Publications Archive
The multidisciplinary work of NCMIR researchers and their collaborators have been published in a variety of journals and presented in local, national, and international forums.
Select a year to view a browsable listing of journal covers, articles, and abstracts.
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2009
Articles
- Bumbarger DJ, Wijeratne S, Carter C, Crum J, Ellisman MH and Baldwin JG. Three-dimensional reconstruction of the amphid sensilla in the microbial feeding nematode, Acrobeles complexus (nematoda: Rhabditida). J Comp Neurol. 2009 Jan 10;512:271-281. PMCID: PMC2750866
- Garcia ML, Rao MV, Fujimoto J, Garcia VB, Shah SB, Crum J, Gotow T, Uchiyama Y, Ellisman M, Calcutt NA, Cleveland DW. Phosphorylation of highly conserved neurofilament medium KSP repeats is not required for myelin-dependent radial axonal growth. J Neurosci. 2009 Feb 4;29(5):1277-84.
- Hayashi T, Martone ME, Yu Z, Thor A, Doi M, Holst MJ, Ellisman MH, Hoshijima M. Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart. J Cell Sci. 2009 Apr 1;122(Pt 7):1005-13.
- Ju WK, Kim KY, Lindsey JD, Angert M, Patel A, Scott RT, Liu Q, Crowston JG, Ellisman MH, Perkins GA and Weinreb RN. Elevated hydrostatic pressure triggers release of OPA1 and cytochrome C, and induces apoptotic cell death in differentiated RGC-5 cells. Mol Vis. 2009 Jan 19;15:120-34. PMCID: PMC2629709
- Perkins G, Bossy-Wetzel E, Ellisman MH. New insights into mitochondrial structure during cell death. Exp Neurol. 2009 Aug;218(2):183-92. PMCID: PMC2712651
- Perkins GA, Sun MG, Frey TG. Chapter 2 Correlated light and electron microscopy/electron tomography of mitochondria in situ. Methods Enzymol. 2009;456:29-52. PMCID: PMC2730195
- Sebba DS, Watson DA, Nolan JP. High throughput single nanoparticle spectroscopy. ACS Nano. 2009 Jun 23;3(6):1477-84. PMCID: PMC2730202
- Serre-Beinier V, Bosco D, Zulianello L, Charollais A, Caille D, Charpantier E, Gauthier BR, Diaferia GR, Giepmans BN, Lupi R, Marchetti P, Deng S, Buhler L, Berney T, Cirulli V, Meda P. Cx36 makes channels coupling human pancreatic beta-cells, and correlates with insulin expression. Hum Mol Genet. 2009 Feb 1;18(3):428-39. PMCID: PMC2638800
- Shawkey MD, Saranathan V, Pálsdóttir H, Crum J, Ellisman MH, Auer M, Prum RO. Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure. J R Soc Interface. 2009 Apr 6;6 Suppl 2:S213-20. PMCID: PMC2706473
- Yamaguchi R, Perkins G. Dynamics of mitochondrial structure during apoptosis and the enigma of Opa1. Biochim Biophys Acta. 2009 Aug;1787(8):963-72.
Oral and Poster Presentations
- Lawrence A, Phan S, and R Singh. Parallel Processing and Large-Field Electron Microscope Tomography. World Congress on Computer Science and Information Engineering (CSIE 2009). Los Angeles, CA, 31 Mar 2009.
- Lawrence, AF. Tutorial on Electron Microscope Tomography. IEEE International Symposium on Biomedical Imaging (ISBI '09). Boston, MA, 28 Jun - 1 Jul 2009.
- Lawrence A, Phan S, Moussavi F. 3D Reconstruction from electron microscope images with TxBR. IEEE International Symposium on Biomedical Imaging (ISBI '09). Boston, MA, 28 Jun - 1 Jul 2009.
