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Mouse BIRN Publications

Mouse BIRN

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Mouse BIRN Peer Reviewed Articles and book chapters

2008
  1. Bug W, Gustafson C, Shahar A, Gefen S, Fan Y, Bertrand L and Nissanov J (2008). Brain spatial normalization: indexing neuroanatomical databases. Neuroinformatics. C. J. Crasto, Humana Press. 401.
  2. Driehuys B, Nouls J, Badea A, Bucholz E, Ghaghada K, Petiet A and Hedlund LW (2008). Small animal imaging with magnetic resonance microscopy. Ilar J 49(1): 35-53.
  3. MacKenzie-Graham A, Boline J and Toga A (2008). Brain Atlases and Neuroanatomic Imaging. Neuroinformatics. C. J. Crasto, Humana Press. 401.
  4. Marenco L, Nadkarni P, Martone ME and Gupta A (2008). Interoperability across Neuroscience Databases. Neuroinformatics. C. J. Crasto, Humana Press. 401.
  5. Rosen GD, Chesler EJ, Manly KF and Williams RW (2008). An Informatics Approach to Systems Neurogenetics. Neuroinformatics. C. J. Crasto, Humana Press. 401.

2007

  1. Ali Sharief A, Badea A, Dale AM and Johnson GA (2007). Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy. Neuroimage 39: 136-45.
  2. Badea A, Ali-Sharief AA and Johnson GA (2007). Morphometric analysis of the C57BL/6J mouse brain. Neuroimage 37(3): 683-93.
  3. Badea A, Nicholls PJ, Johnson GA and Wetsel WC (2007). Neuroanatomical phenotypes in the reeler mouse. Neuroimage 34(4): 1363-74.
  4. Bao L, Peirce JL, Zhou M, Li H, Goldowitz D, Williams RW, Lu L and Cui Y (2007). An integrative genomics strategy for systematic characterization of genetic loci modulating phenotypes. Hum Mol Genet 16(11): 1381-90.
  5. Bearer EL, Falzone TL, Zhang X, Biris O, Rasin A and Jacobs RE (2007). Role of neuronal activity and kinesin on tract tracing by manganese-enhanced MRI (MEMRI). Neuroimage 37(Suplement 1): S37-S46.
  6. Bearer EL, Zhang X and Jacobs RE (2007). Live imaging of neuronal connections by magnetic resonance: Robust transport in the hippocampal-septal memory circuit in a mouse model of Down syndrome. Neuroimage 37(1): 230-42.
  7. Boline J, Hawrylycz M and Williams RW (2007). Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems. Available from Nature Precedings .
  8. Braude I, Marker J, Museth K, Nissanov J and Breen D (2007). Contour-based surface reconstruction using MPU implicit models. Graphical Models 69(2): 139-157.
  9. Chin MH, Geng AB, Khan AH, Qian WJ, Petyuk VA, Boline J, Levy S, Toga AW, Smith RD, Leahy RM and Smith DJ (2007). A genome-scale map of expression for a mouse brain section obtained using voxelation. Physiol Genomics 30(3): 313-21.
  10. Dong H, Martin MV, Colvin J, Ali Z, Wang L, Lu L, Williams RW, Rosen GD, Csernansky JG and Cheverud JM (2007). Quantitative trait loci linked to thalamus and cortex gray matter volumes in BXD recombinant inbred mice. Heredity 99(1): 62-9.
  11. Gustafson C, Bug WJ and Nissanov J (2007). NeuroTerrain – a client-server system for browsing 3 D biomedical image data sets. BMC Bioinformatics 8(1): 40-55.
  12. Johnson GA, Ali-Sharief A, Badea A, Brandenburg J, Cofer G, Fubara B, Gewalt S, Hedlund LW and Upchurch L (2007). High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. Neuroimage 37(1): 82-9.
  13. Larson SD, Fong LL, Gupta A, Condit C, Bug WJ and Martone ME (2007) A formal ontology of subcellular neuroanatomy. Frontiers in Neuroinformatics 1:3 DOI: 10.3389/neuro.11/003.2007
  14. Lee EF, Boline J and Toga AW (2007) A high-resolution anatomical framework of the neonatal mouse brain for managing gene expression data. Frontiers in Neuroinformatics 1:6 DOI: 10.3389/neuro.11/006.2007
  15. Martone ME, Sargis J, Tran J, Wong WW, Jiles H, Mangir C and McIntosh? JR (2007). Database Resources for Cellular Electron Microscopy. Methods in Cell Biology, Academic Press. Volume 79: 799-822.
  16. Mozhui K, Hamre KM, Holmes A, Lu L and Williams RW (2007). Genetic and structural analysis of the basolateral amygdala complex in BXD recombinant inbred mice. Behav Genet 37(1): 223-43.
  17. Ruffins SW, Martin M, Keough L, Truong S, Fraser SE, Jacobs RE and Lansford R (2007). Digital Three-Dimensional Atlas of Quail Development Using High-Resolution MRI. TheScientificWorldJOURNAL? 7: 592-604.
  18. Ruttenberg A, Clark T, Bug W, Samwald M, Bodenreider O, Chen H, Doherty D, Forsberg K, Gao Y, Kashyap V, Kinoshita J, Luciano J, Marshall MS, Ogbuji C, Rees J, Stephens S, Wong GT, Wu E, Zaccagnini D, Hongsermeier T, Neumann E, Herman I and Cheung KH (2007). Advancing translational research with the Semantic Web. BMC Bioinformatics 8 Suppl 3: S2.

