.

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http://dx.doi.org/10.1101/pdb.top94DOI Listing
January 2011

Direct restriction of virus release and incorporation of the interferon-induced protein BST-2 into HIV-1 particles.

PLoS Pathog 2010 Mar 5;6(3):e1000701. Epub 2010 Mar 5.

Department of Medicine, University of California San Diego, La Jolla, California, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1000701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2832767PMC
March 2010

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. Epub 2009 Dec 28.

Department of Medicine, and National Center for Microscopy and Imaging Research, University of California San Diego, La Jolla, CA 92093-0623, USA.

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http://dx.doi.org/10.1016/j.resp.2009.12.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2821748PMC
February 2010

Quantum dots for tracking dendritic cells and priming an immune response in vitro and in vivo.

PLoS One 2008 Sep 29;3(9):e3290. Epub 2008 Sep 29.

Department of Physiology and Biophysics, University of California Irvine, Irvine, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0003290PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538605PMC
September 2008

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 14;161(3):359-71. Epub 2007 Sep 14.

National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, 1070 Basic Science Building MC 0608, 9500 Gilman Drive, La Jolla, CA 92093-0608, USA.

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http://dx.doi.org/10.1016/j.jsb.2007.09.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2459253PMC
March 2008

Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy.

J Struct Biol 2008 Mar 19;161(3):439-46. Epub 2007 Sep 19.

Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1016/j.jsb.2007.09.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2408891PMC
March 2008

The application of fluorescent quantum dots to confocal, multiphoton, and electron microscopic imaging.

Toxicol Pathol 2008 Jan;36(1):112-6

National Center of Microscopy and Imaging Research (NCMIR), Center for Research on Biological Systems, University of California, San Diego (UCSD) School of Medicine, 1000 BSB, 9500 Gilman Drive, MC0608, La Jolla, CA 92093-0608, USA.

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http://dx.doi.org/10.1177/0192623307310950DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2771444PMC
January 2008

Light and electron microscopic localization of multiple proteins using quantum dots.

Methods Mol Biol 2007 ;374:43-53

Department of Neurosciences, The National Center for Microscopy and Imaging Research, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1385/1-59745-369-2:43DOI Listing
December 2007

Isoform-specific PKA dynamics revealed by dye-triggered aggregation and DAKAP1alpha-mediated localization in living cells.

Chem Biol 2007 Sep;14(9):1031-42

Department of Pharmacology, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1016/j.chembiol.2007.07.017DOI Listing
September 2007

Markers for correlated light and electron microscopy.

Methods Cell Biol 2007 ;79:575-91

National Center for Microscopy and Imaging Research and Center for Research in Biological Systems, University of California, San Diego, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1016/S0091-679X(06)79023-9DOI Listing
April 2007

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 13;103(47):17777-82. Epub 2006 Nov 13.

National Center for Microscopy and Imaging Research, Center for Research on Biological Structure, University of California at San Diego, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1073/pnas.0608509103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1635977PMC
November 2006

Correlated light and electron microscopic imaging of multiple endogenous proteins using Quantum dots.

Nat Methods 2005 Oct;2(10):743-9

Department of Neurosciences, National Center for Microscopy and Imaging Research, and Center for Research in Biological Systems, University of California, San Diego, La Jolla, California, 92093-0608, USA.

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http://www.nature.com/doifinder/10.1038/nmeth791
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http://dx.doi.org/10.1038/nmeth791DOI Listing
October 2005

STIM1 is a Ca2+ sensor that activates CRAC channels and migrates from the Ca2+ store to the plasma membrane.

Nature 2005 Oct;437(7060):902-5

Department of Physiology and Biophysics and Center for Immunology, University of California, Irvine, California 92697, USA.

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http://dx.doi.org/10.1038/nature04147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1618826PMC
October 2005

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

National Center for Microscopy and Imaging Research, Department of Neurosciences and the Center for Research on Biological Systems, University of California, San Diego, CA, USA.

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https://papers.cnl.salk.edu/PDFs/Development%20of%20a%20Mode
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http://link.springer.com/10.1385/NI:3:2:133
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http://dx.doi.org/10.1385/NI:3:2:133DOI Listing
September 2005

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

National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, La Jolla, CA 92093, USA.

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November 2004

Activity-dependent regulation of dendritic synthesis and trafficking of AMPA receptors.

Nat Neurosci 2004 Mar 8;7(3):244-53. Epub 2004 Feb 8.

Nancy Friend Pritzker Laboratory, Department of Psychiatry and Behavioral Sciences, 1201 Welch Road, Stanford University School of Medicine, Palo Alto, California 94304, USA.

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http://dx.doi.org/10.1038/nn1189DOI Listing
March 2004

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

Department of Cell Biology and Oncology, Istituto di Ricerche Farmacologiche Mario Negri, Consorzio Mario Negri Sud, 66030 Santa Maria Imbaro, (Chieti), Italy.

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October 2003

Multicolor and electron microscopic imaging of connexin trafficking.

Science 2002 Apr;296(5567):503-7

National Center for Microscopy and Imaging Research, Department of Neurosciences, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.

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http://dx.doi.org/10.1126/science.1068793DOI Listing
April 2002