- Phan S, Bouwer J, Lanman J, Terada M and AF Lawrence. Non-Linear Bundle Adjustment for Electron Tomography. World Congress on Computer Science and Information Engineering (CSIE 2009). Los Angeles, CA, 31 Mar 2009.
2008
Articles
- Boassa D, Qiu F, Dahl G and Sosinsky G. Trafficking dynamics of glycosylated pannexin 1 proteins. Cell Commun Adhes. 2008 May;15(1):119-32. PMCID: PMC2528835
- Boline J, Lee EF and Toga AW. Digital atlases as a framework for data sharing. Front Neurosci. 2008 Jul;2(1):100-6. PMCID: PMC2570073
- Bossy B, Perkins GA and Bossy-Wetzel E. Clearing the brain’s cobwebs, the role of autophagy in neuroprotection. Curr Neuropharmacology. 2008;6:97-101. PMC2647148
- Buccigrossi R, Ellisman M, Grethe J, Haselgrove C, Kennedy DN, Martone M, Preuss N, Reynolds K, Sullivan M, Turner J and Wagner K. The Neuroimaging Informatics Tools and Resources Clearinghouse (NITRC). AMIA Annu Symp Proc. 2008 Nov 6;1000.
- Bug WJ, Ascoli GA, Grethe JS, Gupta A, Fennema-Notestine C, Laird AR, Larson SD, Rubin D, Shepherd GM, Turner JA and Martone ME. The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience. Neuroinformatics. 2008 Sep; 6(3):175-94. PMCID: PMC2743139
- Campbell PH, Hunt DL, Jones Y, Harwood F, Amiel D, Omens JH and McCulloch AD. Effects of biglycan deficiency on myocardial infarct structure and mechanics. Mol Cell Biomech. 2008 Mar;5(1):27-35. PMCID: PMC2679639
- Capani F, Saraceno E, Boti VR, Aon-Bertolino L, Fernández JC, Gato F, Krause MS, Giraldez L, Ellisman MH, Coirini H. A tridimensional view of the organization of actin filaments in the central nervous system by use of fluorescent photooxidation. Biocell. 2008 Apr;32(1):1-8.
- Davalos D, Lee JK, Smith WB, Brinkman B, Ellisman MH, Zheng B and Akassoglou K. Stable in vivo imaging of densely populated glia, axons and blood vessels in the mouse spinal cord using two-photon microscopy. J Neurosci Methods. 2008 Mar 30;169(1):1-7. PMCID: PMC2647134
- Deerinck TJ. The application of fluorescent quantum dots to confocal, multiphoton, and electron microscopic imaging. Toxicol Pathol. 2008;36(1):112-116.
- Gardner D, Akil H, Ascoli GA, Bowden DM, Bug W, Donohue DE, Goldberg DH, Grafstein B, Grethe JS, Gupta A, Halavi M, Kennedy DN, Marenco L, Martone ME, Miller PL, Muller HM, Robert A, Shepherd GM, Sternberg PW, Van Essen DC and Williams RW. The Neuroscience Information Framework: A Data and Knowledge Environment for Neuroscience. Neuroinformatics. 2008 Sep;6(3):149-60. PMCID: PMC2661130
- Garduno E, Wong-Barnum M, Volkmann N and Ellisman MH. Segmentation of electron tomographic data sets using fuzzy set theory principles. J Struct Biol. 2008 Jun;162(3):368-79. PMCID: PMC2494597
- Jin L, Milazzo AC, Kleinfelder S, Li S, Leblanc P, Duttweiler F, Bouwer JC, Peltier ST, Ellisman MH and Xuong NH. Applications of direct detection device in transmission electron microscopy. J Struct Biol. 2008 Mar;161(3):352-8. PMCID: PMC2359769
- Ju WK, Kim KY, Angert M, Duong-Polk KX, Lindsey JD, Ellisman MH and Weinreb RN. Memantine blocks mitochondrial OPA1 and cytochrome c release, and subsequent apoptotic cell death in glaucomatous retina. Invest Ophthalmol Vis Sci. 2008 Oct 20;50(2):707-16. PMCID: PMC2678967
- Ju WK, Kim KY, Lindsey JD, Angert M, Duong-Polk KX, Scott RT, Kim JJ, Kukhmazov I, Ellisman MH, Perkins GA and Weinreb RN. Intraocular Pressure Elevation Induces Mitochondrial Fission and Triggers OPA1 Release in Glaucomatous Optic Nerve. Invest Ophthalmol Vis Sci. 2008 Nov;49(11):4903-11. PMCID: PMC2688012
- Knott AB, Perkins G, Schwarzenbacher R and Bossy-Wetzel E. Mitochondrial fragmentation in neurodegeneration. Nat Rev Neurosci. 2008 Jul;9(7):505-518. PMC2711514
- Kumar VS, Rutt B, Kurc T, Catalyurek UV, Pan TC, Chow S, Lamont S, Martone M and Saltz JH. Large-scale biomedical image analysis in grid environments. IEEE transactions on information technology in biomedicine. 2008 Mar;12(2):154-61.
