Ali AB, Bannister AP, Thomson AM. (2007). Robust correlations between action potential duration and the properties of synaptic connections in layer 4 interneurones in neocortical slices from juvenile rats and adult rat and cat. The Journal of physiology. 580 [PubMed]
Amitai Y. (2001). Thalamocortical synaptic connections: efficacy, modulation, inhibition and plasticity. Reviews in the neurosciences. 12 [PubMed]
Amzica F, Massimini M, Manfridi A. (2002). Spatial buffering during slow and paroxysmal sleep oscillations in cortical networks of glial cells in vivo. The Journal of neuroscience : the official journal of the Society for Neuroscience. 22 [PubMed]
Angulo MC, Rossier J, Audinat E. (1999). Postsynaptic glutamate receptors and integrative properties of fast-spiking interneurons in the rat neocortex. Journal of neurophysiology. 82 [PubMed]
Bannister AP, Thomson AM. (2007). Dynamic properties of excitatory synaptic connections involving layer 4 pyramidal cells in adult rat and cat neocortex. Cerebral cortex (New York, N.Y. : 1991). 17 [PubMed]
Beaulieu C. (1993). Numerical data on neocortical neurons in adult rat, with special reference to the GABA population. Brain research. 609 [PubMed]
Beaulieu C, Colonnier M. (1983). The number of neurons in the different laminae of the binocular and monocular regions of area 17 in the cat, Canada. The Journal of comparative neurology. 217 [PubMed]
Beggs JM, Plenz D. (2003). Neuronal avalanches in neocortical circuits. The Journal of neuroscience : the official journal of the Society for Neuroscience. 23 [PubMed]
Beierlein M, Connors BW. (2002). Short-term dynamics of thalamocortical and intracortical synapses onto layer 6 neurons in neocortex. Journal of neurophysiology. 88 [PubMed]
Beierlein M, Fall CP, Rinzel J, Yuste R. (2002). Thalamocortical bursts trigger recurrent activity in neocortical networks: layer 4 as a frequency-dependent gate. The Journal of neuroscience : the official journal of the Society for Neuroscience. 22 [PubMed]
Beierlein M, Gibson JR, Connors BW. (2000). A network of electrically coupled interneurons drives synchronized inhibition in neocortex. Nature neuroscience. 3 [PubMed]
Beierlein M, Gibson JR, Connors BW. (2003). Two dynamically distinct inhibitory networks in layer 4 of the neocortex. Journal of neurophysiology. 90 [PubMed]
Berger T, Larkum ME, Lüscher HR. (2001). High I(h) channel density in the distal apical dendrite of layer V pyramidal cells increases bidirectional attenuation of EPSPs. Journal of neurophysiology. 85 [PubMed]
Blatow M et al. (2003). A novel network of multipolar bursting interneurons generates theta frequency oscillations in neocortex. Neuron. 38 [PubMed]
Borst JG. (2010). The low synaptic release probability in vivo. Trends in neurosciences. 33 [PubMed]
Boyd J, Matsubara J. (1991). Intrinsic connections in cat visual cortex: a combined anterograde and retrograde tracing study. Brain research. 560 [PubMed]
Brunel N. (2000). Dynamics of sparsely connected networks of excitatory and inhibitory spiking neurons. Journal of computational neuroscience. 8 [PubMed]
Bruno RM, Sakmann B. (2006). Cortex is driven by weak but synchronously active thalamocortical synapses. Science (New York, N.Y.). 312 [PubMed]
Burkhalter A, Gonchar Y, Wang Q. (2008). Multiple distinct subtypes of GABAergic neurons in mouse visual cortex identified by triple immunostaining. Front Neuroanat. 1
Callaway EM. (2008). Transneuronal circuit tracing with neurotropic viruses. Current opinion in neurobiology. 18 [PubMed]
Cauli B et al. (1997). Molecular and physiological diversity of cortical nonpyramidal cells. The Journal of neuroscience : the official journal of the Society for Neuroscience. 17 [PubMed]
Cauli B et al. (2000). Classification of fusiform neocortical interneurons based on unsupervised clustering. Proceedings of the National Academy of Sciences of the United States of America. 97 [PubMed]
Celikel T, Szostak VA, Feldman DE. (2004). Modulation of spike timing by sensory deprivation during induction of cortical map plasticity. Nature neuroscience. 7 [PubMed]
Celio MR. (1986). Parvalbumin in most gamma-aminobutyric acid-containing neurons of the rat cerebral cortex. Science (New York, N.Y.). 231 [PubMed]
Chen N, Sugihara H, Sur M. (2015). An acetylcholine-activated microcircuit drives temporal dynamics of cortical activity. Nature neuroscience. 18 [PubMed]
Cobb SR et al. (1997). Synaptic effects of identified interneurons innervating both interneurons and pyramidal cells in the rat hippocampus. Neuroscience. 79 [PubMed]
Condé F, Lund JS, Jacobowitz DM, Baimbridge KG, Lewis DA. (1994). Local circuit neurons immunoreactive for calretinin, calbindin D-28k or parvalbumin in monkey prefrontal cortex: distribution and morphology. The Journal of comparative neurology. 341 [PubMed]
Connors BW, Gutnick MJ. (1990). Intrinsic firing patterns of diverse neocortical neurons. Trends in neurosciences. 13 [PubMed]
Constantinople CM, Bruno RM. (2011). Effects and mechanisms of wakefulness on local cortical networks. Neuron. 69 [PubMed]
Constantinople CM, Bruno RM. (2013). Deep cortical layers are activated directly by thalamus. Science (New York, N.Y.). 340 [PubMed]
Cragg BG. (1967). The density of synapses and neurones in the motor and visual areas of the cerebral cortex. Journal of anatomy. 101 [PubMed]
Crick FH. (1979). Thinking about the brain. Scientific American. 241 [PubMed]
Cunningham MO et al. (2004). A role for fast rhythmic bursting neurons in cortical gamma oscillations in vitro. Proceedings of the National Academy of Sciences of the United States of America. 101 [PubMed]
Datwani A, Iwasato T, Itohara S, Erzurumlu RS. (2002). NMDA receptor-dependent pattern transfer from afferents to postsynaptic cells and dendritic differentiation in the barrel cortex. Molecular and cellular neurosciences. 21 [PubMed]
De Koninck Y, Mody I. (1997). Endogenous GABA activates small-conductance K+ channels underlying slow IPSCs in rat hippocampal neurons. Journal of neurophysiology. 77 [PubMed]
DeFelipe J. (1993). Neocortical neuronal diversity: chemical heterogeneity revealed by colocalization studies of classic neurotransmitters, neuropeptides, calcium-binding proteins, and cell surface molecules. Cerebral cortex (New York, N.Y. : 1991). 3 [PubMed]
DeFelipe J, Alonso-Nanclares L, Arellano JI. (2002). Microstructure of the neocortex: comparative aspects. Journal of neurocytology. 31 [PubMed]
DeFelipe J et al. (2013). New insights into the classification and nomenclature of cortical GABAergic interneurons. Nature reviews. Neuroscience. 14 [PubMed]
Delattre V, Keller D, Perich M, Markram H, Muller EB. (2015). Network-timing-dependent plasticity. Frontiers in cellular neuroscience. 9 [PubMed]
Denk W, Horstmann H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS biology. 2 [PubMed]
Douglas RJ, Martin KA. (2004). Neuronal circuits of the neocortex. Annual review of neuroscience. 27 [PubMed]
Druckmann S et al. (2007). A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data. Frontiers in neuroscience. 1 [PubMed]
Druckmann S et al. (2011). Effective stimuli for constructing reliable neuron models. PLoS computational biology. 7 [PubMed]
Druckmann S, Hill S, Schürmann F, Markram H, Segev I. (2013). A hierarchical structure of cortical interneuron electrical diversity revealed by automated statistical analysis. Cerebral cortex (New York, N.Y. : 1991). 23 [PubMed]
Dumitriu D, Cossart R, Huang J, Yuste R. (2007). Correlation between axonal morphologies and synaptic input kinetics of interneurons from mouse visual cortex. Cerebral cortex (New York, N.Y. : 1991). 17 [PubMed]
Fairen A, Defelipe J, Redidor J. (1984). Nonpyramidal neurons: General account Cerebral cortex: Cellular components of the cerebral cortex.
Feldmeyer D, Egger V, Lubke J, Sakmann B. (1999). Reliable synaptic connections between pairs of excitatory layer 4 neurones within a single 'barrel' of developing rat somatosensory cortex. The Journal of physiology. 521 Pt 1 [PubMed]
Feldmeyer D, Lübke J, Sakmann B. (2006). Efficacy and connectivity of intracolumnar pairs of layer 2/3 pyramidal cells in the barrel cortex of juvenile rats. The Journal of physiology. 575 [PubMed]
Feldmeyer D, Lübke 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. The Journal of physiology. 538 [PubMed]
Frick A, Feldmeyer D, Helmstaedter M, Sakmann B. (2008). Monosynaptic connections between pairs of L5A pyramidal neurons in columns of juvenile rat somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 18 [PubMed]
Frick A, Feldmeyer D, Sakmann B. (2007). Postnatal development of synaptic transmission in local networks of L5A pyramidal neurons in rat somatosensory cortex. The Journal of physiology. 585 [PubMed]
Fuhrmann G, Segev I, Markram H, Tsodyks M. (2002). Coding of temporal information by activity-dependent synapses. Journal of neurophysiology. 87 [PubMed]
Gentet LJ, Avermann M, Matyas F, Staiger JF, Petersen CC. (2010). Membrane potential dynamics of GABAergic neurons in the barrel cortex of behaving mice. Neuron. 65 [PubMed]
Gentet LJ et al. (2012). Unique functional properties of somatostatin-expressing GABAergic neurons in mouse barrel cortex. Nature neuroscience. 15 [PubMed]
Ghosh A, Shatz CJ. (1993). A role for subplate neurons in the patterning of connections from thalamus to neocortex. Development (Cambridge, England). 117 [PubMed]
Gil Z, Connors BW, Amitai Y. (1999). Efficacy of thalamocortical and intracortical synaptic connections: quanta, innervation, and reliability. Neuron. 23 [PubMed]
Glenn LL, Hada J, Roy JP, Deschênes M, Steriade M. (1982). Anterograde tracer and field potential analysis of the neocortical layer I projection from nucleus ventralis medialis of the thalamus in cat. Neuroscience. 7 [PubMed]
Gonchar Y, Burkhalter A. (1997). Three distinct families of GABAergic neurons in rat visual cortex. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Grange P et al. (2014). Cell-type-based model explaining coexpression patterns of genes in the brain. Proceedings of the National Academy of Sciences of the United States of America. 111 [PubMed]
Gupta A, Wang Y, Markram H. (2000). Organizing principles for a diversity of GABAergic interneurons and synapses in the neocortex. Science (New York, N.Y.). 287 [PubMed]
Haider B, Duque A, Hasenstaub AR, McCormick DA. (2006). Neocortical network activity in vivo is generated through a dynamic balance of excitation and inhibition. The Journal of neuroscience : the official journal of the Society for Neuroscience. 26 [PubMed]
Hallman LE, Schofield BR, Lin CS. (1988). Dendritic morphology and axon collaterals of corticotectal, corticopontine, and callosal neurons in layer V of primary visual cortex of the hooded rat. The Journal of comparative neurology. 272 [PubMed]
Harris KD, Shepherd GM. (2015). The neocortical circuit: themes and variations. Nature neuroscience. 18 [PubMed]
Hasenstaub A et al. (2005). Inhibitory postsynaptic potentials carry synchronized frequency information in active cortical networks. Neuron. 47 [PubMed]
Hay E, Hill S, Schürmann F, Markram H, Segev I. (2011). Models of neocortical layer 5b pyramidal cells capturing a wide range of dendritic and perisomatic active properties. PLoS computational biology. 7 [PubMed]
Heinemann U, Lux HD, Gutnick MJ. (1977). Extracellular free calcium and potassium during paroxsmal activity in the cerebral cortex of the cat. Experimental brain research. 27 [PubMed]
Hendry SH, Jones EG, Emson PC. (1984). Morphology, distribution, and synaptic relations of somatostatin- and neuropeptide Y-immunoreactive neurons in rat and monkey neocortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 4 [PubMed]
Hendry SH et al. (1989). Two classes of cortical GABA neurons defined by differential calcium binding protein immunoreactivities. Experimental brain research. 76 [PubMed]
Hestrin S, Armstrong WE. (1996). Morphology and physiology of cortical neurons in layer I. The Journal of neuroscience : the official journal of the Society for Neuroscience. 16 [PubMed]
Hevner RF et al. (2001). Tbr1 regulates differentiation of the preplate and layer 6. Neuron. 29 [PubMed]
Hill SL, Wang Y, Riachi I, Schürmann F, Markram H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proceedings of the National Academy of Sciences of the United States of America. 109 [PubMed]
Hines M, Kumar S, Schürmann F. (2011). Comparison of neuronal spike exchange methods on a Blue Gene/P supercomputer. Frontiers in computational neuroscience. 5 [PubMed]
Hines ML, Carnevale NT. (1997). The NEURON simulation environment. Neural computation. 9 [PubMed]
Hines ML, Carnevale NT. (2006). The NEURON Book.
