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Bryan William Jones, Ph.D. - PUBLICATIONS

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IN PREPARATION

A P347L Rhodopsin Transgenic Rabbit Model of Retinitis Pigmentosa. B.W. Jones, R.E. Marc, J.R. Anderson, M.V. Shaw, J-H Yang, H. Terasaki, M. Kondo. Retinas of mice lacking Chx10 and p27Kip1 retain cone bipolar cells, but not bipolar cell function. Eric S. Green, Yves Sauve, Bryan W. Jones, Carl B. Watt, Robert E. Marc and Edward M. Levine. 2008 Retinal Remodeling in human retinal degenerations. Bryan W. Jones, Robert E. Marc. 2008 Atlas: A Molecular Phenotypic Atlas of the Mouse Retina. Jones BW, Marc RE. 2008

IN REVIEW

PAPERS IN PRESS/PUBLISHED

Anderson JR, Jones BW, Yang J-H, Shaw MV, Watt CB, Koshevoy P, Spaltenstein J, Jurrus E, Kannan UV, Whitaker R, Mastronarde D, Tasdizen T, Marc R 2008 A computational framework for ultrastructural mapping of neural circuitry. Preprint. Submitted to: PLoS Biology. 8.6 Mb PDF Butterwick A, Huie P, Jones BW, Marmor MF, Marc RE, Palanker D. 2008. Effect of shape and coating of a subretinal prosthesis on its integration with the retina. Experimental Eye Research in press Chapter: Retinal Remodeling and Visual Prosthetics. Visual Prosthetics. 2008 Extreme Retinal Remodeling Triggered by Light Damage: Implications for AMD. RE Marc, BW Jones, CB Watt, F. Vazquez-Chona, DK Vaughan, DT Organisciak. Molecular Vision 14:782-806. . PubMed 40 Mb full res PDF 3 Mb small PDF Marc RE, BW Jones, JR Anderson, K Kinard, DW Marshak, JH Wilson, TG Wensel, RJ Lucas 2007 Neural reprogramming in retinal degenerations. Invest Ophthalmol Vis Sci. PubMed PDF Review: Retinal Remodeling During Retinal Degeneration. Jones BW, Marc RE. Experimental Eye Research 2005, 81: 121-244. PubMed PDF Excitation mapping with the organic cation AGB2+. Marc RE, M Kalloniatis, and BW Jones. 2005. Vision Research, 45: 3454-3468. PubMed PDF Review: Retinal remodeling in retinal degenerations. Jones BW, CB Watt and RE Marc. 2005. Clinical and Experimental Optometry 88: 282-291. PubMed PDF Chapter: Neural plasticity revealed by light-induced photoreceptor lesions. BW Jones, RE Marc, CB Watt, DK Vaughan, DT Organisciak. Retinal Degenerative Diseases, Springer, (New York), pp. 405-410. 2005. Review: Retinal remodeling: Circuitry revisions triggered by photoreceptor degeneration. In Plasticity in the Visual system: Marc RE, BW Jones and CB Watt. 2005, From Genes to Circuits. Eds, Pinaud et al., Springer, pp. 33-54. 2005. Retinal remodeling triggered by photoreceptor degenerations. Jones BW, Watt CB, Frederick JM, Baehr W, Chen CK, Levine EM, Milam AH, LaVail MM, Marc RE. Journal of Comparative Neurology pp. 1-16 Sep, 8;464(1) 2003 PubMed PDF Neural Remodeling in Retinal Degeneration. Marc RE, BW Jones, CB Watt and E Strettoi. Progress in Retinal and Eye Research, pp. 607-655 Sep; 22(5) 2003. PubMed PDF Retinal remodeling in inherited photoreceptor degenerations. Marc RE, BW Jones Molecular Neurobiology 28: 139-148 2003. PubMed PDF Molecular phenotyping of retinal ganglion cells. RE Marc and BW Jones. The Journal of Neuroscience. pp 413-427 Jan, 15 22(2) 2002. PubMed PDF Familial advanced sleep-phase syndrome: A short-period circadian rhythm variant in humans. pp 1062-1065 CR Jones, SS Campbell, SE Zone, F Cooper, A DeSano, PJ Murphy, B Jones, L Czajkowski & Louis J. Ptacek. Nature Medicine 2000 PubMed PDF