- Lanman J, Crum J, Deerinck TJ, Gaietta GM, Schneemann A, Sosinsky GE, Ellisman MH and Johnson JE. Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy. J Struct Biol. 2008 Mar;161(3):439-446. PMCID: PMC2408891
- Lichtenstein A, Gaietta GM, Deerinck TJ, Crum J, Sosinsky GE, Beyer EC and 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. PMCID: PMC2695785
- Lopreore CL, Bartol TM, Coggan JS, Keller DX, Sosinsky GE, Ellisman MH and Sejnowski TJ. Computational modeling of 3D electrodiffusion in biological systems: Application to the node of Ranvier. Biophys J. 2008 Sep 15;95(6):2624-35. PMCID: PMC2527256
- Marenco L, Ascoli GA, Martone ME, Shepherd GM and Miller PL. The NIF LinkOut Broker: A Web Resource to Facilitate Federated Data Integration using NCBI Identifiers. Neuroinformatics. 2008 Sep;6(3):219-27. PMCID: PMC2704600
- Marenco L, Li Y, Martone ME, Sternberg PW, Shepherd GM and Miller PL. Issues in the Design of a Pilot Concept-Based Query Interface for the Neuroinformatics Information Framework. Neuroinformatics. 2008 Sep;6(3):229-39. PMCID: PMC2664632
- Marko M, Ellisman M, Medalia O. The 4th international conference on electron tomography. J Struct Biol. 2008 Mar;161(3):219. PMCID: PMC2289908
- Martone ME, Tran J, Wong WW, Sargis J, Fong L, Larson S, Lamont SP, Gupta A and Ellisman MH. The Cell Centered Database project: An update on building community resources for managing and sharing 3D imaging data. J Struct Biol. 2008 Mar;161(3):220-31. PMCID: PMC2367257
- Miller R, Cirulli V, Diaferia GR, Ninniri S, Hardiman G, Torbett BE, Benezra R and Crisa L. Switching-on survival and repair response programs in islet transplants by bone marrow-derived vasculogenic cells. Diabetes. 2008 Sep;57(9):2402-12. PMCID:PMC2518491
- Mulligan MK, Ponomarev I, Boehm SL 2nd, Owen JA, Levin PS, Berman AE, Blednov YA, Crabbe JC, Williams RW, Miles MF, Bergeson SE. Alcohol trait and transcriptional genomic analysis of C57BL/6 substrains. Genes Brain Behav. 2008 Aug;7(6):677-89.
- Oshima A, Tani K, Hiroaki Y, Fujiyoshi Y, Sosinsky GE. Projection structure of a N-terminal deletion mutant of connexin 26 channel with decreased central pore density. Cell Commun Adhes. 2008 May;15(1):85-93. PMCID: PMC2527467
- Perkins GA, Brown JM, Scott RT, Tjong J, Poquiz PH, Kolson DR, Ellisman MH, Spirou GA. Mitochondria in a central nerve terminal are positioned by a cytoskeletal scaffold and organized for high rate metabolism. J. Neurosci. 2008.
