Bryan W. Jones

Bryan William Jones, Ph.D.


Personal site: Jonesblog

 

Publications

Increasing Electrical Stimulation Efficacy in Degenerated Retina: Stimulus Waveform Design in a Multiscale Computational Model. Kyle Loizos, Robert Marc, Mark Humayun, James R Anderson, Bryan W Jones, Gianluca Lazzi. IEEE Transactions on Neural Systems and Rehabilitation Engineering 26 6 1111-1120. PubMed Direct Link PDF

Corticostriatal circuit defects in Hoxb8 mutant mice. Nagarajan N, Jones BW, West PJ, Marc RE, Capecchi MR. Mol Psychiatry. 2017 Sep 26. doi: 10.1038/mp.2017.180. PubMed Direct Link PDF

Pattern Recognition Analysis Reveals Unique Contrast Sensitivity Isocontours Using Static Perimetry Thresholds Across The Visual Field. 2017 J Phu, S Khuu, L Nivison-Smith, B Zangerl, A Yiu, J Choi, BW Jones, R Pfeiffer, R Marc, and M Kalloniatis. Invest Ophthalmol Vis Sci. 2017;58:4863–4876. DOI:10.1167/ iovs.17-22371 PubMed NCBI PDF

Pattern Recognition analysis of age-related retinal ganglion cell signatures in the human eye 2017
N Yoshioka, B Zangerl, L Nivison-Smith, SK Khuu, BW Jones, RL Pfeiffer, RE Marc, M Kalloniatis
Invest Ophthalmol Vis Sci. 2017 Jun 1;58(7):3086-3099. doi: 10.1167/iovs.17-21450. PubMed Direct Link PDF

Photoreceptor Outer Segment-like Structures in Long-Term 3D Retinas from Human Pluripotent Stem Cells. K. Wahlin, J. Maruotti, S. Srinpathi, J. Ball, J. Angueyra, C. Kim, R. Grebe, W. Li, B.W. Jones, D. Zack. 2017 Nature Scientific Reports 766 doi:10.1038/s41598-017-00774-9 PubMed Direct Link PDF

Graffinity: Visualizing Connectivity in Large Graphs. E. Kerzner, A. Lex, C. Sigulinsky, T. Urness, B.W. Jones, R.E. Marc, M. Meyer. (2017)  EuroVis 2017 Vol 36, Number 3 PMCID Direct LInk PDF

Rod-cone crossover connectome of mammalian bipolar cells. J.S. Lauritzen, C.L. Sigulinsky, J.R. Anderson, M. Kalloniatis, N.T. Nelson, D.P. Emrich, C. Rapp, N. McCarthy, E. Kerzner, M. Meyer, B.W. Jones, R.E. Marc (2016)  Journal Comparative Neurology. PubMed Direct Link PDF

Editorial: Special issue on retinal remodeling. B.W. Jones and G. P. Lewis. Experimental Eye Research 2016 PubMed PubMed Direct Link PDF

Retinal Remodeling and Metabolic Alterations in Human AMD. B.W. Jones, R.L. Pfeiffer, W.D. Ferrell, C.B. Watt, J. Tucker, R.E. Marc (2016)  Frontiers in cellular neuroscience. PubMed Direct Link PDF

Müller cell metabolic chaos during retinal degeneration. R.L. Pfeiffer, R.E. Marc, B.W. Jones 2016 Experimental eye research 150, 62-70 PubMed Direct Link PDF

A Targeted Inhibitor of the Alternative Complement Pathway Accelerates Recovery From Smoke-Induced Ocular Injury. A. Woodell, B.W. Jones, T. Williamson, G. Schnabolk, S. Tomlinson, C. Atkinson, B. Rohrer (2016)  Investigative ophthalmology & visual science 57 (4), 1728-1737 PubMed Direct Link PDF

Retinal Remodeling in Human Retinitis Pigmentosa. B.W. Jones, R.L. Pfeiffer, W.D. Ferrell, C.B. Watt, M. Marmor, R.E. Marc (2016)Experimental eye research 150, 149-165. PubMed Direct Link PDF

Store-Operated Calcium Entry In Müller Glia Is Controlled By Synergistic Activation Of TRPC And Orai Channels. T. Molnár, O. Yarishkin, P. Barabas, A. Iuso, B.W. Jones, R. Marc, T. Phuong, and D. Krizaj. 2016  Journal of Neuroscience 36 (11), 3184-3198 PubMed Direct Link PDF

Eosinophilic Esophagitis in Two Patients with Systemic Sclerosis. T.M. Frech, K. Boynton, E. Downs-Kelly, B. Jones, J.D. Kriesel, K. Peterson 2016. Case reports in rheumatology 2016 PubMed PMCID PDF

Seasonal and post-trauma remodeling in cone-dominant ground squirrel retina. DK Merriman, BS Sajdak, W. Li, Jones BW 2016  Experimental Eye Research. doi 10.1016/j.exer.2016.01.011 PubMed Direct Link PDF