ABSTRACTS/PRESENTATIONS

A P347L Rhodopsin Transgenic Rabbit Model of Retinitis Pigmentosa. B.W. Jones1, R.E. Marc1, J.R. Anderson1, M.V. Shaw1, J-H Yang1, H. Terasaki2, M. Kondo2. 1Ophthalmology, Moran Eye Center, Salt Lake City, UT; 2Ophthalmology, Nagoya University, Graduate School of Medicine, Nagoya, Japan. Retinal Degeneration 2008 Rapid Ionotropic Glutamate Receptor Plasticity in Light-Induced Retinal Stress. Y. Lin, B.W. Jones, K. Rapp, J.R. Anderson, C.B. Watt, M.V. Shaw, J-H Yang, F.R. Vasquez-Chona, R.E. Marc. John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT. Retinal Degeneration 2008 Metabolic Biomarkers of Early Retinal Oxidative Stress. F.R. Vasquez-Chona, W.D. Ferrell, Y. Lin, B.W. Jones, R.E. Marc John A. Moran Eye Center, University of Utah School of Medicine, Salt Lake City, UT. Retinal Degeneration 2008 Computational Molecular Phenotyping and Excitation Mapping in the P347L Rhodopsin Transgenic Rabbit Model of Retinitis Pigmentosa. B.W. Jones1, R.E. Marc1, H. Terasaki2, M. Kondo2. 1Ophthalmology, Moran Eye Center, Salt Lake City, UT; 2Ophthalmology, Nagoya University, Graduate School of Medicine, Nagoya, Japan. ARVO 2008 PDF Excitatory Drive Patterns of TH1 Dopaminergic Polyaxonal Cells in Rabbit Retina. RE Marc, BW Jones, P Pandit, JR Anderson, TM Raleigh. Ophthalmology, School of Medicine, University of Utah Moran Eye Center, Salt Lake City, Utah. 2008. An optimal-path approach for neural circuit reconstruction. E. Jurrus, R. Whitaker, B. W. Jones, R. Marc, and T. Tasdizen. Biomedical Imaging: From Nano to Macro, 2008. ISBI 2008. 5th IEEE International Symposium on, pp. 1609-1612, May 2008. Structure and Function of Microneuromas in Retinal Remodeling. BW Jones1, RE Marc1, CB Watt1, K. Kinard1, D. DeMill1, J-H Yang1, T. Tasdizen2, P. Koshevoy2, E. Jurrus2, R. Whitaker2. 1Moran Eye Center. 2School of Computing/Scientific Computing Institute, University of Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology 2007. PDF Partial Circuitry Rescue By Cones In Retinitis Pigmentosa. BW Jones, K. Kinnard, DW Marshak, RE Marc. John A Moran Eye Center, University of Utah, Salt Lake City, UT. University Texas Medical School, Houston TX. Assoc Res Vision & Ophthalmology 2006. Visualization of Light and Ligand Activated Signaling in the Primate Retina. RE Marc1A, BW Jones1A, JR Anderson1B, DW Marshak2. AOphthalmology, BNeuroscience Program, 1Univ Utah, Salt Lake City, UT; 2Neurobiology & Anatomy, Univ Texas Med Sch, Houston, TX. Assoc Res Vision & Ophthalmology 2006. Assembly of three-dimensional volumes from serial-section transmission electron microscopy. T. Tasdizen, P. A. Koshevoy, B. W. Jones, R. T. Whitaker, and R. E. Marc, in MIAAB, 2006, pp. 10–17. Large-scale computational reconstruction of three-dimensional neural connectivity. T. Tasdizen, BW Jones, P. Koshevoy, E. Jurrus, R. Whitaker, M. Hardy, C.B. Chien, RE Marc and W. Denk. NIH/NSF Collaborative Research in Computational Neuroscience (CRCNS), Washington D.C. 2006 Retinal Migration Into 3-Dimensional Subretinal Prosthetic Implants. P Huie1a, I Chan1b, A Vankov1a, A Butterwick1c, M Marmor1b, MS Blumenkranz1b, BW Jones2, D Palanker1a. (a) Ophthalmology and Hansen Exptl. Physics Lab, (b) Ophthalmology, (c) Hansen Exptl. Physics Lab, 1 Stanford, Stanford, CA; 2 Moran Eye Center, University of Utah, UT. Assoc Res Vision & Ophthalmology 2006. T. Tasdizen, R. Whitaker, R. Marc and B. Jones, "Enhancement of Cell Boundaries in Transmission Microscopy Images", Proceedings of International Conference on Image Processing (ICIP), Vol. 2, pp. 129-132, September, 2005. Bipolar Cell Blindness: Fast, Persistent Second Order Effects of Photoreceptor Degenerations. RE Marc, CB Watt & BW Jones. Moran Eye Center, University of Utah. Salt Lake City, Ut. Occular Cell and Molecular Biology, Assoc Res Vision & Ophthalmology 2005. The Chx10,p27Kip1-Double Null Retina Contains Cone Bipolar Cells, but Remains Severely Compromised in Visual Function. E.M. Levine, Y.Sauve, B.W. Jones, E.S. Green, R.Marc. John A Moran Eye Center, University of Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology 2005. Cell Cycle Alterations in Chx10 Null and Chx10, p27Kip1 Double Null Retinal Progenitor Cells Reveal the Importance of Proliferation Rate in Promoting Retinal Development. T.M. Raleigh, E.S. Green, B.W. Jones, R.Marc, E.M. Levine. John A Moran Eye Center, University of Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology 2005. Excitation Mapping in a Rodent Seizure Model. DK Takahashi, BW Jones, RE Marc, K Wilcox. American Epilepsy Society, 58th Annual Meeting, 2004. Abstract 1.040. Computational Molecular Phenotyping (CMP) of the Platyhelminth Schmidtea Mediterranea. LA Hunt, BW Jones, RE Marc. Program No. 373.3 Society for Neuroscience 2004. Neural plasticity revealed by light-induced photoreceptor lesions.  