- Perkins GA, Sosinsky GE, Ghassemzadeh S, Perez A, Jones Y and Ellisman MH. Electron tomographic analysis of cytoskeletal cross-bridges in the paranodal region of the node of Ranvier in peripheral nerves. J Struct Biol. 2008 Mar;161(3):469-480. PMCID: PMC2346545
- Ragsdale EJ, Crum J, Ellisman MH and Baldwin JG. Three-dimensional reconstruction of the stomatostylet and anterior epidermis in the nematode Aphelenchus avenae (Nematoda: Aphelenchidae) with implications for the evolution of plant parasitism. J Morphol. 2008 Oct;269(10):1181-96. PMCID: PMC2730191
- Saini V, Martyshkin DV, Mirov SB, Perez A, Perkins G, Ellisman MH, Towner VD, Wu H, Pereboeva L, Borovjagin A, Curiel DT and Everts M. An Adenoviral Platform for Selective Self-Assembly and Targeted Delivery of Nanoparticles. Small. 2008 Feb;4(2):262-9.
- Sen D, Deerinck TJ, Ellisman MH, Parker I and 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. PMCID: PMC2538605
- Sosinsky GE, Crum J, Jones YZ, Lanman J, Smarr B, Terada M, Martone ME, Deerinck TJ, Johnson JE and 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. PMCID: PMC2459253
- Yamaguchi R, Lartigue L, Perkins G, Scott RT, Dixit A, Kushnareva Y, Kuwana T, Ellisman MH and Newmeyer DD. Opa1-mediated cristae opening is Bax/Bak and BH3 dependent, required for apoptosis, and independent of Bak oligomerization. Mol Cell. 2008 Aug 22;31(4):557-69. PMCID: PMC2636708
- Yang RJ, Mozhui K, Karlsson RM, Cameron HA, Williams RW, Holmes A. Variation in mouse basolateral amygdala volume is associated with differences in stress reactivity and fear learning. Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology. 2008 Oct;33(11):2595-604.
- Yu Z, Holst JJ, Hayashi T, Bajaj CL, Ellisman MH, McCammon JA and Hoshijima M (in press) Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: Bridging the gap between microscopic imaging and mathematical simulation. J Struct Biol. 2008 Dec;164(3):304-13.
- Zhang J, Bang ML, Gokhin DS, Lu Y, Cui L, Li X, Gu Y, Dalton ND, Scimia MC, Peterson KL, Lieber RL, Chen J. Syncoilin is required for generating maximum isometric stress in skeletal muscle but dispensable for muscle cytoarchitecture. Am J Physiol Cell Physiol. 2008 May;294(5):C1175-82. PMCID: PMC2749034
Books
- Olson, Judith S, Mark Ellisman, Mark James, Jeffrey S. Grethe and Mary Puetz. The Biomedical Informatics Research Network, in Scientific Collaboration on the Internet (Gary M. Olson, Ann Zimmerman and Nathan Bos eds.) Boston, MA: MIT Press, 2008.
- Sosinky G, Gaietta G, Giepmans B. Gap junction morphology and dynamics in situ. In: Harris A, Locke D, editors. Connexins: A Guide. Totowa, NJ: Humana Press. 2008: 241-262.
Oral and Poster Presentations
- Ambrosi C, Boassa D, Smock AE, Pranskevich JN and GE Sosinsky. Isolation of Pannexin1 and Pannexin2 channels reveals structural similarity to gap junction hemichannels. Biophysical Society Annual Meeting. Long Beach, CA, 2-6 Feb 2008.