Hines ML, Eichner H, Schürmann F. (2008). Neuron splitting in compute-bound parallel network simulations enables runtime scaling with twice as many processors. Journal of computational neuroscience. 25 [PubMed]
Hines ML, Markram H, Schürmann F. (2008). Fully implicit parallel simulation of single neurons. Journal of computational neuroscience. 25 [PubMed]
Holmgren C, Harkany T, Svennenfors B, Zilberter Y. (2003). Pyramidal cell communication within local networks in layer 2/3 of rat neocortex. The Journal of physiology. 551 [PubMed]
Honey CJ, Kötter R, Breakspear M, Sporns O. (2007). Network structure of cerebral cortex shapes functional connectivity on multiple time scales. Proceedings of the National Academy of Sciences of the United States of America. 104 [PubMed]
Horton JC, Adams DL. (2005). The cortical column: a structure without a function. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 360 [PubMed]
Hughes SW, Cope DW, Blethyn KL, Crunelli V. (2002). Cellular mechanisms of the slow (<1 Hz) oscillation in thalamocortical neurons in vitro. Neuron. 33 [PubMed]
Häusser M, Roth A. (1997). Estimating the time course of the excitatory synaptic conductance in neocortical pyramidal cells using a novel voltage jump method. The Journal of neuroscience : the official journal of the Society for Neuroscience. 17 [PubMed]
Jones E, Defelipe J. (1988). Cajal on the cerebral cortex: an Annotated Translation of the Complete Writings.
Jones HC, Keep RF. (1988). Brain fluid calcium concentration and response to acute hypercalcaemia during development in the rat. The Journal of physiology. 402 [PubMed]
Kapfer C, Glickfeld LL, Atallah BV, Scanziani M. (2007). Supralinear increase of recurrent inhibition during sparse activity in the somatosensory cortex. Nature neuroscience. 10 [PubMed]
Karagiannis A et al. (2009). Classification of NPY-expressing neocortical interneurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 29 [PubMed]
Karube F, Kubota Y, Kawaguchi Y. (2004). Axon branching and synaptic bouton phenotypes in GABAergic nonpyramidal cell subtypes. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24 [PubMed]
Kasper EM, Larkman AU, Lübke J, Blakemore C. (1994). Pyramidal neurons in layer 5 of the rat visual cortex. II. Development of electrophysiological properties. The Journal of comparative neurology. 339 [PubMed]
Kasthuri N et al. (2015). Saturated Reconstruction of a Volume of Neocortex. Cell. 162 [PubMed]
Kawaguchi Y, Karube F, Kubota Y. (2006). Dendritic branch typing and spine expression patterns in cortical nonpyramidal cells. Cerebral cortex (New York, N.Y. : 1991). 16 [PubMed]
Kawaguchi Y, Kondo S. (2002). Parvalbumin, somatostatin and cholecystokinin as chemical markers for specific GABAergic interneuron types in the rat frontal cortex. Journal of neurocytology. 31 [PubMed]
Kawaguchi Y, Kubota Y. (1993). Correlation of physiological subgroupings of nonpyramidal cells with parvalbumin- and calbindinD28k-immunoreactive neurons in layer V of rat frontal cortex. Journal of neurophysiology. 70 [PubMed]
Kawaguchi Y, Kubota Y. (1997). GABAergic cell subtypes and their synaptic connections in rat frontal cortex. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Keller A, Carlson GC. (1999). Neonatal whisker clipping alters intracortical, but not thalamocortical projections, in rat barrel cortex. The Journal of comparative neurology. 412 [PubMed]
Khazen G, Hill SL, Schürmann F, Markram H. (2012). Combinatorial expression rules of ion channel genes in juvenile rat (Rattus norvegicus) neocortical neurons. PloS one. 7 [PubMed]
Khazipov R, Congar P, Ben-Ari Y. (1995). Hippocampal CA1 lacunosum-moleculare interneurons: modulation of monosynaptic GABAergic IPSCs by presynaptic GABAB receptors. Journal of neurophysiology. 74 [PubMed]
Killackey HP, Gould HJ, Cusick CG, Pons TP, Kaas JH. (1983). The relation of corpus callosum connections to architectonic fields and body surface maps in sensorimotor cortex of new and old world monkeys. The Journal of comparative neurology. 219 [PubMed]
Kisvárday ZF, Martin KA, Whitteridge D, Somogyi P. (1985). Synaptic connections of intracellularly filled clutch cells: a type of small basket cell in the visual cortex of the cat. The Journal of comparative neurology. 241 [PubMed]
Klausberger T et al. (2003). Brain-state- and cell-type-specific firing of hippocampal interneurons in vivo. Nature. 421 [PubMed]
Krimer LS et al. (2005). Cluster analysis-based physiological classification and morphological properties of inhibitory neurons in layers 2-3 of monkey dorsolateral prefrontal cortex. Journal of neurophysiology. 94 [PubMed]
Larkman AU. (1991). Dendritic morphology of pyramidal neurones of the visual cortex of the rat: III. Spine distributions. The Journal of comparative neurology. 306 [PubMed]
Larkman AU. (1991). Dendritic morphology of pyramidal neurones of the visual cortex of the rat: I. Branching patterns. The Journal of comparative neurology. 306 [PubMed]
Larkum ME, Zhu JJ, Sakmann B. (2001). Dendritic mechanisms underlying the coupling of the dendritic with the axonal action potential initiation zone of adult rat layer 5 pyramidal neurons. The Journal of physiology. 533 [PubMed]
Le Bé JV, Silberberg G, Wang Y, Markram H. (2007). Morphological, electrophysiological, and synaptic properties of corticocallosal pyramidal cells in the neonatal rat neocortex. Cerebral cortex (New York, N.Y. : 1991). 17 [PubMed]
Lee SH, Dan Y. (2012). Neuromodulation of brain states. Neuron. 76 [PubMed]
Lefort S, Tomm C, Floyd Sarria JC, Petersen CC. (2009). The excitatory neuronal network of the C2 barrel column in mouse primary somatosensory cortex. Neuron. 61 [PubMed]
Leinekugel X et al. (2002). Correlated bursts of activity in the neonatal hippocampus in vivo. Science (New York, N.Y.). 296 [PubMed]
Ling DS, Benardo LS. (1999). Restrictions on inhibitory circuits contribute to limited recruitment of fast inhibition in rat neocortical pyramidal cells. Journal of neurophysiology. 82 [PubMed]
Livingstone MS. (1996). Oscillatory firing and interneuronal correlations in squirrel monkey striate cortex. Journal of neurophysiology. 75 [PubMed]
Luczak A, Barthó P, Marguet SL, Buzsáki G, Harris KD. (2007). Sequential structure of neocortical spontaneous activity in vivo. Proceedings of the National Academy of Sciences of the United States of America. 104 [PubMed]
Lőrincz ML et al. (2015). A distinct class of slow (~0.2-2 Hz) intrinsically bursting layer 5 pyramidal neurons determines UP/DOWN state dynamics in the neocortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35 [PubMed]
Maffei A, Nelson SB, Turrigiano GG. (2004). Selective reconfiguration of layer 4 visual cortical circuitry by visual deprivation. Nature neuroscience. 7 [PubMed]
Mao BQ, Hamzei-Sichani F, Aronov D, Froemke RC, Yuste R. (2001). Dynamics of spontaneous activity in neocortical slices. Neuron. 32 [PubMed]
Markram H. (2008). Fixing the location and dimensions of functional neocortical columns. HFSP journal. 2 [PubMed]
Markram H, Lübke J, Frotscher M, Roth A, Sakmann B. (1997). Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. The Journal of physiology. 500 ( Pt 2) [PubMed]
Markram H, Schurmann F, Hill S, Anwar H, Riachi I. (2009). An approach to capturing neuron morphological diversity Computational Modeling Methods for Neuroscientists.
