James R. Anderson


James R. Anderson, Ph.D. – PUBLICATIONS

NCBI Library link

Neural Circuit Revision in Retinal Remodeling, A Pathoconnectomics Approach
Rebecca L Pfeiffer, Jeebika Dahal, Crystal L Sigulinsky, James R Anderson, Isabel A Barrera, Jia-Hui Yang, Olivia Haddadin, Alexis R Houser, Jessica C Garcia, Bryan William Jones
bioRxiv, https://doi.org/10.1101/2024.02.14.580149
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Impact of Retinal Degeneration on Response of ON and OFF Cone Bipolar Cells to Electrical Stimulation
Shayan Farzad, Pragya Kosta, Ege Iseri, Steven T Walston, Jean-Marie C Bouteiller, Rebecca L Pfeiffer, Crystal L Sigulinsky, Jia-Hui Yang, Jessica C Garcia, James R Anderson, Bryan W Jones, Gianluca Lazzi
IEEE Trans Neural Syst Rehabil Eng. 2023;31:2424-2437. doi: 10.1109/TNSRE.2023.3276431. Epub 2023 May 26.
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Synaptic inputs to broad thorny ganglion cells in macaque retina.
Bordt AS, Patterson SS, Girresch RJ, Perez D, Tseng L, Anderson JR, Mazzaferri MA, Kuchenbecker JA, Gonzales-Rojas R, Roland A, Tang C, Puller C, Chuang AZ, Ogilvie JM, Neitz J, Marshak DW.
J Comp Neurol. 2021 Apr 12. doi: 10.1002/cne.25156.
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Wide-field amacrine cell inputs to ON parasol ganglion cells in macaque retina
Patterson SS, Bordt AS, Girresch RJ, Linehan CM, Bauss J, Yeo E, Perez D, Tseng L, Navuluri S, Harris NB, Matthews C, Anderson JR, Kuchenbecker JA, Manookin MB, Ogilvie JM, Neitz J, Marshak DW.
J Comp Neurol. 2020 Jun 15;528(9):1588-1598. doi: 10.1002/cne.24840.
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Model-Based Comparison of Current Flow in Rod Bipolar Cells of Healthy and Early-Stage Degenerated Retina
Pragya Kosta, Ege Iseri, Kyle Loizos, Javad Paknahad, Rebecca L. Pfeiffer, Crystal L. Sigulinsky, James R. Anderson, Bryan W. Jones, and Gianluca Lazzi.
Exp Eye Res. March 30, 2021
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A pathoconnectome of early neurodegeneration: Network changes in retinal degeneration
Rebecca L. Pfeiffer, James R. Anderson, Jeebika Dahal, Jessica C Garcia, Jia-Hui Yang, Crystal L. Sigulinsky, Kevin Rapp, Daniel P. Emrich, Carl B. Watt, Hope AB Johnstun, Alexis R. Houser, Robert E. Marc, and Bryan W. Jones.
Exp Eye Res. Aug 15 2020, 199:108196
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Network architecture of gap junctional coupling among parallel processing channels in the mammalian retina
Crystal L. Sigulinsky, James R. Anderson, Ethan Kerzner, Christopher N. Rapp, Rebecca L. Pfeiffer, Taryn M. Rodman, Daniel P. Emrich, Kevin D. Rapp, Noah T. Nelson, J. Scott Lauritzen, Miriah Meyer, Robert E. Marc, and Bryan W. Jones.
J. Neurosci 3 June 2020, 40 (23) 4483-4511
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Pathoconnectome Analysis of Müller Cells in Early Retinal Remodeling
Rebecca L Pfeiffer, James R Anderson, Daniel P Emrich, Jeebika Dahal, Crystal L Sigulinsky, Hope AB Morrison, Jia-Hui Yang, Carl B Watt, Kevin D Rapp, Mineo Kondo, Hiroko Terasaki, Jessica C Garcia, Robert E Marc, Bryan W Jones
Chapter: Retinal Degenerative Diseases pp365-370 2019 PubMed Direct Link PDF

