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van Ooyen A, Carnell A, de Ridder S, Tarigan B, Mansvelder HD, Bijma F, de Gunst M, van Pelt (2014) Independently outgrowing neurons and geometry-based synapse formation produce networks with realistic synaptic connectivity. PLoS One 9:e85858[PubMed]

   NETMORPH: creates NNs with realistic neuron morphologies (Koene et al. 2009, van Ooyen et al. 2014)

References and models cited by this paper

References and models that cite this paper

Amirikian B (2005) A phenomenological theory of spatially structured local synaptic connectivity. PLoS Comput Biol 1:e11 [PubMed]

Arendt T, Schindler C, Bruckner MK, Eschrich K, Bigl V, Zedlick D, Marcova L (1997) Plastic neuronal remodeling is impaired in patients with Alzheimer's disease carrying apolipoprotein epsilon 4 allele. J Neurosci 17:516-29 [PubMed]

Ascoli GA (2006) Mobilizing the base of neuroscience data: the case of neuronal morphologies. Nat Rev Neurosci 7:318-24 [PubMed]

Barabási AL (2009) Scale-free networks: a decade and beyond. Science 325:412-3 [PubMed]

Bassett DS, Bullmore E (2006) Small-world brain networks. Neuroscientist 12:512-23 [PubMed]

Benson DL, Colman DR, Huntley GW (2001) Molecules, maps and synapse specificity. Nat Rev Neurosci 2:899-909 [PubMed]

Bettencourt LM, Stephens GJ, Ham MI, Gross GW (2007) Functional structure of cortical neuronal networks grown in vitro. Phys Rev E Stat Nonlin Soft Matter Phys 75:021915-34 [PubMed]

Bullmore E, Sporns O (2009) Complex brain networks: graph theoretical analysis of structural and functional systems. Nat Rev Neurosci 10:186-98 [PubMed]

Chen W, Maex R, Adams R, Steuber V, Calcraft L, Davey N (2011) Clustering predicts memory performance in networks of spiking and non-spiking neurons. Front Comput Neurosci 5:14 [PubMed]

Chklovskii DB, Mel BW, Svoboda K (2004) Cortical rewiring and information storage. Nature 431:782-8 [PubMed]

Cline HT (2001) Dendritic arbor development and synaptogenesis. Curr Opin Neurobiol 11:118-26 [PubMed]

Cook SC, Wellman CL (2004) Chronic stress alters dendritic morphology in rat medial prefrontal cortex. J Neurobiol 60:236-48 [PubMed]

Costa Lda F, Manoel ET, Faucereau F, Chelly J, van Pelt J, Ramakers G (2002) A shape analysis framework for neuromorphometry. Network 13:283-310 [PubMed]

Courchesne E, Redcay E, Morgan JT, Kennedy DP (2005) Autism at the beginning: microstructural and growth abnormalities underlying the cognitive and behavioral phenotype of autism. Dev Psychopathol 17:577-97 [PubMed]

Cullen TJ, Walker MA, Eastwood SL, Esiri MM, Harrison PJ, Crow TJ (2006) Anomalies of asymmetry of pyramidal cell density and structure in dorsolateral prefrontal cortex in schizophrenia. Br J Psychiatry 188:26-31 [PubMed]

da Silva S, Wang F (2011) Retrograde neural circuit specification by target-derived neurotrophins and growth factors. Curr Opin Neurobiol 21:61-7 [PubMed]

Feldmeyer D, bke J, Silver RA, Sakmann B (2002) Synaptic connections between layer 4 spiny neurone-layer 2-3 pyramidal cell pairs in juvenile rat barrel cortex: physiology and anatomy of interlaminar signalling within a cortical column. J Physiol 538:803-22 [PubMed]

Gaiteri C, Rubin JE (2011) The interaction of intrinsic dynamics and network topology in determining network burst synchrony. Front Comput Neurosci 5:10 [PubMed]

Gerhard F, Pipa G, Lima B, Neuenschwander S, Gerstner W (2011) Extraction of Network Topology From Multi-Electrode Recordings: Is there a Small-World Effect? Front Comput Neurosci 5:4-25 [PubMed]

He Y, Chen ZJ, Evans AC (2007) Small-world anatomical networks in the human brain revealed by cortical thickness from MRI. Cereb Cortex 17:2407-19 [PubMed]

Hellwig B (2000) A quantitative analysis of the local connectivity between pyramidal neurons in layers 2-3 of the rat visual cortex. Biol Cybern 82:111-21 [PubMed]

Hill SL, Wang Y, Riachi I, Schurmann F, Markram H (2012) Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proc Natl Acad Sci U S A 109:E2885-94 [PubMed]

Holmgren C, Harkany T, Svennenfors B, Zilberter Y (2003) Pyramidal cell communication within local networks in layer 2-3 of rat neocortex. J Physiol 551:139-53 [PubMed]