Markram H et al. (2004). Interneurons of the neocortical inhibitory system. Nature reviews. Neuroscience. 5 [PubMed]
Markram H, Wang Y, Tsodyks M. (1998). Differential signaling via the same axon of neocortical pyramidal neurons. Proceedings of the National Academy of Sciences of the United States of America. 95 [PubMed]
Mason A, Nicoll A, Stratford K. (1991). Synaptic transmission between individual pyramidal neurons of the rat visual cortex in vitro. The Journal of neuroscience : the official journal of the Society for Neuroscience. 11 [PubMed]
Massimini M, Amzica F. (2001). Extracellular calcium fluctuations and intracellular potentials in the cortex during the slow sleep oscillation. Journal of neurophysiology. 85 [PubMed]
Mazurek ME, Shadlen MN. (2002). Limits to the temporal fidelity of cortical spike rate signals. Nature neuroscience. 5 [PubMed]
McCormick DA, Connors BW, Lighthall JW, Prince DA. (1985). Comparative electrophysiology of pyramidal and sparsely spiny stellate neurons of the neocortex. Journal of neurophysiology. 54 [PubMed]
McCormick DA et al. (2003). Persistent cortical activity: mechanisms of generation and effects on neuronal excitability. Cerebral cortex (New York, N.Y. : 1991). 13 [PubMed]
McGarry LM et al. (2010). Quantitative classification of somatostatin-positive neocortical interneurons identifies three interneuron subtypes. Frontiers in neural circuits. 4 [PubMed]
Mercer A et al. (2005). Excitatory connections made by presynaptic cortico-cortical pyramidal cells in layer 6 of the neocortex. Cerebral cortex (New York, N.Y. : 1991). 15 [PubMed]
Meyer AH, Katona I, Blatow M, Rozov A, Monyer H. (2002). In vivo labeling of parvalbumin-positive interneurons and analysis of electrical coupling in identified neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 22 [PubMed]
Meyer HS et al. (2011). Inhibitory interneurons in a cortical column form hot zones of inhibition in layers 2 and 5A. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Meyer HS et al. (2010). Cell type-specific thalamic innervation in a column of rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 20 [PubMed]
Meyer HS et al. (2010). Number and laminar distribution of neurons in a thalamocortical projection column of rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 20 [PubMed]
Micheva KD, Busse B, Weiler NC, O'Rourke N, Smith SJ. (2010). Single-synapse analysis of a diverse synapse population: proteomic imaging methods and markers. Neuron. 68 [PubMed]
Micheva KD, Smith SJ. (2007). Array tomography: a new tool for imaging the molecular architecture and ultrastructure of neural circuits. Neuron. 55 [PubMed]
Migliore M, Cannia C, Lytton WW, Markram H, Hines ML. (2006). Parallel network simulations with NEURON. Journal of computational neuroscience. 21 [PubMed]
Mott DD, Li Q, Okazaki MM, Turner DA, Lewis DV. (1999). GABAB-Receptor-mediated currents in interneurons of the dentate-hilus border. Journal of neurophysiology. 82 [PubMed]
Nelson S. (2002). Cortical microcircuits: diverse or canonical? Neuron. 36 [PubMed]
Nevian T, Larkum ME, Polsky A, Schiller J. (2007). Properties of basal dendrites of layer 5 pyramidal neurons: a direct patch-clamp recording study. Nature neuroscience. 10 [PubMed]
O'Connor DH, Huber D, Svoboda K. (2009). Reverse engineering the mouse brain. Nature. 461 [PubMed]
Oberlaender M et al. (2012). Cell type-specific three-dimensional structure of thalamocortical circuits in a column of rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 22 [PubMed]
Ohana O, Sakmann B. (1998). Transmitter release modulation in nerve terminals of rat neocortical pyramidal cells by intracellular calcium buffers. The Journal of physiology. 513 ( Pt 1) [PubMed]
Okun M, Lampl I. (2008). Instantaneous correlation of excitation and inhibition during ongoing and sensory-evoked activities. Nature neuroscience. 11 [PubMed]
Okun M et al. (2015). Diverse coupling of neurons to populations in sensory cortex. Nature. 521 [PubMed]
Oláh S et al. (2007). Output of neurogliaform cells to various neuron types in the human and rat cerebral cortex. Frontiers in neural circuits. 1 [PubMed]
Packer AM, Yuste R. (2011). Dense, unspecific connectivity of neocortical parvalbumin-positive interneurons: a canonical microcircuit for inhibition? The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]
Perin R, Berger TK, Markram H. (2011). A synaptic organizing principle for cortical neuronal groups. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Perrenoud Q, Rossier J, Geoffroy H, Vitalis T, Gallopin T. (2013). Diversity of GABAergic interneurons in layer VIa and VIb of mouse barrel cortex. Cerebral cortex (New York, N.Y. : 1991). 23 [PubMed]
Peters A. (1987). Number of neurons and synapses in primaryvisual cortex Cerebralcortex: Further Aspects Of Cortical Function, Including Hippocampus.
Peters A, Kaiserman-Abramof IR. (1970). The small pyramidal neuron of the rat cerebral cortex. The perikaryon, dendrites and spines. The American journal of anatomy. 127 [PubMed]
Petilla Interneuron Nomenclature Group et al. (2008). Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nature reviews. Neuroscience. 9 [PubMed]
Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]
Ramaswamy S et al. (2012). Intrinsic morphological diversity of thick-tufted layer 5 pyramidal neurons ensures robust and invariant properties of in silico synaptic connections. The Journal of physiology. 590 [PubMed]
Ramaswamy S, Markram H. (2015). Anatomy and physiology of the thick-tufted layer 5 pyramidal neuron. Frontiers in cellular neuroscience. 9 [PubMed]
Ramon y Cajal S. (1911). Histologie du Systeme Nerveux de lHomme et des Vertebrates. .
Ramon y cajal s . (1909). Histologie du systeme nerveux de l'homme et des vertebres.
Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H. (2015). An algorithm to predict the connectome of neural microcircuits. Frontiers in computational neuroscience. 9 [PubMed]
Renart A et al. (2010). The asynchronous state in cortical circuits. Science (New York, N.Y.). 327 [PubMed]
Reyes A et al. (1998). Target-cell-specific facilitation and depression in neocortical circuits. Nature neuroscience. 1 [PubMed]
Reyes A, Sakmann B. (1999). Developmental switch in the short-term modification of unitary EPSPs evoked in layer 2/3 and layer 5 pyramidal neurons of rat neocortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 19 [PubMed]
Reyes-Puerta V, Sun JJ, Kim S, Kilb W, Luhmann HJ. (2015). Laminar and Columnar Structure of Sensory-Evoked Multineuronal Spike Sequences in Adult Rat Barrel Cortex In Vivo. Cerebral cortex (New York, N.Y. : 1991). 25 [PubMed]
Rinaldi T, Silberberg G, Markram H. (2008). Hyperconnectivity of local neocortical microcircuitry induced by prenatal exposure to valproic acid. Cerebral cortex (New York, N.Y. : 1991). 18 [PubMed]
Romand S, Wang Y, Toledo-Rodriguez M, Markram H. (2011). Morphological development of thick-tufted layer v pyramidal cells in the rat somatosensory cortex. Frontiers in neuroanatomy. 5 [PubMed]
Rozov A, Burnashev N, Sakmann B, Neher E. (2001). Transmitter release modulation by intracellular Ca2+ buffers in facilitating and depressing nerve terminals of pyramidal cells in layer 2/3 of the rat neocortex indicates a target cell-specific difference in presynaptic calcium dynamics. The Journal of physiology. 531 [PubMed]
Rudy B, Fishell G, Lee S, Hjerling-Leffler J. (2011). Three groups of interneurons account for nearly 100% of neocortical GABAergic neurons. Developmental neurobiology. 71 [PubMed]
Sakata S, Harris KD. (2009). Laminar structure of spontaneous and sensory-evoked population activity in auditory cortex. Neuron. 64 [PubMed]
Salinas E, Sejnowski TJ. (2001). Correlated neuronal activity and the flow of neural information. Nature reviews. Neuroscience. 2 [PubMed]
Sancesario G, Pisani A, D'Angelo V, Calabresi P, Bernardi G. (1998). Morphological and functional study of dwarf neurons in the rat striatum. The European journal of neuroscience. 10 [PubMed]
Sanchez-Vives MV, McCormick DA. (2000). Cellular and network mechanisms of rhythmic recurrent activity in neocortex. Nature neuroscience. 3 [PubMed]
Santana R, McGarry LM, Bielza C, Larrañaga P, Yuste R. (2013). Classification of neocortical interneurons using affinity propagation. Frontiers in neural circuits. 7 [PubMed]
Sarid L, Bruno R, Sakmann B, Segev I, Feldmeyer D. (2007). Modeling a layer 4-to-layer 2/3 module of a single column in rat neocortex: interweaving in vitro and in vivo experimental observations. Proceedings of the National Academy of Sciences of the United States of America. 104 [PubMed]
Schroeder CE, Foxe JJ. (2002). The timing and laminar profile of converging inputs to multisensory areas of the macaque neocortex. Brain research. Cognitive brain research. 14 [PubMed]
Schurmann F et al. (2014). Rebasing I/O for Scientific Computing: Leveraging Storage Class Memory in an IBM BlueGene/Q Supercomputer .
Schurmann F, Hernando J, Pastor L. (2012). Towards real-time visualization of detailed neural tissue models: View frustum culling for parallel rendering BioVis.