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

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

A high-resolution morphological and ultrastructural map of anterior sensory cilia and glia in Caenorhabditis elegans. Doroquez DB, Berciu C, Anderson JR, Sengupta P, Nicastro D. eLife. 2014; 3:e01948. PMID: 24668170 PMCID: PMC3965213

The AII amacrine cell connectome: a dense network hub. Marc RE, Anderson JR, Jones BW, Sigulinsky CL, Lauritzen JS. Frontiers in neural circuits. 2014; 8:104. PMID: 25237297 PMCID: PMC4154443

A multi-scale computational model for the study of retinal prosthetic stimulation. Loizos K, Lazzi G, Lauritzen JS, Anderson J, Jones BW, et al. Conference proceedings : … Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual Conference. 2014; 2014:6100-3. NIHMSID: NIHMS703810 PMID: 25571389 PMCID: PMC4490688

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

Robust segmentation based tracing using an adaptive wrapper for inducing priors. Jagadeesh V, Manjunath BS, Anderson J, Jones BW, Marc R, et al. IEEE transactions on image processing : a publication of the IEEE Signal Processing Society. 2013; 22(12):4952-63.
PMID: 23996562

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

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 2012
J Comp Neurol 521:977-1000 doi: 10.1002/cne.23244. [epub ahead of print]
PubMed PMID 23042441

Retinal Connectomics: A new era for connectivity analysis. Marc RE, Jones BW, Lauritzen JS, Watt CB, Anderson JR. 2013 New Visual Neurosciences. In Press.

Building retinal connectomes. Marc RE, Anderson JR, Jones BW, Watt CB 2012
Current Opinion in Neurobiology 22:568-574. :: PubMed PMID 22498714::

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. Jones BW, Kondo M, Terasaki H, Watt CB, Rapp K, Anderson J, Lin Y, Shaw MV, Yang J-H, Marc R J Comp Neurol. 2011 1;519(14):2713-2733 :: PubMed PMID 21681749::

Increased expression of multifunctional serine protease, HTRA1, in retinal pigment epithelium induces polypoidal choroidal vasculopathy in mice.
Jones A, Kumar S, Zhang N, Tong Z, Yang JH, Watt C, Anderson J, Amrita, Fillerup H, McCloskey M, Luo L, Yang Z, Ambati B, Marc R, Oka C, Zhang K, Fu Y 2011 Proc Natl Acad Sci U S A. 108:14578-83. Epub 2011 Aug 15 :: PubMed PMID 21844367:: PubMedCentral PMC3167497::

Exploring the retinal connectome. Anderson JR, Jones BW, Watt CB, Shaw MV, Yang J.-H., DeMill D, Lauritzen J.S., Lin Y., Rapp KD, Mastronarde D, Koshevoy P, Grimm B, Tasdizen T, Whitaker R, Marc RE 2011  ∞ Molecular Vision 17:355-379 :: PubMed PMID 21311605:: ∞ 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 R 2011 J Microscopy: 241:13-28. doi: 10.1111/j.1365-2818.2010.03402.x. PubMed PMID 21118201:: PubMedCentral PMC 3017751::

Detection of neuron membranes in electron microscopy images using a serial neural network architecture. Jurrus E, Paiva ARC, Watanabe S, Jorgensen EM, Anderson JR, Jones BW, Whitaker R, Marc R, Tasdizen T 2010  Medical Image Analysis 14:770-783.
PubMed PMID 20598935:: ∞ PDF

Automatic mosaicking and volume assembly for high-throughput serial-section transmission electron microscopy. Tasdizen T, Koshevoy P,Grimm B, Anderson JR, Jones BW, Whitaker R, Marc RE  J Neuroscience Methods: 193:132-44.
PubMed PMID 20713087:: ∞ 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 2009  PLoS Biol 7(3): e1000074 [doi:10.1371/journal.pbio.1000074]
PubMed PMID 19855814:: PubMedCentral PMC2661966

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 48: 3364-3371.PubMed PMID 17591910 :: PubMedCentral PMC2408857