Isbister CM, O'Connor TP (1999) Filopodial adhesion does not predict growth cone steering events in vivo J Neurosci. 19(7):2589-600 [PubMed]

Kaiser M, Hilgetag CC, van Ooyen A (2009) A simple rule for axon outgrowth and synaptic competition generates realistic connection lengths and filling fractions. Cereb Cortex 19:3001-10 [PubMed]

Kaufmann WE, Moser HW (2000) Dendritic anomalies in disorders associated with mental retardation. Cereb Cortex 10:981-91 [PubMed]

Koene RA, Tijms B, van Hees P, Postma F, de Ridder A, Ramakers GJ, van Pelt J, van Ooyen A (2009) NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7:195-210 [Journal] [PubMed]

   NETMORPH: creates NNs with realistic neuron morphologies (Koene et al. 2009, van Ooyen et al. 2014) [Model]

Kvajo M, McKellar H, Arguello PA, Drew LJ, Moore H, MacDermott AB, Karayiorgou M, Gogos JA (2008) A mutation in mouse Disc1 that models a schizophrenia risk allele leads to specific alterations in neuronal architecture and cognition. Proc Natl Acad Sci U S A 105:7076-81 [PubMed]

Lago-Fernandez LF, Huerta R, Corbacho F, Siguenza JA (2000) Fast response and temporal coherent oscillations in small-world networks. Phys Rev Lett 84:2758-61 [PubMed]

Larkman AU (1991) Dendritic morphology of pyramidal neurones of the visual cortex of the rat: I. Branching patterns. J Comp Neurol 306:307-19 [PubMed]

Le Be JV, Silberberg G, Wang Y, Markram H (2007) Morphological, electrophysiological, and synaptic properties of corticocallosal pyramidal cells in the neonatal rat neocortex. Cereb Cortex 17:2204-13 [PubMed]

Liu Y, Liang M, Zhou Y, He Y, Hao Y, Song M, Yu C, Liu H, Liu Z, Jiang T (2008) Disrupted small-world networks in schizophrenia. Brain 131:945-61 [PubMed]

Lohmann H, Rörig B (1994) Long-range horizontal connections between supragranular pyramidal cells in the extrastriate visual cortex of the rat. J Comp Neurol 344:543-58 [PubMed]

Maass W, Natschlager T, Markram H (2002) Real-time computing without stable states: a new framework for neural computation based on perturbations. Neural Comput 14:2531-60 [PubMed]

Magarinos AM, McEwen BS, Flugge G, Fuchs E (1996) Chronic psychosocial stress causes apical dendritic atrophy of hippocampal CA3 pyramidal neurons in subordinate tree shrews. J Neurosci 16:3534-40 [PubMed]

Magee JC (2000) Dendritic integration of excitatory synaptic input. Nat Rev Neurosci 1:181-90 [PubMed]

Micheloyannis S, Pachou E, Stam CJ, Breakspear M, Bitsios P, Vourkas M, Erimaki S, Zervakis M (2006) Small-world networks and disturbed functional connectivity in schizophrenia. Schizophr Res 87:60-6 [PubMed]

Moolman DL, Vitolo OV, Vonsattel JP, Shelanski ML (2004) Dendrite and dendritic spine alterations in Alzheimer models. J Neurocytol 33:377-87 [PubMed]

Morelli LG, Abramson G, Kuperman MN (2004) Associative memory on a small-world neural network Eur Phys J 38:495-500

Neymotin SA, Jacobs KM, Fenton AA, Lytton WW (2011) Synaptic information transfer in computer models of neocortical columns. J Comput Neurosci. 30(1):69-84 [Journal] [PubMed]

   Synaptic information transfer in computer models of neocortical columns (Neymotin et al. 2010) [Model]

Nuñez JL, Kim BY, Juraska JM (1998) Neonatal cryoanesthesia affects the morphology of the visual cortex in the adult rat. Brain Res Dev Brain Res 111:89-98 [PubMed]

Perin R, Berger TK, Markram H (2011) A synaptic organizing principle for cortical neuronal groups. Proc Natl Acad Sci U S A 108:5419-24 [PubMed]

Pernice V, Staude B, Cardanobile S, Rotter S (2011) How structure determines correlations in neuronal networks. PLoS Comput Biol 7:e1002059 [PubMed]

Polinsky M, Balazovich K, Tosney KW (2000) Identification of an invariant response: stable contact with schwann cells induces veil extension in sensory growth cones. J Neurosci 20:1044-55 [PubMed]

Polleux F (2005) Genetic mechanisms specifying cortical connectivity: let's make some projections together. Neuron 46:395-400 [PubMed]

