Al-Humaidi A. (2011). Resistor Networks and Finite Element Models.
Anastassiou CA, Koch C. (2015). Ephaptic coupling to endogenous electric field activity: why bother? Current opinion in neurobiology. 31 [PubMed]
Anderson RW, Farokhniaee A, Gunalan K, Howell B, McIntyre CC. (2018). Action potential initiation, propagation, and cortical invasion in the hyperdirect pathway during subthalamic deep brain stimulation. Brain stimulation. 11 [PubMed]
Ascoli GA, Krichmar JL. (2000). L-Neuron: a modeling tool for the efficient generation and parsimonious description of dendritic morphology. Neurocomputing. 32
Berger TW, Bouteiller JM. (2017). The role of simulations in neuropharmacology Computational Neurology and Psychiatry. 6
Bindocci E et al. (2017). Three-dimensional Ca2+ imaging advances understanding of astrocyte biology. Science (New York, N.Y.). 356 [PubMed]
Bingham CS et al. (2016). A large-scale detailed neuronal model of electrical stimulation of the dentate gyrus and perforant path as a platform for electrode design and optimization. Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference. 2016 [PubMed]
Bingham CS et al. (2018). Model-Based Analysis of Electrode Placement and Pulse Amplitude for Hippocampal Stimulation. IEEE transactions on bio-medical engineering. 65 [PubMed]
Bossetti CA, Birdno MJ, Grill WM. (2008). Analysis of the quasi-static approximation for calculating potentials generated by neural stimulation. Journal of neural engineering. 5 [PubMed]
Budd JM, Kisvárday ZF. (2012). Communication and wiring in the cortical connectome. Frontiers in neuroanatomy. 6 [PubMed]
Budd JM et al. (2010). Neocortical axon arbors trade-off material and conduction delay conservation. PLoS computational biology. 6 [PubMed]
Cayley A. (1889). A theorem on Trees The Quarterly Journal of Pure and Applied Mathematics. 23
Chen J. (2003). Dijkstra's shortest path algorithm Journal of Formalized Mathematics. 15
Chew L. (1989). Constrained delaunay triangulations Algoritmica. 4
Claiborne BJ, Amaral DG, Cowan WM. (1990). Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. The Journal of comparative neurology. 302 [PubMed]
Clark JW, Plonsey R. (1970). A mathematical study of nerve fiber interaction. Biophysical journal. 10 [PubMed]
Cuntz H, Borst A, Segev I. (2007). Optimization principles of dendritic structure. Theoretical biology & medical modelling. 4 [PubMed]
Cuntz H, Forstner F, Borst A, Häusser M. (2010). One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS computational biology. 6 [PubMed]
Desmond NL, Levy WB. (1985). Granule cell dendritic spine density in the rat hippocampus varies with spine shape and location. Neuroscience letters. 54 [PubMed]
Foutz TJ, Arlow RL, McIntyre CC. (2012). Theoretical principles underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron. Journal of neurophysiology. 107 [PubMed]
Fries P. (2005). A mechanism for cognitive dynamics: neuronal communication through neuronal coherence. Trends in cognitive sciences. 9 [PubMed]
Gaarskjaer FB. (1978). Organization of the mossy fiber system of the rat studied in extended hippocampi. I. Terminal area related to number of granule and pyramidal cells. The Journal of comparative neurology. 178 [PubMed]
Grill WM. (1999). Modeling the effects of electric fields on nerve fibers: influence of tissue electrical properties. IEEE transactions on bio-medical engineering. 46 [PubMed]
Hagberg A, Schult D, Swart P. (2005). Networkx: Python Software for the Analysis of Networks. .
Hama K, Arii T, Kosaka T. (1989). Three-dimensional morphometrical study of dendritic spines of the granule cell in the rat dentate gyrus with HVEM stereo images. Journal of electron microscopy technique. 12 [PubMed]
Hampson RE et al. (2018). Developing a hippocampal neural prosthetic to facilitate human memory encoding and recall. Journal of neural engineering. 15 [PubMed]
Hartigan J, Wong M. (1979). Algorithm AS 136: a k-means clustering algorithm Journal of the Royal Statistical Society. 28
Hendrickson PJ, Yu GJ, Song D, Berger TW. (2016). A Million-Plus Neuron Model of the Hippocampal Dentate Gyrus: Critical Role for Topography in Determining Spatiotemporal Network Dynamics. IEEE transactions on bio-medical engineering. 63 [PubMed]
Hines ML, Carnevale NT. (2003). NEURON simulation environment The Handbook of Brain Theory and Neural Networks (2nd Ed).