Shu Y, Hasenstaub A, McCormick DA. (2003). Turning on and off recurrent balanced cortical activity. Nature. 423 [PubMed]
Sigalas C, Rigas P, Tsakanikas P, Skaliora I. (2015). High-Affinity Nicotinic Receptors Modulate Spontaneous Cortical Up States In Vitro. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35 [PubMed]
Silberberg G. (2008). Polysynaptic subcircuits in the neocortex: spatial and temporal diversity. Current opinion in neurobiology. 18 [PubMed]
Silberberg G, Markram H. (2007). Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron. 53 [PubMed]
Silberberg G, Wu C, Markram H. (2004). Synaptic dynamics control the timing of neuronal excitation in the activated neocortical microcircuit. The Journal of physiology. 556 [PubMed]
Silva LR, Amitai Y, Connors BW. (1991). Intrinsic oscillations of neocortex generated by layer 5 pyramidal neurons. Science (New York, N.Y.). 251 [PubMed]
Silver RA, Lubke J, Sakmann B, Feldmeyer D. (2003). High-probability uniquantal transmission at excitatory synapses in barrel cortex. Science (New York, N.Y.). 302 [PubMed]
Simkus CR, Stricker C. (2002). Properties of mEPSCs recorded in layer II neurones of rat barrel cortex. The Journal of physiology. 545 [PubMed]
Singer W. (1993). Synchronization of cortical activity and its putative role in information processing and learning. Annual review of physiology. 55 [PubMed]
Somogyi P, Freund TF, Cowey A. (1982). The axo-axonic interneuron in the cerebral cortex of the rat, cat and monkey. Neuroscience. 7 [PubMed]
Somogyi P, Tamás G, Lujan R, Buhl EH. (1998). Salient features of synaptic organisation in the cerebral cortex. Brain research. Brain research reviews. 26 [PubMed]
Sporns O, Kötter R. (2004). Motifs in brain networks. PLoS biology. 2 [PubMed]
Spruston N. (2008). Pyramidal neurons: dendritic structure and synaptic integration. Nature reviews. Neuroscience. 9 [PubMed]
Stepanyants A, Martinez LM, Ferecskó AS, Kisvárday ZF. (2009). The fractions of short- and long-range connections in the visual cortex. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]
Steriade M, Nuñez A, Amzica F. (1993). A novel slow (< 1 Hz) oscillation of neocortical neurons in vivo: depolarizing and hyperpolarizing components. The Journal of neuroscience : the official journal of the Society for Neuroscience. 13 [PubMed]
Svoboda K, Denk W, Kleinfeld D, Tank DW. (1997). In vivo dendritic calcium dynamics in neocortical pyramidal neurons. Nature. 385 [PubMed]
Szabadics J et al. (2006). Excitatory effect of GABAergic axo-axonic cells in cortical microcircuits. Science (New York, N.Y.). 311 [PubMed]
Tamás G, Somogyi P, Buhl EH. (1998). Differentially interconnected networks of GABAergic interneurons in the visual cortex of the cat. The Journal of neuroscience : the official journal of the Society for Neuroscience. 18 [PubMed]
Tan AY, Chen Y, Scholl B, Seidemann E, Priebe NJ. (2014). Sensory stimulation shifts visual cortex from synchronous to asynchronous states. Nature. 509 [PubMed]
Thomson AM, Bannister AP. (1998). Postsynaptic pyramidal target selection by descending layer III pyramidal axons: dual intracellular recordings and biocytin filling in slices of rat neocortex. Neuroscience. 84 [PubMed]
Thomson AM, Deuchars J. (1997). Synaptic interactions in neocortical local circuits: dual intracellular recordings in vitro. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Thomson AM, Deuchars J, West DC. (1993). Large, deep layer pyramid-pyramid single axon EPSPs in slices of rat motor cortex display paired pulse and frequency-dependent depression, mediated presynaptically and self-facilitation, mediated postsynaptically. Journal of neurophysiology. 70 [PubMed]
Thomson AM, Lamy C. (2007). Functional maps of neocortical local circuitry. Frontiers in neuroscience. 1 [PubMed]
Thomson AM, West DC, Hahn J, Deuchars J. (1996). Single axon IPSPs elicited in pyramidal cells by three classes of interneurones in slices of rat neocortex. The Journal of physiology. 496 ( Pt 1) [PubMed]
Timofeev I, Grenier F, Bazhenov M, Sejnowski TJ, Steriade M. (2000). Origin of slow cortical oscillations in deafferented cortical slabs. Cerebral cortex (New York, N.Y. : 1991). 10 [PubMed]
Toledo-Rodriguez M et al. (2004). Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. Cerebral cortex (New York, N.Y. : 1991). 14 [PubMed]
Toledo-Rodriguez M, Goodman P, Illic M, Wu C, Markram H. (2005). Neuropeptide and calcium-binding protein gene expression profiles predict neuronal anatomical type in the juvenile rat. The Journal of physiology. 567 [PubMed]
Tsodyks MV, Markram H. (1997). The neural code between neocortical pyramidal neurons depends on neurotransmitter release probability. Proceedings of the National Academy of Sciences of the United States of America. 94 [PubMed]
Wang Y, Gupta A, Toledo-Rodriguez M, Wu CZ, Markram H. (2002). Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 12 [PubMed]
Wang Y et al. (2006). Heterogeneity in the pyramidal network of the medial prefrontal cortex. Nature neuroscience. 9 [PubMed]
Wang Y et al. (2004). Anatomical, physiological and molecular properties of Martinotti cells in the somatosensory cortex of the juvenile rat. The Journal of physiology. 561 [PubMed]
Wang Z, McCormick DA. (1993). Control of firing mode of corticotectal and corticopontine layer V burst-generating neurons by norepinephrine, acetylcholine, and 1S,3R-ACPD. The Journal of neuroscience : the official journal of the Society for Neuroscience. 13 [PubMed]
West MJ, Gundersen HJ. (1990). Unbiased stereological estimation of the number of neurons in the human hippocampus. The Journal of comparative neurology. 296 [PubMed]
Westerink BH, Hofsteede HM, Damsma G, de Vries JB. (1988). The significance of extracellular calcium for the release of dopamine, acetylcholine and amino acids in conscious rats, evaluated by brain microdialysis. Naunyn-Schmiedeberg's archives of pharmacology. 337 [PubMed]
Wickersham IR, Finke S, Conzelmann KK, Callaway EM. (2007). Retrograde neuronal tracing with a deletion-mutant rabies virus. Nature methods. 4 [PubMed]
Williams RW, Rakic P. (1988). Three-dimensional counting: an accurate and direct method to estimate numbers of cells in sectioned material. The Journal of comparative neurology. 278 [PubMed]
Williams SR, Mitchell SJ. (2008). Direct measurement of somatic voltage clamp errors in central neurons. Nature neuroscience. 11 [PubMed]
Wilson NR, Runyan CA, Wang FL, Sur M. (2012). Division and subtraction by distinct cortical inhibitory networks in vivo. Nature. 488 [PubMed]
Wimmer VC, Bruno RM, de Kock CP, Kuner T, Sakmann B. (2010). Dimensions of a projection column and architecture of VPM and POm axons in rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 20 [PubMed]
Yoshimura Y, Kimura F, Tsumoto T. (1999). Estimation of single channel conductance underlying synaptic transmission between pyramidal cells in the visual cortex. Neuroscience. 88 [PubMed]
Yuste R. (2005). Origin and classification of neocortical interneurons. Neuron. 48 [PubMed]
Yuste R, Tank DW, Kleinfeld D. (1997). Functional study of the rat cortical microcircuitry with voltage-sensitive dye imaging of neocortical slices. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Zagha E, McCormick DA. (2014). Neural control of brain state. Current opinion in neurobiology. 29 [PubMed]
Zhu JJ. (2000). Maturation of layer 5 neocortical pyramidal neurons: amplifying salient layer 1 and layer 4 inputs by Ca2+ action potentials in adult rat tuft dendrites. The Journal of physiology. 526 Pt 3 [PubMed]
van Vreeswijk C, Sompolinsky H. (1996). Chaos in neuronal networks with balanced excitatory and inhibitory activity. Science (New York, N.Y.). 274 [PubMed]
Abdellah M et al. (2017). Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies. BMC bioinformatics. 18 [PubMed]
Aberra AS, Peterchev AV, Grill WM. (2018). Biophysically realistic neuron models for simulation of cortical stimulation. Journal of neural engineering. 15 [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.
Andreozzi E, Carannante I, D'Addio G, Cesarelli M, Balbi P. (2019). Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms Scientific reports. 9 [PubMed]
Antunes G, Faria da Silva SF, Simoes de Souza FM. (2018). Mirror Neurons Modeled Through Spike-Timing-Dependent Plasticity are Affected by Channelopathies Associated with Autism Spectrum Disorder. International journal of neural systems. 28 [PubMed]
Arkhipov A et al. (2018). Visual physiology of the layer 4 cortical circuit in silico. PLoS computational biology. 14 [PubMed]
Balbi P, Massobrio P, Hellgren Kotaleski J. (2017). A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms. PLoS computational biology. 13 [PubMed]
Barros-Zulaica N et al. (2019). Estimating the Readily-Releasable Vesicle Pool Size at Synaptic Connections in the Neocortex Frontiers in Synaptic Neuroscience. 11
Ben-Shalom R et al. (2022). NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs Journal of neuroscience methods. 366 [PubMed]
Bezaire MJ, Raikov I, Burk K, Vyas D, Soltesz I. (2016). Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit. eLife. 5 [PubMed]
Carlu M et al. (2020). A mean-field approach to the dynamics of networks of complex neurons, from nonlinear Integrate-and-Fire to Hodgkin-Huxley models. Journal of neurophysiology. 123 [PubMed]
Cavarretta F et al. (2018). Parallel odor processing by mitral and middle tufted cells in the olfactory bulb. Scientific reports. 8 [PubMed]
Crone JC et al. (2019). Enabling Large-Scale Simulations With the GENESIS Neuronal Simulator Frontiers in Neuroinformatics. 13
Duggins P, Stewart TC, Choo X, Eliasmith C. (2017). The Effects of Guanfacine and Phenylephrine on a Spiking Neuron Model of Working Memory. Topics in cognitive science. 9 [PubMed]
Dura-Bernal S et al. (2023). Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics. Cell reports. 42 [PubMed]
Dura-Bernal S et al. (2016). Restoring Behavior via Inverse Neurocontroller in a Lesioned Cortical Spiking Model Driving a Virtual Arm. Frontiers in neuroscience. 10 [PubMed]
Eyal G et al. (2018). Human Cortical Pyramidal Neurons: From Spines to Spikes via Models. Frontiers in cellular neuroscience. 12 [PubMed]
Eyal G et al. (2016). Unique membrane properties and enhanced signal processing in human neocortical neurons. eLife. 5 [PubMed]
Farokhniaee A, McIntyre CC. (2019). Theoretical principles of deep brain stimulation induced synaptic suppression. Brain stimulation. 12 [PubMed]
Gal E et al. (2017). Rich cell-type-specific network topology in neocortical microcircuitry. Nature neuroscience. 20 [PubMed]
Galloni AR, Laffere A, Rancz E. (2020). Apical length governs computational diversity of layer 5 pyramidal neurons. eLife. 9 [PubMed]
Gandolfi D et al. (2022). A realistic morpho-anatomical connection strategy for modelling full-scale point-neuron microcircuits Scientific reports. 12 [PubMed]
Geminiani A et al. (2018). Complex Dynamics in Simplified Neuronal Models: Reproducing Golgi Cell Electroresponsiveness. Frontiers in neuroinformatics. 12 [PubMed]
Giacopelli G, Tegolo D, Spera E, Migliore M. (2021). On the structural connectivity of large-scale models of brain networks at cellular level. Scientific reports. 11 [PubMed]
Golomb D et al. (2017). Mechanisms underlying a thalamocortical transformation during active tactile sensation PLoS Comput Biol. 13(6)
Günay C, Doloc-Mihu A, Lamb DG, Calabrese RL. (2019). Synaptic Strengths Dominate Phasing of Motor Circuit: Intrinsic Conductances of Neuron Types Need Not Vary across Animals. eNeuro. 6 [PubMed]
Hagen E et al. (2017). Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37 [PubMed]
Halnes G et al. (2016). Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue. PLoS computational biology. 12 [PubMed]
Hiratani N, Fukai T. (2018). Redundancy in synaptic connections enables neurons to learn optimally. Proceedings of the National Academy of Sciences of the United States of America. 115 [PubMed]
Hjorth JJJ et al. (2020). The microcircuits of striatum in silico. Proceedings of the National Academy of Sciences of the United States of America. 117 [PubMed]
Huang C, Zeldenrust F, Celikel T. (2022). Cortical Representation of Touch in Silico Neuroinformatics. 20 [PubMed]
Jacob T et al. (2019). A Proposed Mechanism for Spontaneous Transitions between Interictal and Ictal Activity. The Journal of neuroscience : the official journal of the Society for Neuroscience. 39 [PubMed]
Kumaravelu K, Sombeck J, Miller LE, Bensmaia SJ, Grill WM. (2022). Stoney vs. Histed: Quantifying the spatial effects of intracortical microstimulation Brain stimulation. 15 [PubMed]
Lytton WW et al. (2017). Evolutionary algorithm optimization of biological learning parameters in a biomimetic neuroprosthesis. IBM Journal of Research and Development (Computational Neuroscience special issue). 61(2/3)
Magalhães B, Hines M, Sterling T, Schüermann F. (2019). Exploiting Flow Graph of System of ODEs to Accelerate the Simulation of Biologically-Detailed Neural Networks 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS).
Magalhães BR, Sterling T, Hines M, Schürmann F. (2019). Fully-Asynchronous Cache-Efficient Simulation of Detailed Neural Networks Computational Science -- ICCS 2019.