BW Jones, RE Marc, CB Watt, DK Vaughan, DT Organisciak. Univ Utah/Moran Eye Center, Salt Lake City, UT; Biology, University of Wisconsin Oshkosh, Oshkosh, WI; Biochemistry and Molecular Biology, Wright State University, Dayton, OH.  XI International Symposium on Retinal Degeneration, Perth Australia, 2004. Dopamine Amacrine and Interplexiform Cells Exhibit Glutamatergic Signatures. BW Jones, CB Watt, RE Marc. Ophthalmology, Univ Utah/Moran Eye Center, Salt Lake City, UT Assoc Res Vision & Ophthalmology 2004. PDF Excitatory Self Signaling in Retinal Remodeling. Marc RE, BW Jones. Ophthalmology, Univ Utah/Moran Eye Center, Salt Lake City, UT Assoc Res Vision & Ophthalmology 2004. PDF Complex Rewiring in Retinal Remodeling. CB Watt, BW Jones, J-H Yang, RE Marc. Ophthalmology, Univ Utah/Moran Eye Center, Salt Lake City, UT Assoc Res Vision & Ophthalmology 2004. PDF Phenotyping neurons with pattern recognition of molecular mixtures. Marc RE, BW Jones 2003. IEEE, Intermational Symposium on Signal Processing and its Applications, S1571. PDF Retinal Remodeling Triggered by Light Damage in the Albino Rat. B. W. Jones, C. B. Watt, R. E. Marc. Ophthalmology, Univ Utah/Moran Eye Center, Salt Lake City, UT Assoc Res Vision & Ophthalmology 2003. PDF Severe remodeling of the mouse neural retina triggered by rod degeneration. Jones BW, Chen CK, Watt CB, Frederick JM, Huang W, Baehr W, Marc RE. 2002 Ophthalmology, Univ Utah/Moran Eye Center, Salt Lake City, UT Assoc Res Vision & Ophthalmology. Circuitry in the rabbit inner plexiform layer: Enhanced analysis with deep-etch EM immunogold. Watt CB, Yang J, Jones BW, Shaw MV, Marc RE. 2002 Ophthalmology, Univ Utah/Moran Eye Center, Salt Lake City, UT Assoc Res Vision & Ophthalmology. Aberrant remodeling of the neural retina in the GHL transgenic mouse. Jones BW, Marc RE, Frederick JM, Baehr W, et al. 2001 Moran Eye Center, Univ Utah, Salt Lake City, UT Fifth Annual Vision research Conference. PDF Molecular phenotyping of the neural retina in retinitis pigmentosa. Marc RE, Jones BW, Yang JH, Shaw MV and Milam AH. 2001 Moran Eye Center, Univ Utah, Salt Lake City, UT; Scheie Eye Institute, Univ Penn, Philadelphia, PA. Assoc Res Vision & Ophthalmology. Nested feedback and Concatenated Inhibition In The Rabbit Inner Plexiform Layer. Watt CB, Yang JH, Jones BW and Marc RE. 2001 Moran Eye Center, Univ. of Utah, Salt Lake City, UT Assoc Res Vision & Ophthalmology. Computational molecular phenotyping. Visualizing cellular chemistry. Marc RE , Jones BW. 2001 Moran Eye Center, Univ. of Utah, Salt Lake City, UT First International Symposium on computational Cell Biology Biochemical signature analysis of the human ganglion cell layer. BW Jones, Marc RE , Watt CB, Shaw MV and Yang JH. 2000 Moran Eye Center, Univ.Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology Studies examining the neurotransmitter properties of horizontal cell populations in the goldfish retina. CB Watt, M Kalloniatis, BW Jones and RE Marc 2000 Moran Eye Center, Univ. of Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology The molecular signature of all types of rabbit retinal ganglion cells. RE Marc, BW Jones, CB Watt, MV Shaw and J-H Yang 2000 Moran Eye Center, Univ. Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology Ionotropic glutamatergic drive histories of amacrine cell layer neurons reported by 1-amino-4-guanidobutane (AGB) in vivo. BW Jones, J Howard, A Beg, CB Watt, and RE Marc 1999 Moran Eye Center, Univ. Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology Neurochemical subtypes of LGNd neurons in the cat LGNd and PGN. MT Schmolesky, BW Jones, Y-C, Wang, AG Leventhal, and RE Marc 1999 Department of Neurobiology and Anatomy1 and Moran Eye Center2, Univ. Utah, Salt Lake City, UT. Assoc Res Vision & Ophthalmology TECHNICAL REPORTS