2006

  1. Ali-Sharief AA and Johnson GA (2006). Enhanced T2 contrast for MR histology of the mouse brain. Magnetic Resonance in Medicine 56(4): 717-725.
  2. Kempermann G, Chesler EJ, Lu L, Williams RW and Gage FH (2006). Natural variation and genetic covariance in adult hippocampal neurogenesis. Proceedings of the National Academy of Sciences 103(3): 780-785.
  3. Lan H, Chen M, Flowers JB, Yandell BS, Stapleton DS, Mata CM, Mui ETK, Flowers MT, Schueler KL, Manly KF, Williams RW, Kendziorski C and Attie AD (2006). Combined expression trait correlations and expression quantitative trait locus mapping. PLoS? Genetics, 2(1):0051-0061.
  4. Li H, Chen H, Bao L, Manly KF, Chesler EJ, Lu L, Wang J, Zhou M, Williams RW, Cui Y (2006). Integrative genetic analysis of transcription modules: towards filling the gap between genetic loci and inherited traits. Hum Mol Genet. Feb 1;15(3):481-92.
  5. MacKenzie-Graham A, Tinsley MR, Shah KP, Aguilar C, Strickland LV, Boline J, Martin M, Morales L, Shattuck DW, Jacobs RE, Voskuhl RR and Toga AW (2006). Cerebellar cortical atrophy in experimental autoimmune encephalomyelitis. Neuroimage 32(3): 1016-23.
  6. Martin MV, Dong H, Vallera D, Lee D, Lu L, Williams RW, Rosen GD, Cheverud JM and Csernansky JG (2006). Independent quantitative trait loci influence ventral and dorsal hippocampal volume in recombinant inbred strains of mice. Genes Brain Behav 5(8): 614-23.
  7. Price DL, Chow SK, MacLean? NAB, Hakozaki H, Peltier S, Martone ME and Ellisman MH (2006). High-resolution large-scale mosaic imaging using multiphoton microscopy to characterize transgenic mouse models of human neurological disorders. NeuroInformatics? 4(1): 65-80.
  8. Williams RW (2006). Animal models in biomedical research: ethics, challenges, and opportunities. Principles of molecular medicine. M. Runge and C. Patterson. Totowa, New Jersey, Humana Press: 53-60.
  9. Williams RW (2006). Expression genetics and the phenotype revolution. Mammalian Genome, 17:496-502.
  10. Williams RW (2006). Genomics and dyslexia: Bridging the gap. The Dyslexic Brain: New Pathways in Neuroscience Discovery, G. D. Rosen, ed. Lawrence Erlbaum Associates: 167-190.