- Astakhov V, Grethe J, Gupta A, Martone M, Sanders B, Ross E, Little DR, Bug WJ, Xufei, Condit C and Ellisman MH. Semantic architecture for data integration and discovery within the biomedical informatics research network. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain, Stockholm, 7-9 Sep 2008. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.115
- Bouwer JC. Electron Tomography Offers a New Frontier in Applied Mathematics. Society for Industrial and Applied Mathematics, Imaging Science Conference, 7-9 Jul 2008.
- Bouwer JC and MH Ellisman. Advances in Electron Microscope Instrumentation and Exploration of Biological Structures. SIAM Natl. Meeting, San Diego, CA, Jul 11, 2008.
- Bouwer JC, Molina T, Shone T, Khodjasaryan K, Hakozaki H, Hakozaki Y, Jin L, Milazzo A, Peltier S, Xuong NH and Ellisman MH. An 8k x 8k lens-coupled detector for wide-field, high-resolution transmission electron microscopy (TEM). Microscopy and Microanalysis 2008 Meeting. 3-7 Aug 2008.
- Bug WJ, Ascoli GA, Grethe JS, Gupta A, Lamont S, Larson S, Shepherd GM, Martone ME. The NIFSTD vocabulary: empowering concept-driven queries against diverse, online neuroscience resources. Society for Neuroscience. Washington, D.C., 17 Nov 2008.
- Ellisman MH. Integrating neuroscience knowledge: brain research in the digital age. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain, Stockholm, 7-9 Sep 2008. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.146.
- Fox DA, Perkins GA, Johnson JE, Scott RT, Poquiz PH, Kim J and Ellisman MH. Differential Susceptibility of Cone Photoreceptor Synaptic and Non-Synaptic Mitochondria to Postnatal Lead Exposure and Protection by Bcl-xL. ARVO Meeting. Fort Lauderdale, FL, May 2008.
- Gaietta GM, Prendergast S, Jones Y, Obayashi J, Deerinck TJ, Bowman G, Yeh YC, Shapiro L, McAdams H and MH Ellisman. Development of methods for correlated light and electron microscopic analysis of protein complexes: applications to Caulobacter crescentus. Joint Genomics: GTL Awardee Workshop VI and Metabolic Engineering 2008 and USDA-DOE Plant Feedstock Genomics for Bioenergy Awardee Workshop. Bethesda, MD., 10-13 Feb 2008.
- Gardner D, Goldberg DH, Grafstein B, Robert A, Gardner EP. BrainML08: Investigator-derived semantics of a data-description language for neuroinformatics. Society for Neuroscience. Washington, D.C., 17 Nov 2008.
- Gupta, Bug W, Qian X, Condit C, Grethe JS, Astakhov V, Sanders B, Marenco L, Miller PL, Shepherd GM, Rangarajan A, Mueller HM, Sternberg PW, Lamont S, Larson S, Ascoli G, Polavaram S, ME Martone. Finding neuroscience information from heterogeneous information sources with NIF (Neuroscience Information Framework). Society for Neuroscience. Washington, D.C., 17 Nov 2008.
- Halavi M, Hamilton KA, Polavaram S, Donohue DE, Ascoli GA. Dense coverage of digitally reconstructed dendrites and axons in NeuroMorpho.Org through extensive literature mining. Society for Neuroscience. Washington, D.C., 17 Nov 2008.
- Jin L, Milazzo AC, Kleinfelder S, Li S, Leblanc P, Duttweiler F, Bouwer J, Peltier SP, Ellisman MH and Xuong NH. Characterization of the Direct Detection Detector for Electron Microscopy. Microscopy & Microanalysis 2008 Meeting. Albuquerque, New Mexico, 4 Aug 2008.
- Larson S and Martone M. A spatial framework for multi-scale computational neuroanatomy. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain, Stockholm, 7-9 Sep 2008. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.134
- Lawrence AF. Mathematics of Electron Microscope Tomography. SIAM Natl. Meeting, San Diego, CA, 11 Jul 2008.