Magalhães BRC, Sterling T, Hines M, Schürmann F. (2019). Asynchronous Branch-Parallel Simulation of Detailed Neuron Models. Frontiers in neuroinformatics. 13 [PubMed]
Manninen T, Havela R, Linne M-L. (2017). Reproducibility and comparability of computational models for astrocyte calcium excitability Front. Neuroinform..
Manninen T, Saudargiene A, Linne ML. (2020). Astrocyte-mediated spike-timing-dependent long-term depression modulates synaptic properties in the developing cortex. PLoS computational biology. 16 [PubMed]
McDougal RA, Bulanova AS, Lytton WW. (2016). Reproducibility in Computational Neuroscience Models and Simulations. IEEE transactions on bio-medical engineering. 63 [PubMed]
Mäki-Marttunen T et al. (2018). A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. Journal of neuroscience methods. 293 [PubMed]
Mäki-Marttunen T, Iannella N, Edwards AG, Einevoll GT, Blackwell KT. (2020). A unified computational model for cortical post-synaptic plasticity. eLife. 9 [PubMed]
Mäki-Marttunen T et al. (2019). Alterations in Schizophrenia-Associated Genes Can Lead to Increased Power in Delta Oscillations. Cerebral cortex (New York, N.Y. : 1991). 29 [PubMed]
Mäki-Marttunen T et al. (2017). Pleiotropic effects of schizophrenia-associated genetic variants in neuron firing and cardiac pacemaking revealed by computational modeling. Translational psychiatry. 7 [PubMed]
Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]
Reimann MW, Horlemann AL, Ramaswamy S, Muller EB, Markram H. (2017). Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]
Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H. (2015). An algorithm to predict the connectome of neural microcircuits. Frontiers in computational neuroscience. 9 [PubMed]
Reimann MW et al. (2017). Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function. Frontiers in computational neuroscience. 11 [PubMed]
Rich S et al. (2019). Inhibitory Network Bistability Explains Increased Interneuronal Activity Prior to Seizure Onset. Frontiers in neural circuits. 13 [PubMed]
Schmidt M, Bakker R, Hilgetag CC, Diesmann M, van Albada SJ. (2018). Multi-scale account of the network structure of macaque visual cortex. Brain structure & function. 223 [PubMed]
Schmidt M et al. (2018). A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas. PLoS computational biology. 14 [PubMed]
Schwarzacher SW, Cuntz H, Jedlicka P, Beining M, Mongiat LA. (2017). T2N as a new tool for robust electrophysiological modeling demonstrated for mature and adult-born dentate granule cells eLife.
Spratt PWE et al. (2021). Paradoxical hyperexcitability from NaV1.2 sodium channel loss in neocortical pyramidal cells Cell reports. 36 [PubMed]
Venkadesh S et al. (2018). Evolving Simple Models of Diverse Intrinsic Dynamics in Hippocampal Neuron Types. Frontiers in neuroinformatics. 12 [PubMed]
Zerlaut Y, Chemla S, Chavane F, Destexhe A. (2018). Modeling mesoscopic cortical dynamics using a mean-field model of conductance-based networks of adaptive exponential integrate-and-fire neurons. Journal of computational neuroscience. 44 [PubMed]
Berger TK, Perin R, Silberberg G, Markram H. (2009). Frequency-dependent disynaptic inhibition in the pyramidal network: a ubiquitous pathway in the developing rat neocortex. The Journal of physiology. 587 [PubMed]
Burkhalter A, Gonchar Y, Wang Q. (2008). Multiple distinct subtypes of GABAergic neurons in mouse visual cortex identified by triple immunostaining. Front Neuroanat. 1
Connors BW, Gutnick MJ. (1990). Intrinsic firing patterns of diverse neocortical neurons. Trends in neurosciences. 13 [PubMed]
DeFelipe J. (1993). Neocortical neuronal diversity: chemical heterogeneity revealed by colocalization studies of classic neurotransmitters, neuropeptides, calcium-binding proteins, and cell surface molecules. Cerebral cortex (New York, N.Y. : 1991). 3 [PubMed]
DeFelipe J, Alonso-Nanclares L, Arellano JI. (2002). Microstructure of the neocortex: comparative aspects. Journal of neurocytology. 31 [PubMed]
Feldmeyer D, Egger V, Lubke J, Sakmann B. (1999). Reliable synaptic connections between pairs of excitatory layer 4 neurones within a single 'barrel' of developing rat somatosensory cortex. The Journal of physiology. 521 Pt 1 [PubMed]
Feldmeyer D, Lübke J, Sakmann B. (2006). Efficacy and connectivity of intracolumnar pairs of layer 2/3 pyramidal cells in the barrel cortex of juvenile rats. The Journal of physiology. 575 [PubMed]
Feldmeyer D, Lübke 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. The Journal of physiology. 538 [PubMed]
Gonchar Y, Burkhalter A. (1997). Three distinct families of GABAergic neurons in rat visual cortex. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Gupta A, Wang Y, Markram H. (2000). Organizing principles for a diversity of GABAergic interneurons and synapses in the neocortex. Science (New York, N.Y.). 287 [PubMed]
Kasper EM, Larkman AU, Lübke J, Blakemore C. (1994). Pyramidal neurons in layer 5 of the rat visual cortex. II. Development of electrophysiological properties. The Journal of comparative neurology. 339 [PubMed]
Kawaguchi Y, Kondo S. (2002). Parvalbumin, somatostatin and cholecystokinin as chemical markers for specific GABAergic interneuron types in the rat frontal cortex. Journal of neurocytology. 31 [PubMed]
Kawaguchi Y, Kubota Y. (1997). GABAergic cell subtypes and their synaptic connections in rat frontal cortex. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Kole MH, Hallermann S, Stuart GJ. (2006). Single Ih channels in pyramidal neuron dendrites: properties, distribution, and impact on action potential output. The Journal of neuroscience : the official journal of the Society for Neuroscience. 26 [PubMed]
Korngreen A, Sakmann B. (2000). Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats: subtypes and gradients. The Journal of physiology. 525 Pt 3 [PubMed]
Larkman AU. (1991). Dendritic morphology of pyramidal neurones of the visual cortex of the rat: I. Branching patterns. The Journal of comparative neurology. 306 [PubMed]
Larkum ME, Nevian T, Sandler M, Polsky A, Schiller J. (2009). Synaptic integration in tuft dendrites of layer 5 pyramidal neurons: a new unifying principle. Science (New York, N.Y.). 325 [PubMed]
Larkum ME, Waters J, Sakmann B, Helmchen F. (2007). Dendritic spikes in apical dendrites of neocortical layer 2/3 pyramidal neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27 [PubMed]
Ledergerber D, Larkum ME. (2010). Properties of layer 6 pyramidal neuron apical dendrites. The Journal of neuroscience : the official journal of the Society for Neuroscience. 30 [PubMed]
Lübke J, Roth A, Feldmeyer D, Sakmann B. (2003). Morphometric analysis of the columnar innervation domain of neurons connecting layer 4 and layer 2/3 of juvenile rat barrel cortex. Cerebral cortex (New York, N.Y. : 1991). 13 [PubMed]
Markram H, Lübke J, Frotscher M, Roth A, Sakmann B. (1997). Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. The Journal of physiology. 500 ( Pt 2) [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Markram H et al. (2004). Interneurons of the neocortical inhibitory system. Nature reviews. Neuroscience. 5 [PubMed]
Meyer HS et al. (2011). Inhibitory interneurons in a cortical column form hot zones of inhibition in layers 2 and 5A. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Meyer HS et al. (2010). Number and laminar distribution of neurons in a thalamocortical projection column of rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 20 [PubMed]
Narayanan RT et al. (2015). Beyond Columnar Organization: Cell Type- and Target Layer-Specific Principles of Horizontal Axon Projection Patterns in Rat Vibrissal Cortex. Cerebral cortex (New York, N.Y. : 1991). 25 [PubMed]
Nevian T, Larkum ME, Polsky A, Schiller J. (2007). Properties of basal dendrites of layer 5 pyramidal neurons: a direct patch-clamp recording study. Nature neuroscience. 10 [PubMed]
O'Connor DH, Huber D, Svoboda K. (2009). Reverse engineering the mouse brain. Nature. 461 [PubMed]
Oberlaender M et al. (2011). Three-dimensional axon morphologies of individual layer 5 neurons indicate cell type-specific intracortical pathways for whisker motion and touch. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Oberlaender M et al. (2012). Cell type-specific three-dimensional structure of thalamocortical circuits in a column of rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 22 [PubMed]
Perin R, Berger TK, Markram H. (2011). A synaptic organizing principle for cortical neuronal groups. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Petilla Interneuron Nomenclature Group et al. (2008). Petilla terminology: nomenclature of features of GABAergic interneurons of the cerebral cortex. Nature reviews. Neuroscience. 9 [PubMed]
Ramaswamy S, Markram H. (2015). Anatomy and physiology of the thick-tufted layer 5 pyramidal neuron. Frontiers in cellular neuroscience. 9 [PubMed]
Reyes A et al. (1998). Target-cell-specific facilitation and depression in neocortical circuits. Nature neuroscience. 1 [PubMed]
Romand S, Wang Y, Toledo-Rodriguez M, Markram H. (2011). Morphological development of thick-tufted layer v pyramidal cells in the rat somatosensory cortex. Frontiers in neuroanatomy. 5 [PubMed]
Santana R, McGarry LM, Bielza C, Larrañaga P, Yuste R. (2013). Classification of neocortical interneurons using affinity propagation. Frontiers in neural circuits. 7 [PubMed]
Silberberg G, Markram H. (2007). Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron. 53 [PubMed]
Somogyi P, Tamás G, Lujan R, Buhl EH. (1998). Salient features of synaptic organisation in the cerebral cortex. Brain research. Brain research reviews. 26 [PubMed]
Stuart GJ, Sakmann B. (1994). Active propagation of somatic action potentials into neocortical pyramidal cell dendrites. Nature. 367 [PubMed]
Thomson AM, Deuchars J. (1997). Synaptic interactions in neocortical local circuits: dual intracellular recordings in vitro. Cerebral cortex (New York, N.Y. : 1991). 7 [PubMed]
Thomson AM, Deuchars J, West DC. (1993). Large, deep layer pyramid-pyramid single axon EPSPs in slices of rat motor cortex display paired pulse and frequency-dependent depression, mediated presynaptically and self-facilitation, mediated postsynaptically. Journal of neurophysiology. 70 [PubMed]
Toledo-Rodriguez M et al. (2004). Correlation maps allow neuronal electrical properties to be predicted from single-cell gene expression profiles in rat neocortex. Cerebral cortex (New York, N.Y. : 1991). 14 [PubMed]
Toledo-Rodriguez M, Goodman P, Illic M, Wu C, Markram H. (2005). Neuropeptide and calcium-binding protein gene expression profiles predict neuronal anatomical type in the juvenile rat. The Journal of physiology. 567 [PubMed]
Tsodyks MV, Markram H. (1997). The neural code between neocortical pyramidal neurons depends on neurotransmitter release probability. Proceedings of the National Academy of Sciences of the United States of America. 94 [PubMed]
Wang Y, Gupta A, Toledo-Rodriguez M, Wu CZ, Markram H. (2002). Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 12 [PubMed]
Wang Y et al. (2006). Heterogeneity in the pyramidal network of the medial prefrontal cortex. Nature neuroscience. 9 [PubMed]
Wang Y et al. (2004). Anatomical, physiological and molecular properties of Martinotti cells in the somatosensory cortex of the juvenile rat. The Journal of physiology. 561 [PubMed]