2005

  1. Ali AA, Dale AM, Badea A and Johnson GA (2005). Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. Neuroimage 27(2): 425-35.
  2. Bug W (2005). The impact of the NIH public access policy on literature informatics: What role can the neuroinformaticists play? Neuroinformatics 3(2): 81-91.
  3. Cyr M, Caron MG, Johnson GA and Laakso A (2005). Magnetic resonance imaging at microscopic resolution reveals subtle morphological changes in a mouse model of dopaminergic hyperfunction. Neuroimage 26(1): 83-90.
  4. Lee EF, Jacobs RE, Dinov I, Leow A and Toga AW (2005). Standard atlas space for C57BL/6J neonatal mouse brain. Anat Embryol (Berl) 210(4): 245-63.
  5. Li CX, Wei X, Lu L, Peirce JL, Williams RW, Waters RS (2005). Genetic analysis of barrel field size in the first somatosensory area (SI) in inbred and recombinant inbred strains of mice. Somat Motor Res 22:141-150.

2004

  1. Martone ME, Gupta A and Ellisman MH (2004). E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains. Nat Neurosci 7(5): 467-72.

2003

  1. Gupta A, Ludascher B, Grethe JS and Martone ME (2003). Towards a formalization of disease-specific ontologies for neuroinformatics. Neural Networks 16(9): 1277-92.
  2. Martone ME, Zhang S, Gupta A, Qian X, He H, Price DL, Wong M, Santini S, Ellisman MH (2003). The Cell Centered Database: A Database for Multiscale Structural and Protein Localization Data from Light and Electron Microscopy. Neuroinformatics, 1(4):379-95.

Mouse BIRN Abstracts

2007
  1. Badea A, Williams RW, Gustafson C, Nissanov J, and Johnson GA (2007). Phenotypic differences in a set of BXD recombinant inbred mice. Society for Neuroscience, Abstract #100.15
  2. Boline JK, Zaslavsky I, Bug WJ, Williams RW, Martone ME, Anderson S, Wong W, Yuan H, Memon A, Ng Q, Grethe JS, Sforza DM, MacKenzie-Graham A, Nissanov J, Gustafson C, Toga AW (2007). Accessing a sharing infrastructure with the Mouse BIRN atlasing toolkit (MBAT). Society for Neuroscience, Abstract #100.12
  3. Bug WJ, Wong W, , Gustafson C, Johnson GA, Martone ME, Price D, Rosen G, Zaslavsky I, and Nissanov J (2007). Brain atlasing tool interoperation: neuroterrain-smart atlas synergistic visualization and analysis environment, 3rd International IEEE EMBS Conference on Neural Engineering, May 2-5, Kohala Coast, Hawaii.
  4. Bug WJ, Wong W, Badea A, Brandenburg J, Gustafson C, MacKenzie-Graham A, Memon A, Price D, Rosen G, Yuan H, Zaslavsky I, Boline J, Johnson GA, Martone ME, Nissanov J, Toga AW, and Williams RW (2007). The BIRN Atlasing System Interoperability Service: an interface for exchange of registration coordinates, segmentation geometries, and registered images amongst neuroanatomical atlasing systems. Society for Neuroscience, Abstract #100.13
  5. Fong, L.L., Larson, S.D., Gupta, A., Condit, C., Bug, W.J., Chen, L., West, R., Lamont, S., Terada, M., Martone, M.E. (2007). An Ontology-Driven Knowledge Environment for Subcellular Neuroanatomy. CEUR Workshop Proceedings 258, ISNN 1613-0073.
  6. Gupta A, Astakhov V, Boline J, Bug WJ, Fennema-Notestine C, Grethe JS, Kennedy DN, Martone ME, Rubin DL, Sanders B, Turner JA (2007). Data Federation in the Biomedical Informatics Research Network: Tools for semantic annotation and query of distributed multiscale brain data. Society for Neuroscience, Abstract #100.16
  7. Larson, S.D. and Martone, M.E. (2007). Rule-based reasoning with a multi-scale neuroanatomical ontology. CEUR Workshop Proceedings 258, ISSN 1613-0073.
  8. Lee EF, Boline J, Yuan H, and Toga AW (2007). A digital atlas as a framework for data management and cross-data comparison. Society for Neuroscience, Abstract #100.11
  9. MacKenzie-Graham A, Aguilar C, Strickland LV, Morales L, Fubara B, Martin M, Jacobs RE, Johnson GA, Toga AW, Voskuhl RR, Tiwari-Woodruff S (2007) Purkinje Cell death underlies Grey Matter Atrophy in Experimental Autoimmune Encephalomyelitis, American Academy of Neurology, Abstract
  10. MacKenzie-Graham A, Aguilar C, Vo KT, Strickland LV, Morales L, Fubara B, Martin M, Jacobs RE, Johnson GA, Toga AW, Voskuhl RR, Tiwari-Woodruff SK (2007) Purkinje Cell Death Underlies Cerebellar Atrophy in Experimental Autoimmune Encephalomyelitis. Neurology 68 (12, Suppl. 1) : A340
  11. MacKenzie-Graham A, Tiwari-Woodruff S, Aguilar C, Vo KT, Strickland LV, Morales L, Fubara B, Martin M, Jacobs RE, Johnson GA, Voskuhl RR, and Toga AW (2007). Purkinje cell death underlies cerebellar atrophy in experimental autoimmune encephalomyelitis. Society for Neuroscience, Abstract # 901.8
  12. Martone ME, Wong WW, Tran J, Sargis J, Fong L, Larson S, Terada M, Obyashi J, Gupta A, and Ellisman MH (2007). The Cell Centered Database: An on-line resource for managing, sharing and mining light and electron microscopic data. Society for Neuroscience, Abstract #101.7
  13. Price, D. L., Rockenstein, E., Phung, V., Masliah, E., Ellisman, M. H. mGluR5 antagonism reverses motor deficits in a transgenic mouse model of Parkinsonism Alzheimer’s disease/Parkinson’s disease meeting, Salzburg, Austria March 2007