Development of Animal Models of Local Retinal Degeneration. H. Lorach, J. Kung, C. Beier, Y. Mandel, R. Dalal, P. Huie, J. Wang, S. Lee, A. Sher, B.W. Jones and D. Palanker (2015). 56(8): 4644-52. Invest Ophthalmol Vis Sci. PubMed Direct Link PDF

The AII Amacrine Cell Connectome: A Dense Network Hub. R.E. Marc, J.R. Anderson, B.W. Jones, C. Sigulinsky and J. Scott Lauritzen (2014).  Front Neural Circuits. PubMed Direct Link PDF

A Multi-Scale Computational Model For The Study of Retinal Prosthetic Stimulation. Kyle Loizos, Gianluca Lazzi, J. Scott Lauritzen, James R. Anderson, Bryan W. Jones and Robert E. Marc (2014).  IEEE Computer Graphics and Applications. PubMed Direct Link PDF

Retinal Prosthetics, optogenetics, and chemical photoswitches. R.E. Marc, R. Pfeiffer, B.W. Jones (2014). ACS Chem Neurosci. PubMed Direct Link PDF

Synapse Classification and Localization in Electron Micrographs. V. Jagadeesh, J. Anderson, B.W. Jones, R.E. Marc, S. Fisher and B.S. Manjunath 2014 2013. Pattern Recognition Letters. Direct Link PDF

Quantitative Analyses of Retinal Vascular Area and Density after Different Methods to Reduce VEGF in a Rat Model of Retinopathy of Prematurity. Wang H, Yang Z, Jiang Y, Flannery JG, Hammond S, Kafri T, Vemuri SK, Jones B, Hartnett ME (2014). Invest Ophthalmol Vis Sci. PubMed Direct Link PDF

Robust Segmentation based Tracking using an Adaptive Wrapper for Inducing Priors. Vignesh Jagadeesh, James Anderson, B.W.Jones, Robert E. Marc, Steven K Fisher and B.S Manjunath (2013).  IEEE Trans Image Process. Direct Link PDF

Alternative Complement Pathway Deficiency Amerliorates Chronic Smoked-Induced Functional And Morphological Ocular Injury. A. Woodell, B. Coughlin, K. Kunchithapautham, S. Casey, T. Williamson, W.D. Ferrell, C. Atkinson, B.W.Jones, B. Rohrer (2013).  PLoS ONE. PubMed Direct Link PDF

Retinal Connectomics: Towards Complete, Accurate Networks. Marc RE, Jones BW, Watt CB, C. Sigulinsky, Anderson JR, Lauritzen JS (2013).  Prog Retin Eye Res. PubMed Direct Link PDF

Restoration of Retinal Structure and Function After Selective Photocoagulation. A. Sher, B.W. Jones, P. Huie, Y. Paulus, L.S. Leung, H. Nomoto, R.E. Marc, D. Palanker (2013). J Neurosci. PubMed Direct Link PDF

The Role of ELOVL4 And Very Long Chain Polyunsaturated Fatty Acids In Mouse Models of Stargardt Type 3 Retinal Degeneration. P. Barabas, A. Liu, W. Xing, C-K. Jason Chen, Z. Tong, C. B. Watt, B.W. Jones, P. S Bernstein, D. Križaj (2013). Proc Natl Acad Sci U S A. PubMed Direct Link PDF

ON cone bipolar cell axonal synapses in the OFF inner plexiform layer of the rabbit retina. Lauritzen JS, Anderson JR, Jones BW, Watt CB, Mohammed S, Hoang JV, Marc RE (2013). J Comp Neurol. PubMed Direct Link PDF

Retinal Remodeling. B.W. Jones, M. Kondo, H. Terasaki, Y. Lin, M. McCall, R.E. Marc (July 2012). Jpn J Ophthalmol, 56(4), 289-306. PubMed Direct Link PDF

Computational molecular phenotyping of retinal sheet transplants to rats with retinal degeneration. Seiler MJ, Jones BW, Aramant RB, Yang PB, Keirstead HS, Marc RE (June 2012). Eur J Neurosci, 35(11), 1692-1704. PubMed Direct Link PDF

Building retinal connectomes. Marc RE, Anderson JR, Jones BW, Watt CB (April 2012). Curr Opin Neurobiol. PubMed Direct Link PDF

Rapid glutamate receptor 2 trafficking during retinal degeneration. Lin Y, Jones BW, Liu A, Vazquez-Chona FR, Lauritzen JS, Ferrell WD, Marc RE (February 2012).  Mol Neurodegener. Feb 10 doi: 10.1186. PubMed Direct Link PDF

Dysmorphic Photoreceptors in a P23H Mutant Rhodopsin Model of Retinitis Pigmentosa are Metabolically Active and Capable of Regenerating to Reverse Retinal Degeneration. D. Lee, F.V-Chona, W. Ferrell, B. Tam, B.W. Jones, R.E. Marc, O. Moritz (February 2012). J Neurosci, 32(6), 2121-2128. PubMed Direct Link PDF