Wimmer VC, Bruno RM, de Kock CP, Kuner T, Sakmann B. (2010). Dimensions of a projection column and architecture of VPM and POm axons in rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 20 [PubMed]
Zhu JJ. (2000). Maturation of layer 5 neocortical pyramidal neurons: amplifying salient layer 1 and layer 4 inputs by Ca2+ action potentials in adult rat tuft dendrites. The Journal of physiology. 526 Pt 3 [PubMed]
Abdellah M et al. (2017). Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies. BMC bioinformatics. 18 [PubMed]
Aberra AS, Peterchev AV, Grill WM. (2018). Biophysically realistic neuron models for simulation of cortical stimulation. Journal of neural engineering. 15 [PubMed]
Antunes G, Faria da Silva SF, Simoes de Souza FM. (2018). Mirror Neurons Modeled Through Spike-Timing-Dependent Plasticity are Affected by Channelopathies Associated with Autism Spectrum Disorder. International journal of neural systems. 28 [PubMed]
Barros-Zulaica N et al. (2019). Estimating the Readily-Releasable Vesicle Pool Size at Synaptic Connections in the Neocortex Frontiers in Synaptic Neuroscience. 11
Ben-Shalom R et al. (2022). NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs Journal of neuroscience methods. 366 [PubMed]
Bezaire MJ, Raikov I, Burk K, Vyas D, Soltesz I. (2016). Interneuronal mechanisms of hippocampal theta oscillations in a full-scale model of the rodent CA1 circuit. eLife. 5 [PubMed]
Dura-Bernal S et al. (2023). Data-driven multiscale model of macaque auditory thalamocortical circuits reproduces in vivo dynamics. Cell reports. 42 [PubMed]
Hagen E et al. (2017). Focal Local Field Potential Signature of the Single-Axon Monosynaptic Thalamocortical Connection. The Journal of neuroscience : the official journal of the Society for Neuroscience. 37 [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
McDougal RA, Bulanova AS, Lytton WW. (2016). Reproducibility in Computational Neuroscience Models and Simulations. IEEE transactions on bio-medical engineering. 63 [PubMed]
Reimann MW, Horlemann AL, Ramaswamy S, Muller EB, Markram H. (2017). Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]
Reimann MW et al. (2017). Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function. Frontiers in computational neuroscience. 11 [PubMed]
Anderson JC, Binzegger T, Douglas RJ, Martin KA. (2002). Chance or design? Some specific considerations concerning synaptic boutons in cat visual cortex. Journal of neurocytology. 31 [PubMed]
Arellano JI, Benavides-Piccione R, Defelipe J, Yuste R. (2007). Ultrastructure of dendritic spines: correlation between synaptic and spine morphologies. Frontiers in neuroscience. 1 [PubMed]
Beierlein M, Connors BW. (2002). Short-term dynamics of thalamocortical and intracortical synapses onto layer 6 neurons in neocortex. Journal of neurophysiology. 88 [PubMed]
Bienenstock EL, Cooper LN, Munro PW. (1982). Theory for the development of neuron selectivity: orientation specificity and binocular interaction in visual cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 2 [PubMed]
Bonhoeffer T, Staiger V, Aertsen A. (1989). Synaptic plasticity in rat hippocampal slice cultures: local "Hebbian" conjunction of pre- and postsynaptic stimulation leads to distributed synaptic enhancement. Proceedings of the National Academy of Sciences of the United States of America. 86 [PubMed]
Bopp R, Maçarico da Costa N, Kampa BM, Martin KA, Roth MM. (2014). Pyramidal cells make specific connections onto smooth (GABAergic) neurons in mouse visual cortex. PLoS biology. 12 [PubMed]
Braitenberg V. (2001). Brain size and number of neurons: an exercise in synthetic neuroanatomy. Journal of computational neuroscience. 10 [PubMed]
Braitenberg V, Schuz A. (1998). Cortex Statistics and Geometry of Neuronal Connectivity 2nd ed.
Chklovskii DB, Mel BW, Svoboda K. (2004). Cortical rewiring and information storage. Nature. 431 [PubMed]
Chklovskii DB, Vitaladevuni S, Scheffer LK. (2010). Semi-automated reconstruction of neural circuits using electron microscopy. Current opinion in neurobiology. 20 [PubMed]
DeFelipe J. (1999). Chandelier cells and epilepsy. Brain : a journal of neurology. 122 ( Pt 10) [PubMed]
Denk W, Horstmann H. (2004). Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS biology. 2 [PubMed]
Deuchars J, West DC, Thomson AM. (1994). Relationships between morphology and physiology of pyramid-pyramid single axon connections in rat neocortex in vitro. The Journal of physiology. 478 Pt 3 [PubMed]
Egger R, Dercksen VJ, Udvary D, Hege HC, Oberlaender M. (2014). Generation of dense statistical connectomes from sparse morphological data. Frontiers in neuroanatomy. 8 [PubMed]
Fares T, Stepanyants A. (2009). Cooperative synapse formation in the neocortex. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]
Feldmeyer D, Egger V, Lubke J, Sakmann B. (1999). Reliable synaptic connections between pairs of excitatory layer 4 neurones within a single 'barrel' of developing rat somatosensory cortex. The Journal of physiology. 521 Pt 1 [PubMed]
Feldmeyer D, Lübke J, Sakmann B. (2006). Efficacy and connectivity of intracolumnar pairs of layer 2/3 pyramidal cells in the barrel cortex of juvenile rats. The Journal of physiology. 575 [PubMed]
Feldmeyer D, Lübke 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. The Journal of physiology. 538 [PubMed]
Fino E, Yuste R. (2011). Dense inhibitory connectivity in neocortex. Neuron. 69 [PubMed]
Frick A, Feldmeyer D, Helmstaedter M, Sakmann B. (2008). Monosynaptic connections between pairs of L5A pyramidal neurons in columns of juvenile rat somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 18 [PubMed]
Gupta A, Wang Y, Markram H. (2000). Organizing principles for a diversity of GABAergic interneurons and synapses in the neocortex. Science (New York, N.Y.). 287 [PubMed]
Hellwig B. (2000). A quantitative analysis of the local connectivity between pyramidal neurons in layers 2/3 of the rat visual cortex. Biological cybernetics. 82 [PubMed]
Hill SL, Wang Y, Riachi I, Schürmann F, Markram H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proceedings of the National Academy of Sciences of the United States of America. 109 [PubMed]
Hofer SB, Mrsic-Flogel TD, Bonhoeffer T, Hübener M. (2009). Experience leaves a lasting structural trace in cortical circuits. Nature. 457 [PubMed]
Holmgren C, Harkany T, Svennenfors B, Zilberter Y. (2003). Pyramidal cell communication within local networks in layer 2/3 of rat neocortex. The Journal of physiology. 551 [PubMed]
Holtmaat A, Svoboda K. (2009). Experience-dependent structural synaptic plasticity in the mammalian brain. Nature reviews. Neuroscience. 10 [PubMed]
Howard A, Tamas G, Soltesz I. (2005). Lighting the chandelier: new vistas for axo-axonic cells. Trends in neurosciences. 28 [PubMed]
Kalisman N, Silberberg G, Markram H. (2005). The neocortical microcircuit as a tabula rasa. Proceedings of the National Academy of Sciences of the United States of America. 102 [PubMed]
Karube F, Kubota Y, Kawaguchi Y. (2004). Axon branching and synaptic bouton phenotypes in GABAergic nonpyramidal cell subtypes. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24 [PubMed]
Kawaguchi Y, Karube F, Kubota Y. (2006). Dendritic branch typing and spine expression patterns in cortical nonpyramidal cells. Cerebral cortex (New York, N.Y. : 1991). 16 [PubMed]
Kleinfeld D et al. (2011). Large-scale automated histology in the pursuit of connectomes. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]
Kozloski J, Hamzei-Sichani F, Yuste R. (2001). Stereotyped position of local synaptic targets in neocortex. Science (New York, N.Y.). 293 [PubMed]
Kubota Y, Hatada S, Kondo S, Karube F, Kawaguchi Y. (2007). Neocortical inhibitory terminals innervate dendritic spines targeted by thalamocortical afferents. The Journal of neuroscience : the official journal of the Society for Neuroscience. 27 [PubMed]
Lamprecht R, LeDoux J. (2004). Structural plasticity and memory. Nature reviews. Neuroscience. 5 [PubMed]
Le Bé JV, Markram H. (2006). Spontaneous and evoked synaptic rewiring in the neonatal neocortex. Proceedings of the National Academy of Sciences of the United States of America. 103 [PubMed]
Le Bé JV, Silberberg G, Wang Y, Markram H. (2007). Morphological, electrophysiological, and synaptic properties of corticocallosal pyramidal cells in the neonatal rat neocortex. Cerebral cortex (New York, N.Y. : 1991). 17 [PubMed]
Lübke J, Roth A, Feldmeyer D, Sakmann B. (2003). Morphometric analysis of the columnar innervation domain of neurons connecting layer 4 and layer 2/3 of juvenile rat barrel cortex. Cerebral cortex (New York, N.Y. : 1991). 13 [PubMed]
Markram H et al. (2012). Accelerating range queries for brain simulations Proceedings of the 28th International Conference on Data Engineering Washington DC.
Markram H et al. (2008). Identifying, tabulating, and analyzing contacts between branched neuron morphologies Ibm J Res Dev. 52
Markram H, Lübke J, Frotscher M, Roth A, Sakmann B. (1997). Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. The Journal of physiology. 500 ( Pt 2) [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Markram H et al. (2004). Interneurons of the neocortical inhibitory system. Nature reviews. Neuroscience. 5 [PubMed]
Mishchenko Y et al. (2010). Ultrastructural analysis of hippocampal neuropil from the connectomics perspective. Neuron. 67 [PubMed]
Neves G, Cooke SF, Bliss TV. (2008). Synaptic plasticity, memory and the hippocampus: a neural network approach to causality. Nature reviews. Neuroscience. 9 [PubMed]
Nimchinsky EA, Sabatini BL, Svoboda K. (2002). Structure and function of dendritic spines. Annual review of physiology. 64 [PubMed]
Perin R, Berger TK, Markram H. (2011). A synaptic organizing principle for cortical neuronal groups. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Peters A, Feldman ML. (1976). The projection of the lateral geniculate nucleus to area 17 of the rat cerebral cortex. I. General description. Journal of neurocytology. 5 [PubMed]
Peters A, Proskauer CC, Feldman ML, Kimerer L. (1979). The projection of the lateral geniculate nucleus to area 17 of the rat cerebral cortex. V. Degenerating axon terminals synapsing with Golgi impregnated neurons. Journal of neurocytology. 8 [PubMed]
Petersen CC, Sakmann B. (2000). The excitatory neuronal network of rat layer 4 barrel cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 20 [PubMed]
Reyes A, Sakmann B. (1999). Developmental switch in the short-term modification of unitary EPSPs evoked in layer 2/3 and layer 5 pyramidal neurons of rat neocortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 19 [PubMed]
Romand S, Wang Y, Toledo-Rodriguez M, Markram H. (2011). Morphological development of thick-tufted layer v pyramidal cells in the rat somatosensory cortex. Frontiers in neuroanatomy. 5 [PubMed]
Royer S, Paré D. (2003). Conservation of total synaptic weight through balanced synaptic depression and potentiation. Nature. 422 [PubMed]
Sala C, Segal M. (2014). Dendritic spines: the locus of structural and functional plasticity. Physiological reviews. 94 [PubMed]
Schuman EM, Madison DV. (1994). Locally distributed synaptic potentiation in the hippocampus. Science (New York, N.Y.). 263 [PubMed]
Seung S. (). Connectome: How the Brain’s Wiring Makes Us Who We are.