2006

  1. Badea A, Nicholls PJ, Wetsel WC, Johnson GA, (2006) Neuroanatomical Phenotypes in the Reeler Mouse Society for Neuroscience, Abstract #763.2
  2. Boline JK, MacKenzie-Graham A, Shattuck D, Yuan H, Anderson S, Sforza DM, Wang J, Williams RW, Wong W, Martone ME, Zaslavsky I, Toga AW (2006) A Digital Atlas and Neuroinformatics Framework for Query and Display of Disparate Data. Society for Neuroscience, Abstract #100.12
  3. Bug WJ, Gupta A, Gustafson C, Martone ME, Nissanov J, Wong WW, Zaslavsky I (2006) Integrating Brain Atlas Tools for Broad-field Morphometric Analysis and Semantic Data Integration. Society for Neuroscience, Abstract #490.10
  4. Gupta A, Bean C, Bug W, Fennema-Notestine C, Martone ME, Turner JA, Grethe JS (2006) Creating a Community-Based Knowledge Management Framework for Integrating Neuroscience Data Via Ontologies. Society for Neuroscience, Abstract #100.7
  5. MacKenzie-Graham A, Tiwari-Woodruff S, Strickland LV, Aguilar C, Peterson RS, Fubara B, Johnson GA, Toga AW, Voskuhl RR (2006) The neuropathology underlying gray matter atrophy in autoimmune demyelinating disease. Society for Neuroscience, Abstract #474.4
  6. Price DL, Rockenstein E, MacLean? NAB, Phung V, Masliah E, Ellisman MH (2006) Altered dopamine receptor immunoreactivity in CNS of transgenic mice overexpressing alpha-synuclein. ICAD, Abstract, Madrid, Spain July 16
  7. Price DL, Rockenstein E, Phung V, MacLean? NAB, Masliah E, Ellisman MH (2006) A Parkinsonian mouse model overexpressing alpha-synuclein: assessment of changes in behavior and glutamate and dopamine receptor immunoreactivity. Soc. Neuroscience, Abstract #75.20.
  8. Sforza DM, Hartenstein P, Lacan G, Melega WP, Toga AW (2006) Mapping of multiple brain region gene expression in a mouse MPTP model of Parkinson’s disease. Society for Neuroscience, Abstract #755.1
  9. Turner JA, Fennema-Notestine C, Martone ME, Laird AR, Grethe JS, Bug W, Gupta A, Bean C (2006) You say potato, I say potahto: ontological engineering applied within the Biomedial Informatics Research Network. Society for Neuroscience, Abstract #100.6