- Lawrence AF and S Phan. Generalized Radon Transforms in Electron Microscope Tomography. SIAM Natl. Meeting, San Diego, CA, 11 July 2008.
- Lawrence, AF. Electron Microscope Tomography, Three Dimensional Reconstruction and Data Analysis, Minisymposium on Electron Microscope Tomography. SIAM Annual Meeting (SIAM AN08). San Diego, CA, 2008.
- Lawrence, AF. Tomography Day 2008. Jacobs School of Engineering, UC San Diego, CA, 10 Jul 2008.
- Martone M, Gupta A, Bug W, Xufei , Condit C, Marenco L and Miller P. The Neuroscience Information Framework (NIF): accessing diverse neuroscience resources through a single interface. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain, Stockholm, 7-9 Sep 2008. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.124.
- Perkins GA, Ma Y, Mackey M, Taylor SS and Ellisman MH. D-AKAP1 Association with Mitochondria and Structural Alterations Upon Overexpression. New Frontiers in Mitochondrial Science. Janelia Farm, VA, Mar 2008.
- Petrilli Guinart A, Liot G, Bossy B, Lubitz S, Knott AB, Poquiz PH, Tjong J, Pouladi M, Ghassemzadeh S, Hayden M, Masliah E, Ellisman MH, Rouiller I, Perkins GA and Bossy-Wetzel E. Mitochondrial Fission and Fusion Imbalance in Huntington’s Disease. The Milton Wexler Celebration of Life Symposium. Cambridge, MA, Aug 2008.
- Polavaram S, Halavi M, Donohue DE, Ascoli GA. NeuroMorpho.Org implementation of digital neuroanatomy: public distribution of 3D reconstructions and deep registration with the Neuroscience Information Framework. Society for Neuroscience. Washington, D.C., 17 Nov 2008.
- Ruiz M, Jones N, Grethe JS. Simplifying the Utilization of Grid Computation using Grid Wizard Enterprise. MICCAI Grid Workshop Proceedings 13-22. New York City, NY, 6 Sep 2008.
- Saini V, Martyshkin DV, Mirov SB, Towner VD, Wu H, Pereboeva L, Borovjagin A, Perkins G, Ellisman MH, Curiel DT and Everts M. Adenovirus as a platform for selective assembly and targeted delivery of gold nanoparticles to tumor cells. American Association for Cancer Research. San Diego, CA, Apr 2008.
- Saini V, Martyshkin DV, Mirov SB, Towner VD, Wu H, Pereboeva L, Perkins G, Ellisman MH, Curiel DT and Everts M. Adenovirus as a platform for selective assembly and targeted delivery of gold nanoparticles to tumor cells. Trainee Research Symposium. Birmingham, AL, Mar 2008.
- Sosinsky GE, Lanman J, Crum J, Jones Y, Terada M, Perkins GA, Martone ME, Deerinck T, Johnson JE and Ellisman MH. High pressure cryo-fixation for electron microscopy. High Pressure Bioscience and Biotechnology Conference. Scripps Institute of Oceanography, CA, Sep 2008.
- Spirou GA, Perkins G and Ellisman MH. Roles of Mitochondria in Synapse Formation and Dysfunction. Winter Conference on Brain Research. Snowbird, UT, Jan 2008.
- Yamaguchi R, Lartigue L, Perkins G, Scott RT, Dixit A, Ellisman MH and Newmeyer DD. Opa1 Regulates Crista Junction Sizes and Cytochrome c Accessibility. 3rd International Mitochondria Minisymposium. Bethesda, MD, Jan 2008.
- Zaslavsky I, Memon A and Martone M. Spatial registration, visualization and annotation of mouse brain images at different scales. 1st INCF Congress of Neuroinformatics: Databasing and Modeling the Brain, Stockholm, 7-9 Sep 2008. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.128