Generation of an inbred miniature pig model of retinitis pigmentosa. Ross JW, Fernandez de Castro JP, Zhao J, Samuel M, Walters E, Rios C, Bray-Ward P, Jones BW, Marc RE, Wang W, Zhou L, Noel JM, McCall MA, DeMarco PJ, Prather RS, Kaplan HJ (January 2012). Invest Ophthalmol Vis Sci, 53(1), 501-507. PubMed Direct Link PDF

Online parameter estimation in dynamic Markov Random Fields for image sequence analysis. V Jagadeesh, BS Manjunath, J Anderson, B Jones, R Marc, SK Fisher (2012). ICIP. Direct Link PDF

Retinal Remodeling in the Tg P347L Rabbit, a Large-Eye Model of Retinal Degeneration. B.W. Jones, M. Kondo, H. Terasaki, C.B. Watt, K. Rapp, J. Anderson, Y. Lin, M.V. Shaw, J-H Yang, R.E. Marc (October 2011). J Comp Neurol, 519(14). PubMed Direct Link PDF

Retinoid Receptors Trigger Neuritogenesis in Retinal Degenerations. Y. Lin, B.W. Jones, A. Liu, J.F. Tucker, K. Rapp, L. Luo, W. Baehr, P.S. Bernstein, C.B. Watt, J-H Yang, M.V. Shaw, R.E. Marc (September 2011). FASEB J. PubMed Direct Link PDF

Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy. T. Tasdizen, P. Koshevoy, B. Grimm, J. Anderson, B.W. Jones, R.T. Whitaker, R.E. Marc (2010). J Neurosci Methods. PubMed Direct Link PDF

Exploring The Retinal Connectome. J.R. Anderson, B.W. Jones, C.B. Watt, M.V. Shaw, J-H. Yang, D. DeMill, J.S. Lauritzen, Y. Lin, Kevin D. Rapp, D. Mastronarde, P. Koshevoy, B. Grimm, T. Tasdizen, R. Whitaker, R.E. Marc (2010). Mol Vis. PubMed Direct Link PDF

Detection of neuron membranes in electron microscopy images using auto-context. Jurrus E, Paiva ARC, Watanabe S, Jorgensen EM, Anderson JR, Jones BW, Whitaker R, Marc R, Tasdizen T (2010). Med Image Anal. PubMed Direct Link PDF

The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets. Anderson JR, Mohammed S, Grimm B, Jones BW, Koshevoy P, Tasdizen T, Whitaker R, Marc (2010). J Microsc. PubMed Direct Link PDF

A computational framework for ultrastructural mapping of neural circuitry. 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 PLoS Biol 7(3): e1000074 [doi:10.1371/journal.pbio.1000074].  PubMed Direct Link PDF  8.6 Mb PDF

An optimal-path approach for neural circuit reconstruction. E. Jurrus, R. Whitaker, B. W. Jones, R. Marc, and T. Tasdizen (2008). IEEE Biomedical Engineering Days. 1609-1612. PubMed Direct Link PDF

Effect of shape and coating of a subretinal prosthesis on its integration with the retina. Experimental Eye Research Butterwick A, Huie P, Jones BW, Marmor MF, Marc RE, Palanker D. 2008. Experimental Eye Research. 2009 88(1):22-9 PubMed Direct Link PDF

 

 

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 Direct Link PDF . PubMed 40 Mb full res PDF 3 Mb small PDF

Neural reprogramming in retinal degenerations. Marc RE, BW Jones, JR Anderson, K Kinard, DW Marshak, JH Wilson, TG Wensel, RJ Lucas 2007  Invest Ophthalmol Vis Sci. PubMed Direct Link PDF PubMed PDF

Review: Retinal Remodeling During Retinal Degeneration. Jones BW, Marc RE. Experimental Eye Research 2005, 81: 121-244. PubMed Direct Link PDF PubMed PDF

Excitation mapping with the organic cation AGB2+. Marc RE, M Kalloniatis, and BW Jones. 2005. Vision Research, 45: 3454-3468.PubMed Direct Link PDF PubMed PDF

Review: Retinal remodeling in retinal degenerations. Jones BW, CB Watt and RE Marc. 2005. Clinical and Experimental Optometry 88: 282-291. PubMed Direct Link PDF PubMed PDF

Chapter: Neural plasticity revealed by light-induced photoreceptor lesions. BW Jones, RE Marc, CB Watt, DK Vaughan, DT Organisciak. PubMed Direct Link PDF 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. PubMed Direct Link PDF 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 Direct Link PDF 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 Direct Link PDF PubMed PDF

Retinal remodeling in inherited photoreceptor degenerations. Marc RE, BW Jones Molecular Neurobiology 28: 139-148 2003. PubMed Direct Link PDF 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 Direct Link PDF 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 Direct Link PDF PubMed PDF

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.