2005

  1. Martone ME, Chen L, Sargis J, Tran J, Grethe J & Gupta A (2005) Development of an ontology for the subcellular anatomy of the nervous system. Soc. Neuroscience, Abstract, #510.10.
  2. Price DL, Rockenstein E, MacLean? NAB, Martone ME, Masliah E & Ellisman MH (2005) Behavioral Deficits and Increased mGluR5 Immunoreactivity in CNS of Transgenic Mice Overexpressing Alphasynuclein. 7th Annual International Conference AD/PD, Sorrento, Italy, Abstract #352.
  3. Price DL, Rockenstein E, MacLean? NAB, Phung V, Martone ME, Masliah E, Ellisman MH (2005) Multidisciplinary approaches to characterizing behavioral deficits and altered mGluR5 immunoreactivity in CNS of transgenic mice overexpressing alpha-synuclein. Society for Neuroscience, Abstract. #85.15.

2004

  1. Martone ME, Gupta A, Wang Y, Sun L, Zaslavsky I, He H, Price DL, Tran J, Ellisman MH (2004) The Cell Centered Database Project: Advanced Informatics for Federation of Distributed Multi-scale Imaging Data Human Brain Project, Annual Meeting.
  2. Martone ME, Zaslavsky I, He H, Tran J, Wang Y, Sun J, Price DL, Ellisman MH, Gupta A (2004) The SMART Atlas: A web-based spatial data management and data mining tool for the mouse brain. Society for Neuroscience, Abstract.
  3. Price DL, Chow SK, Hakozaki H, Phung V, Smarr B, Peltier S, Martone ME, Ellisman MH (2004) Application of a Multi-Photon HighResolution? Large-Scale Montage Imaging Technique to Characterize Transgenic Mouse Models of Human Neurodisorders. Microscopy and Microanalysis Abstract, Annual Meeting Savannah, GA.
  4. Price DL, Rockenstein E, MacLean? NAB, Martone ME, Masliah E, Ellisman MH (2004) Changes in mGluR5 immunoreactivity in CNS of transgenic mice overexpressing alpha-synuclein. Society for Neuroscience Abstract, #561.4.
  5. Rodrigues EM, Price DL, MacLean? NAB, Martone ME, Bash R, Van Dyke T, Ellisman MH (2004) Diffusely transformed astrocytes by sv40 expression as a model for brain cancer: Alterations in filamentous-actin levels. Society for Neuroscience Abstract, #462.12.

2003

  1. Johnson GA, Jacobs R, Toga A, Ellisman MH, Martone ME, MacKenzie-Graham A, Ruffins S, Price DL, Gewalt S, Merchant E, Crawford K, Zhang S, Fehnel M (2003) Multi-Scale Investigations of Animal Models of Human Disease: The Mouse BIRN Project. BISTI Abstract.
  2. Mackenzie-Graham, A., Martin, M., Jones, E., Shattuck, D., Jacobs, R., Voskuhl, R., and Toga, A.W. (2003) An atlas of experimental autoimmune encephalomyelitis in the C57BL/6 brain. Society for Neuroscience Nov 2003, New Orleans, LA.
  3. Martone ME, Gupta A, Zhang S, Santini S, He H, Zaslavsky I, Price DL, Thor A, Terada M, Ellisman MH (2003) Data Mining of neuronal structural and protein localization data using the cell centered database. Society for Neuroscience Abstract, #428.8.
  4. Price DL, Martone ME, Masliah E, Ellisman MH (2003) High-Resolution Large Scale 3-D Mapping Studies of Alpha-Synuclein Immunoreactivity in Transgenic Mice Overexpressing Human Alpha-Synuclein. Society for Neuroscience Abstract, #297.10.
  5. Zhang S, Price DL, Qian X, Gupta A, Wong M, Ellisman MH, Martone ME (2003) A Cell Centered Database (CCDB) for Multi-Scale Microscopy Data Management. Microscopy and Microanalysis, Proceedings August 3-7, 2003, San Antonio, Texas.