Shepherd GM, Stepanyants A, Bureau I, Chklovskii D, Svoboda K. (2005). Geometric and functional organization of cortical circuits. Nature neuroscience. 8 [PubMed]
Silberberg G, Markram H. (2007). Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron. 53 [PubMed]
Silver RA, Lubke J, Sakmann B, Feldmeyer D. (2003). High-probability uniquantal transmission at excitatory synapses in barrel cortex. Science (New York, N.Y.). 302 [PubMed]
Somogyi P. (1977). A specific 'axo-axonal' interneuron in the visual cortex of the rat. Brain research. 136 [PubMed]
Somogyi P, Freund TF, Cowey A. (1982). The axo-axonic interneuron in the cerebral cortex of the rat, cat and monkey. Neuroscience. 7 [PubMed]
Somogyi P, Tamás G, Lujan R, Buhl EH. (1998). Salient features of synaptic organisation in the cerebral cortex. Brain research. Brain research reviews. 26 [PubMed]
Stepanyants A, Chklovskii DB. (2005). Neurogeometry and potential synaptic connectivity. Trends in neurosciences. 28 [PubMed]
Stepanyants A, Hof PR, Chklovskii DB. (2002). Geometry and structural plasticity of synaptic connectivity. Neuron. 34 [PubMed]
Szabadics J et al. (2006). Excitatory effect of GABAergic axo-axonic cells in cortical microcircuits. Science (New York, N.Y.). 311 [PubMed]
Wang Y, Gupta A, Toledo-Rodriguez M, Wu CZ, Markram H. (2002). Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 12 [PubMed]
White G, Levy WB, Steward O. (1990). Spatial overlap between populations of synapses determines the extent of their associative interaction during the induction of long-term potentiation and depression. Journal of neurophysiology. 64 [PubMed]
Wilbrecht L, Holtmaat A, Wright N, Fox K, Svoboda K. (2010). Structural plasticity underlies experience-dependent functional plasticity of cortical circuits. The Journal of neuroscience : the official journal of the Society for Neuroscience. 30 [PubMed]
van Ooyen A et al. (2014). Independently outgrowing neurons and geometry-based synapse formation produce networks with realistic synaptic connectivity. PloS one. 9 [PubMed]
Barros-Zulaica N et al. (2019). Estimating the Readily-Releasable Vesicle Pool Size at Synaptic Connections in the Neocortex Frontiers in Synaptic Neuroscience. 11
Gandolfi D et al. (2022). A realistic morpho-anatomical connection strategy for modelling full-scale point-neuron microcircuits Scientific reports. 12 [PubMed]
Giacopelli G, Tegolo D, Spera E, Migliore M. (2021). On the structural connectivity of large-scale models of brain networks at cellular level. Scientific reports. 11 [PubMed]
Jacob T et al. (2019). A Proposed Mechanism for Spontaneous Transitions between Interictal and Ictal Activity. The Journal of neuroscience : the official journal of the Society for Neuroscience. 39 [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Reimann MW, Horlemann AL, Ramaswamy S, Muller EB, Markram H. (2017). Morphological Diversity Strongly Constrains Synaptic Connectivity and Plasticity. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]
Reimann MW et al. (2017). Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function. Frontiers in computational neuroscience. 11 [PubMed]
Abdellah M. (2017). Physically-plausible Reconstruction of Neocortical Somata. Blue Brain Project. 2017. https://www.youtube.com/watch?v= XJ8uVBL8CA8&feature=youtu.be.
Abdellah M, Bilgili A, Eilemann S, Markram H, Schürmann F. (2015). Physically-based in silico light sheet microscopy for visualizing fluorescent brain models. BMC bioinformatics. 16 Suppl 11 [PubMed]
Abdellah M et al. (2017). Bio-physically plausible visualization of highly scattering fluorescent neocortical models for in silico experimentation. BMC bioinformatics. 18 [PubMed]
Ascoli GA, Scorcioni R, Donohue DE. (2002). Generation and description of neuronal morphology using L-Neuron: A case study Computational Neuroanatomy: Principles and Methods.
Azimipour M et al. (2014). Extraction of optical properties and prediction of light distribution in rat brain tissue. Journal of biomedical optics. 19 [PubMed]
Berndt A et al. (2011). High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Bhalla US, Bower JM, Wilson MA, Uhley JD. (1989). GENESIS: a system for simulating neural networks Advances In Neural Information Processing Systems.
Blender Institute Amsterdam. (2016). Blender - 3D Modelling and Rendering Package http://www.blender.org/.
Blender Online Community. (2016). Mesh Primitives, Blender Reference Manual, Version 2.77 http://www.blender.org.
Brito JP et al. (2013). Neuronize: a tool for building realistic neuronal cell morphologies. Frontiers in neuroanatomy. 7 [PubMed]
Burtsev S, Kuzmin YP. (1993). An efficient flood-filling algorithm Comput Graph. 17(5)
Chemla S, Chavane F. (2010). Voltage-sensitive dye imaging: Technique review and models. Journal of physiology, Paris. 104 [PubMed]
Chen H, Fang S. (2000). Hardware accelerated voxelization Hardware accelerated voxelization. 24(3)
Cignoni P, Corsini M, Ranzuglia G. (2008). Meshlab: an Open-Source 3D mesh processing system Ercim News. 73(45-46)
Dagum L, Menon R. (1998). Openmp: An industry-standard api for shared-memory programming Ieee Computational Science Engineering. 5
Di Ventura B, Lemerle C, Michalodimitrakis K, Serrano L. (2006). From in vivo to in silico biology and back. Nature. 443 [PubMed]
Eisemann E, Décoret X. (2006). Fast scene voxelization and applications Proceedings of the 2006 Symposium on Interactive 3D Graphics and Games. ACM.
Eisemann E, Décoret X.. (2008). Single-pass GPU solid voxelization for real-time applications Single-pass GPU solid voxelization for real-time applications.
Geschwind DH, Konopka G. (2009). Neuroscience in the era of functional genomics and systems biology. Nature. 461 [PubMed]
Glaser JR, Glaser EM. (1990). Neuron imaging with Neurolucida--a PC-based system for image combining microscopy. Computerized medical imaging and graphics : the official journal of the Computerized Medical Imaging Society. 14 [PubMed]
Gleeson P, Steuber V, Silver RA. (2007). neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron. 54 [PubMed]
Halavi M et al. (2008). NeuroMorpho.Org implementation of digital neuroscience: dense coverage and integration with the NIF. Neuroinformatics. 6 [PubMed]
He W et al. (2003). Automated three-dimensional tracing of neurons in confocal and brightfield images. Microscopy and microanalysis : the official journal of Microscopy Society of America, Microbeam Analysis Society, Microscopical Society of Canada. 9 [PubMed]
Humphreys G, Pharr M. (2010). Physically Based Rendering, Second Edition: From Theory To Implementation.
Humphreys G, Pharr M. (2012). Physically-based Rendering. From Theory to Implementation. 2012. http://www.pbrt.org/.
Kaufman A, Cohen-Or D. (1997). 3D line voxelization and connectivity control IEEE Comput Graph Appl.. 17(6)
Kazhdan M, Hoppe H. (2013). Screened poisson surface reconstruction ACM Trans Graph. 32(3)
Koene RA et al. (2009). NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics. 7 [PubMed]
Lasserre S et al. (2012). A neuron membrane mesh representation for visualization of electrophysiological simulations. IEEE transactions on visualization and computer graphics. 18 [PubMed]
Lippert T, Orth B. (2014). Supercomputing infrastructure for simulations of the human brain Brain-Inspired Computing. 8603
Llamas I. (2007). Real-time voxelization of triangle meshes on the GPU SIGGRAPH Sketches. San Diego: The 34th international conference and exhibition on computer graphics and interactive techniques.
Luo T, Sanes JR, Lichtman JW, Cai D, Cohen KB. (2013). Improved tools for thebrainbowtoolbox NatMethods. 10(6)
Markram H. (2006). The blue brain project. Nature reviews. Neuroscience. 7 [PubMed]
Markram H et al. (2011). Introducing the human brain project Procedia Comput Sci.. 7
Markram H et al. (2008). Identifying, tabulating, and analyzing contacts between branched neuron morphologies Ibm J Res Dev. 52
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Markram H, Schürmann F, Abdellah M, Bilgili A, Eilemann S. (2015). A computational model of light-sheet fluorescence microscopy using physically-based rendering Eurographics 2015.
Mills MJL, Sale KL, Simmons BA, Popelier PLA. (2017). Rhorix: An interface between quantum chemical topology and the 3D graphics program blender. Journal of computational chemistry. 38 [PubMed]
Moser MB, Moser EI, Freeman J, Marcus G. (2014). The Future of the Brain: Essays by the World's Leading Neuroscientists.
Müller M, Nealen A, Keiser R, Boxerman E, Carlson M. (2006). Physically based deformable models in computer graphics Computer Graphics Forum.
Oberlaender M, Bruno RM, Sakmann B, Broser PJ. (2007). Transmitted light brightfield mosaic microscopy for three-dimensional tracing of single neuron morphology. Journal of biomedical optics. 12 [PubMed]
Pawelzik H, Hughes DI, Thomson AM. (2002). Physiological and morphological diversity of immunocytochemically defined parvalbumin- and cholecystokinin-positive interneurones in CA1 of the adult rat hippocampus. The Journal of comparative neurology. 443 [PubMed]
Peng H, Meijering E, Ascoli GA. (2015). From DIADEM to BigNeuron. Neuroinformatics. 13 [PubMed]
Platt J, Terzopoulos D, Barr A, Fleischer K. (1987). Elastically deformable models ACM Siggraph Computer Graphics. ACM.
Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]
Sanbonmatsu KY, Tung CS. (2007). High performance computing in biology: multimillion atom simulations of nanoscale systems. Journal of structural biology. 157 [PubMed]
Schultz S, Nikolic K, Grossman N, Jarvis S. (2013). Computational models of optogenetic tools for controlling neural circuits with light 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).
Schurmann F, Hernando J, Pastor L. (2012). Towards real-time visualization of detailed neural tissue models: View frustum culling for parallel rendering BioVis.
Schwarz M, Seidel HP. (2010). Fast parallel surface and solid voxelization on gpus ACM Transactions on Graphics (TOG).