Hjorth-Simonsen A, Jeune B. (1972). Origin and termination of the hippocampal perforant path in the rat studied by silver impregnation. The Journal of comparative neurology. 144 [PubMed]
Holt GR, Koch C. (1999). Electrical interactions via the extracellular potential near cell bodies. Journal of computational neuroscience. 6 [PubMed]
Howell B, McIntyre CC. (2017). Role of Soft-Tissue Heterogeneity in Computational Models of Deep Brain Stimulation. Brain stimulation. 10 [PubMed]
Hu T. (1974). Optimum communication spanning trees Siam Journal on Computing. 3
Huang J, Hu T, Alpert C, Kahng A, Karger D. (1995). Prim-Dijkstra tradeoffs for improved performance-driven routing tree design IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems . 14
Johnson MD, McIntyre CC. (2008). Quantifying the neural elements activated and inhibited by globus pallidus deep brain stimulation. Journal of neurophysiology. 100 [PubMed]
Joucla S, Yvert B. (2009). The "mirror" estimate: an intuitive predictor of membrane polarization during extracellular stimulation. Biophysical journal. 96 [PubMed]
Khuller S, Raghavachari B, Young NFront. Neuroinform. (1995). Balancing minimum spanning trees and shortest-path trees Algorithmica. 14
Kim JH, Lee HJ, Choi W, Lee KJ. (2019). Encoding information into autonomously bursting neural network with pairs of time-delayed pulses. Scientific reports. 9 [PubMed]
Lujan JL et al. (2013). Tractography-activation models applied to subcallosal cingulate deep brain stimulation. Brain stimulation. 6 [PubMed]
López-Aguado L, Ibarz JM, Herreras O. (2001). Activity-dependent changes of tissue resistivity in the CA1 region in vivo are layer-specific: modulation of evoked potentials. Neuroscience. 108 [PubMed]
McIntyre CC, Grill WM. (1999). Excitation of central nervous system neurons by nonuniform electric fields. Biophysical journal. 76 [PubMed]
McKinney W. (2010). Data structures for statistical computing in python Proceedings of the 9th Python in Science Conference.
Mcintyre C. (2009). Computational modeling of deep brain stimulation. Neuromodulation.
Michailidou I et al. (2015). Complement C1q-C3-associated synaptic changes in multiple sclerosis hippocampus. Annals of neurology. 77 [PubMed]
Newman MEJ, Gastner MT. (2006). Shape and efficiency in spatial distribution networks Journal of Statistical Mechanics. 2006
Nowak LG, Bullier J. (1996). Spread of stimulating current in the cortical grey matter of rat visual cortex studied on a new in vitro slice preparation. Journal of neuroscience methods. 67 [PubMed]
Nowak LG, Bullier J. (1998). Axons, but not cell bodies, are activated by electrical stimulation in cortical gray matter. I. Evidence from chronaxie measurements. Experimental brain research. 118 [PubMed]
Patton PE, McNaughton B. (1995). Connection matrix of the hippocampal formation: I. The dentate gyrus. Hippocampus. 5 [PubMed]
Quilichini P, Sirota A, Buzsáki G. (2010). Intrinsic circuit organization and theta-gamma oscillation dynamics in the entorhinal cortex of the rat. The Journal of neuroscience : the official journal of the Society for Neuroscience. 30 [PubMed]
Ramachandran P. (2001). MayaVi: a free tool for CFD data visualization Proceedings Of The 4Th Annual CFD Symposium, Aeronautical Society Of India.
Ranck JB. (1975). Which elements are excited in electrical stimulation of mammalian central nervous system: a review. Brain research. 98 [PubMed]
Rattay F, Paredes LP, Leao RN. (2012). Strength-duration relationship for intra- versus extracellular stimulation with microelectrodes. Neuroscience. 214 [PubMed]
Rozenberg G, Salomaa A. (1980). The Mathematical Theory of L Systems.
Saalfeld A. (1999). Topologically consistent line simplification with the DouglasPeucker algorithm Cartography and Geographic Information Science. 26
Schwartz SP, Coleman PD. (1981). Neurons of origin of the perforant path. Experimental neurology. 74 [PubMed]
Scorcioni R, Ascoli G. (2005). Algorithmic reconstruction of complete axonal arborizations in rat hippocampal neurons. Neurocomputing. 65
Scorcioni R, Polavaram S, Ascoli GA. (2008). L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nature protocols. 3 [PubMed]
Song D et al. (2018). Developing a hippocampal neural prosthetic to facilitate human memory encoding and recall J. Neural Eng. 15
Tamamaki N, Nojyo Y. (1993). Projection of the entorhinal layer II neurons in the rat as revealed by intracellular pressure-injection of neurobiotin. Hippocampus. 3 [PubMed]
Türetken E, González G, Blum C, Fua P. (2011). Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors. Neuroinformatics. 9 [PubMed]
Whittington MA, Stanford IM, Colling SB, Jefferys JG, Traub RD. (1997). Spatiotemporal patterns of gamma frequency oscillations tetanically induced in the rat hippocampal slice. The Journal of physiology. 502 ( Pt 3) [PubMed]
Witter M, Kjonigsen L, Leergaard T, Kjode J, Bjaalie J. (2008). Interactive histological atlas system for anatomical parcellation of the rat hippocampus proper, fasciola and associated parahippocampal cortex Frontiers in Neuroinformatics . 2
Witter MP. (2007). The perforant path: projections from the entorhinal cortex to the dentate gyrus. Progress in brain research. 163 [PubMed]
Wu B, Tang C, Chao K-M. (2000). Approximation algorithms for some optimum communication spanning tree problems. Discrete Appl. Math. 102