Radley JJ, Sisti HM, Hao J, Rocher AB, McCall T, Hof PR, McEwen BS, Morrison JH (2004) Chronic behavioral stress induces apical dendritic reorganization in pyramidal neurons of the medial prefrontal cortex. Neuroscience 125:1-6 [PubMed]

Roxin A (2011) The role of degree distribution in shaping the dynamics in networks of sparsely connected spiking neurons. Front Comput Neurosci 5:8 [PubMed]

Shepherd GM, Svoboda K (2005) Laminar and columnar organization of ascending excitatory projections to layer 2-3 pyramidal neurons in rat barrel cortex. J Neurosci 25:5670-9 [PubMed]

Song S, Sjostrom PJ, Reigl M, Nelson S, Chklovskii DB (2005) Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol 3:e68-88 [PubMed]

Sousa N, Lukoyanov NV, Madeira MD, Almeida OF, Paula-Barbosa MM (2000) Reorganization of the morphology of hippocampal neurites and synapses after stress-induced damage correlates with behavioral improvement. Neuroscience 97:253-66 [PubMed]

Sporns O, Chialvo DR, Kaiser M, Hilgetag CC (2004) Organization, development and function of complex brain networks. Trends Cogn Sci 8:418-25 [PubMed]

Sporns O, Tononi G, Edelman GM (2000) Theoretical neuroanatomy: relating anatomical and functional connectivity in graphs and cortical connection matrices. Cereb Cortex 10:127-41 [PubMed]

Sporns O, Zwi JD (2004) The small world of the cerebral cortex. Neuroinformatics 2:145-62 [PubMed]

Stam CJ, Reijneveld JC (2007) Graph theoretical analysis of complex networks in the brain. Nonlinear Biomed Phys 1:3 [PubMed]

Stepanyants A, Chklovskii DB (2005) Neurogeometry and potential synaptic connectivity. Trends Neurosci 28:387-94 [PubMed]

Stepanyants A, Tamás G, Chklovskii DB (2004) Class-specific features of neuronal wiring. Neuron 43:251-9 [PubMed]

Supekar K, Menon V, Rubin D, Musen M, Greicius MD (2008) Network analysis of intrinsic functional brain connectivity in Alzheimer's disease. PLoS Comput Biol 4:e1000100 [PubMed]

Takahashi N, Sasaki T, Matsumoto W, Matsuki N, Ikegaya Y (2010) Circuit topology for synchronizing neurons in spontaneously active networks. Proc Natl Acad Sci U S A 107:10244-9 [PubMed]

Tessier-Lavigne M (1994) Axon guidance by diffusible repellants and attractants. Curr Opin Genet Dev 4:596-601 [PubMed]

Tigerholm J, Migliore M, Fransén E (2013) Integration of synchronous synaptic input in CA1 pyramidal neuron depends on spatial and temporal distributions of the input. Hippocampus 23:87-99 [PubMed]

Uylings HB, van Pelt J, Parnavelas JG, Ruiz-Marcos A (1994) Geometrical and topological characteristics in the dendritic development of cortical pyramidal and non-pyramidal neurons. Prog Brain Res 102:109-23

van den Heuvel MP, Sporns O (2011) Rich-club organization of the human connectome. J Neurosci 31:15775-86 [PubMed]

van Pelt J, Carnell A, de Ridder S, Mansvelder HD, van Ooyen A (2010) An algorithm for finding candidate synaptic sites in computer generated networks of neurons with realistic morphologies. Front Comput Neurosci 4:148 [PubMed]

Van Pelt J, Van Ooyen A, Uylings HB (2001) Modeling dendritic geometry and the development of nerve connections. Computational Neuroscience, Realistic Modeling for Experimentalists, E De Schutter, ed. pp.179

van Pelt J, van Ooyen A, Uylings HB (2001) The need for integrating neuronal morphology databases and computational environments in exploring neuronal structure and function. Anat Embryol (Berl) 204:255-65 [PubMed]

Voges N, Perrinet L (2012) Complex dynamics in recurrent cortical networks based on spatially realistic connectivities. Front Comput Neurosci 6:41 [PubMed]

Watts DJ, Strogatz SH (1998) Collective dynamics of 'small-world' networks. Nature 393:440-2 [PubMed]

Yamada M, Wada Y, Tsukagoshi H, Otomo E, Hayakawa M (1988) A quantitative Golgi study of basal dendrites of hippocampal CA1 pyramidal cells in senile dementia of Alzheimer type. J Neurol Neurosurg Psychiatry 51:1088-90 [PubMed]

Yu S, Huang D, Singer W, Nikolic D (2008) A small world of neuronal synchrony. Cereb Cortex 18:2891-901 [PubMed]

Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H (2015) An algorithm to predict the connectome of neural microcircuits. Front Comput Neurosci 9:120 [Journal] [PubMed]

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