Tolga Tasdizen, Ross Whitaker, Robert Marc and Bryan Jones, "Automatic Correction of Non-uniform Illumination in Transmission Electron Microscopy Images", SCI Institute Technical Report, UUSCI-2005-008, University of Utah, September, 2005.

INVITED PRESENTATIONS

Torsten Wiesel Research Institute, West China Hospital, Sichuan University, 2008. GlaxoSmithKline, 2008. University of Texas Health Sciences Center, 2008. Huntsman Cancer Institute, 2008. Ophthalmic Photographers Society, Moran Eye Center, 2008. Scientific Computing Institute, University of Utah, 2007. University of Leicester Dept. of Toxicology, 2007. Microscopy and Microanalysis, 2007. Bio Image Informatics, UCSB, 2006. USU Center for Integrated BioSystems, 2006. NIH/NCRR Center for Integrative Biomedical Computing, 2006. Medical University South Carolina, Dept. of Ophthalmology, 2006. UCSB Center for Bio-Image and Informatics, 2006. ARUP Laboratories Institute for Clinical and Experimental Pathology, 2005. Ophthalmology Grand Rounds Moran Eye Center, 2004. St. Louis University, Dept of Pharmacology & Physiological Science, 2004. University of Michigan, Depts of Bioinformatics and Pharmacology, 2004. Stanford University, Department of Ophthalmology, 2004. University of Utah, Department of Ophthalmology Moran Eye Center, 2002. University of Utah, Department of Bioninfomatics, 2001.

CURRENT COLLABORATIONS

University of Texas Health Sciences Center, Charles Keller Stanford University: Daniel Palanker and Philip Huie Medical University South Carolina: Baerbel Rohrer St. Louis University: Steven Fliesler University of Utah, Moran Eye Center: Edward Levine University of Michigan: Pamela Raymond Wright State University: Daniel Organisciak University of Wisconsin Oshkosh: Dana Vaughan University of California Santa Barbara: Steven Fisher and Geoff Lewis University of Utah, Dept of Pathology: David Stillman

AWARDS

Career Development Award (Research Prevent Blindness) 2006. National Eye Institute (NEI) Travel Fellowship Grant, 2002. Young Investigator Award, RD2004.