2002

  1. Martone ME, Gupta A, Qian X, Wong M, Zhang S, Ludaescher B, Zaslavsky I, Price DL, Ellisman MH (2002) The Cell-Centered Database: An online resource for high resolution cell

Attachment sort Action Size Date Who Comment
Neuroimage2005Ali.pdf manage 969.4 K 02 May 2005 - 17:46 MouseBIRN G. Allan Johnson; accepted for publication in NeuroImage?
Cyr.Neuro_Img.pdf manage 467.8 K 02 May 2005 - 17:47 MouseBIRN G. Allan Johnson; published article in NeuroImage?
Gupta_2003_NNetworks.pdf manage 251.0 K 11 Jul 2005 - 23:07 MouseBIRN  
Johnson_2003BISTI_abstract.pdf manage 182.0 K 23 Sep 2005 - 21:52 DianaPrice 2003 BISTI abstract
Martone_2002SFNAbstract.pdf manage 13.2 K 23 Sep 2005 - 21:53 DianaPrice 2002 SFN abstract - Martone et al.
Martone2003_Neuroinformatics.pdf manage 6540.9 K 23 Sep 2005 - 21:55 DianaPrice 2003 Neuroinformatics accepted publication: Martone et al.
Zhang_2003_MMProceedings.pdf manage 353.6 K 23 Sep 2005 - 21:57 DianaPrice 2003 M&M Proceedings: Zhang et al.
Martone_2003SFNAbstract.pdf manage 13.3 K 23 Sep 2005 - 21:59 DianaPrice 2003 SFN abstract: Martone et al.
Price_2003SFNAbstract.pdf manage 13.8 K 23 Sep 2005 - 22:00 DianaPrice 2003 SFN abstract: Price et al.
Martone_2004_NatureNS.pdf manage 739.2 K 23 Sep 2005 - 22:00 DianaPrice 2004 Nature Neuroscience accepted publication: Martone et al.
Martone_2004HBP.pdf manage 13.6 K 23 Sep 2005 - 22:02 DianaPrice 2004 HBP meeting abstract: Martone et al.
Price_2004MSA_abstract.pdf manage 213.6 K 23 Sep 2005 - 22:02 DianaPrice 2004 MSA meeting abstract: Price et al.
Martone_2004SFNAbstract.pdf manage 13.5 K 23 Sep 2005 - 22:03 DianaPrice 2004 SFN abstract: Martone et al.
Price_2004SFNAbstract.pdf manage 14.0 K 23 Sep 2005 - 22:04 DianaPrice 2004 SFN abstract: Price et al.
Rodrigues_2004SFNAbstract.pdf manage 13.4 K 23 Sep 2005 - 22:04 DianaPrice 2004 SFN abstract: Rodrigues et al.
Price_ADPD2005_abstract.pdf manage 17.9 K 23 Sep 2005 - 22:05 DianaPrice 2005 SFN abstract: Price et al.
Ali_NeuroImage2005.pdf manage 1779.5 K 25 Jan 2006 - 20:47 JylBoline G. Allan Johnson; published in NeuroImage?
SfN2006_digital_atlas_MBAT.pdf manage 14.3 K 08 Jan 2007 - 17:04 JylBoline 2006 SFN Abstract: MBAT and digital atals display
SfN2006_atlas_integration.pdf manage 14.0 K 08 Jan 2007 - 17:12 JylBoline 2006 SFN Abstract: atlas interoperability
Ruffins_Lansford_quail.pdf manage 575.9 K 06 May 2008 - 21:24 SethRuffins