Segev I, Koch C. (1998). Methods In Neuronal Modeling.
Stosiek C, Garaschuk O, Holthoff K, Konnerth A. (2003). In vivo two-photon calcium imaging of neuronal networks. Proceedings of the National Academy of Sciences of the United States of America. 100 [PubMed]
Tomer R, Ye L, Hsueh B, Deisseroth K. (2014). Advanced CLARITY for rapid and high-resolution imaging of intact tissues. Nature protocols. 9 [PubMed]
Torben-Nielsen B, Tuyls K, Postma E. (2008). EvOL-NEURON: Neuronal morphology generation Neurocomputing. 71
Zhang H, Bao H, Chen W, Dong Z, Peng Q. (2004). Real-time voxelization for complex polygonal models Computer Graphics and Applications, 2004. PG 2004. Proceedings. 12th Pacific Conference On. IEEE.
Zhu X, Jin X, Guo X. (2013). Efficient polygonization of tree trunks modeled by convolution surfaces Sci China Inf Sci.. 56(3)
Abeles M. (1982). Local Cortical Circuits: An Electrophysiological Study.
Bale MR, Ince RA, Santagata G, Petersen RS. (2015). Efficient population coding of naturalistic whisker motion in the ventro-posterior medial thalamus based on precise spike timing. Frontiers in neural circuits. 9 [PubMed]
Bassett DS, Sporns O. (2017). Network neuroscience. Nature neuroscience. 20 [PubMed]
Berger E, Aharoni R, Meshulam R. (2005). Eigenvalues and homology of flag complexes and vector representations of graphs Geom. Funct. Anal.. 15
Bienenstock E. (1995). A model of nerocortex Comput Neural Syst. 6
Braitenberg V, Schuz A. (1998). Cortex Statistics and Geometry of Neuronal Connectivity 2nd ed.
Brody CD. (1999). Correlations without synchrony Neural computation. 11 [PubMed]
Bullmore E, Sporns O. (2009). Complex brain networks: graph theoretical analysis of structural and functional systems. Nature reviews. Neuroscience. 10 [PubMed]
Chambers B, MacLean JN. (2016). Higher-Order Synaptic Interactions Coordinate Dynamics in Recurrent Networks. PLoS computational biology. 12 [PubMed]
Chklovskii DB, Mel BW, Svoboda K. (2004). Cortical rewiring and information storage. Nature. 431 [PubMed]
Engel AK, Singer W. (2001). Temporal binding and the neural correlates of sensory awareness. Trends in cognitive sciences. 5 [PubMed]
Erdos P, Renyi A. (1960). On the evolution of random graphs Publ Math Instit Hungar Acad Sci. 5
Et AL et al. (2011). Scikit-learn: Machine Learning in Python J Mach Learn Res.. 12
Giusti C, Pastalkova E, Curto C, Itskov V. (2015). Clique topology reveals intrinsic geometric structure in neural correlations. Proceedings of the National Academy of Sciences of the United States of America. 112 [PubMed]
Gong P, Leeuwen Cv. (2004). Evolution to a small-world network with chaotic units EPL. 67
Harris KD, Shepherd GM. (2015). The neocortical circuit: themes and variations. Nature neuroscience. 18 [PubMed]
Hebb DO. (1949). The Organization Of Behavior.
Holtmaat A, Svoboda K. (2009). Experience-dependent structural synaptic plasticity in the mammalian brain. Nature reviews. Neuroscience. 10 [PubMed]
Hu Y, Trousdale J, Josić K, Shea-Brown E. (2014). Local paths to global coherence: cutting networks down to size. Physical review. E, Statistical, nonlinear, and soft matter physics. 89 [PubMed]
Jarvis RM, Broadhurst D, Johnson H, O'Boyle NM, Goodacre R. (2006). PYCHEM: a multivariate analysis package for python. Bioinformatics (Oxford, England). 22 [PubMed]
Knoblauch A, Palm G, Sommer FT. (2010). Memory capacities for synaptic and structural plasticity. Neural computation. 22 [PubMed]
Latora V, Marchiori M. (2001). Efficient behavior of small-world networks. Physical review letters. 87 [PubMed]
Le Bé JV, Markram H. (2006). Spontaneous and evoked synaptic rewiring in the neonatal neocortex. Proceedings of the National Academy of Sciences of the United States of America. 103 [PubMed]
Luczak A, McNaughton BL, Harris KD. (2015). Packet-based communication in the cortex. Nature reviews. Neuroscience. 16 [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Meyer HS et al. (2010). Cell type-specific thalamic innervation in a column of rat vibrissal cortex. Cerebral cortex (New York, N.Y. : 1991). 20 [PubMed]
Miller JE, Ayzenshtat I, Carrillo-Reid L, Yuste R. (2014). Visual stimuli recruit intrinsically generated cortical ensembles. Proceedings of the National Academy of Sciences of the United States of America. 111 [PubMed]
Munkres JR. (1984). Elements of Algebraic Topology.
Pajevic S, Plenz D. (2012). The organization of strong links in complex networks. Nature physics. 8 [PubMed]
Palm G, Aertsen AM, Gerstein GL. (1988). On the significance of correlations among neuronal spike trains. Biological cybernetics. 59 [PubMed]
Perin R, Berger TK, Markram H. (2011). A synaptic organizing principle for cortical neuronal groups. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Peters A, Feldman ML. (1976). The projection of the lateral geniculate nucleus to area 17 of the rat cerebral cortex. I. General description. Journal of neurocytology. 5 [PubMed]
Petri G et al. (2014). Homological scaffolds of brain functional networks. Journal of the Royal Society, Interface. 11 [PubMed]
Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]
Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H. (2015). An algorithm to predict the connectome of neural microcircuits. Frontiers in computational neuroscience. 9 [PubMed]
Renart A et al. (2010). The asynchronous state in cortical circuits. Science (New York, N.Y.). 327 [PubMed]
Rosenbaum R, Smith MA, Kohn A, Rubin JE, Doiron B. (2017). The spatial structure of correlated neuronal variability. Nature neuroscience. 20 [PubMed]
Shepherd GM, Stepanyants A, Bureau I, Chklovskii D, Svoboda K. (2005). Geometric and functional organization of cortical circuits. Nature neuroscience. 8 [PubMed]
Song S, Sjöström PJ, Reigl M, Nelson S, Chklovskii DB. (2005). Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS biology. 3 [PubMed]
Stepanyants A, Chklovskii DB. (2005). Neurogeometry and potential synaptic connectivity. Trends in neurosciences. 28 [PubMed]
Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB. (2011). Structural properties of the Caenorhabditis elegans neuronal network. PLoS computational biology. 7 [PubMed]
Wagner H, Bauer U, Kerber M, Reininghaus J. (2017). PHATPersistent Homology Algorithms Toolbox J. Symb. Comput.. 78
Willshaw DJ, Buneman OP, Longuet-Higgins HC. (1969). Non-holographic associative memory. Nature. 222 [PubMed]
Abeles M, Kanter I, Cohen D, Kopelowitz E. (2012). Sensitivity of global network dynamics to local parameters versus motif structure in a cortex-like neuronal model. Phys. Rev. E. 85
Amaral LA, Scala A, Barthelemy M, Stanley HE. (2000). Classes of small-world networks. Proceedings of the National Academy of Sciences of the United States of America. 97 [PubMed]
Atkinson SE, Williams SR. (2009). Postnatal development of dendritic synaptic integration in rat neocortical pyramidal neurons. Journal of neurophysiology. 102 [PubMed]
Baker ST et al. (2015). Developmental Changes in Brain Network Hub Connectivity in Late Adolescence. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35 [PubMed]
Barabasi AL, Albert R. (1999). Emergence of scaling in random networks Science (New York, N.Y.). 286 [PubMed]
Barbour DL, Callaway EM. (2008). Excitatory local connections of superficial neurons in rat auditory cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]
Barthélemy M. (2011). Spatial networks Phys. Rep.. 499
Bassett DS, Sporns O. (2017). Network neuroscience. Nature neuroscience. 20 [PubMed]
Bettencourt LM, Stephens GJ, Ham MI, Gross GW. (2007). Functional structure of cortical neuronal networks grown in vitro. Physical review. E, Statistical, nonlinear, and soft matter physics. 75 [PubMed]
Bonifazi P et al. (2009). GABAergic hub neurons orchestrate synchrony in developing hippocampal networks. Science (New York, N.Y.). 326 [PubMed]
Briggman KL, Helmstaedter M, Denk W. (2011). Wiring specificity in the direction-selectivity circuit of the retina. Nature. 471 [PubMed]
Chklovskii DB, Vitaladevuni S, Scheffer LK. (2010). Semi-automated reconstruction of neural circuits using electron microscopy. Current opinion in neurobiology. 20 [PubMed]
Egger R, Dercksen VJ, Udvary D, Hege HC, Oberlaender M. (2014). Generation of dense statistical connectomes from sparse morphological data. Frontiers in neuroanatomy. 8 [PubMed]
Fagiolo G. (2007). Clustering in complex directed networks. Physical review. E, Statistical, nonlinear, and soft matter physics. 76 [PubMed]
Flammini A, Vespignani A, Colizza V, Serrano MA. (2006). Detecting rich-club ordering in complex networks Nat. Phys.. 2
Fornito A, Zalesky A, Breakspear M. (2015). The connectomics of brain disorders. Nature reviews. Neuroscience. 16 [PubMed]
Hanel R, Corominas-Murtra B, Liu B, Thurner S. (2017). Fitting power-laws in empirical data with estimators that work for all exponents. PloS one. 12 [PubMed]
Helmstaedter M et al. (2013). Connectomic reconstruction of the inner plexiform layer in the mouse retina. Nature. 500 [PubMed]
Kasthuri N et al. (2015). Saturated Reconstruction of a Volume of Neocortex. Cell. 162 [PubMed]
Lago-Fernández LF, Huerta R, Corbacho F, Sigüenza JA. (2000). Fast response and temporal coherent oscillations in small-world networks. Physical review letters. 84 [PubMed]
Landau ID, Egger R, Dercksen VJ, Oberlaender M, Sompolinsky H. (2016). The Impact of Structural Heterogeneity on Excitation-Inhibition Balance in Cortical Networks. Neuron. 92 [PubMed]
Larkman AU. (1991). Dendritic morphology of pyramidal neurones of the visual cortex of the rat: I. Branching patterns. The Journal of comparative neurology. 306 [PubMed]
Lefort S, Tomm C, Floyd Sarria JC, Petersen CC. (2009). The excitatory neuronal network of the C2 barrel column in mouse primary somatosensory cortex. Neuron. 61 [PubMed]
London M, Roth A, Beeren L, Häusser M, Latham PE. (2010). Sensitivity to perturbations in vivo implies high noise and suggests rate coding in cortex. Nature. 466 [PubMed]
Lorenzon NM, Foehring RC. (1993). The ontogeny of repetitive firing and its modulation by norepinephrine in rat neocortical neurons. Brain research. Developmental brain research. 73 [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Milo R et al. (2002). Network motifs: simple building blocks of complex networks. Science (New York, N.Y.). 298 [PubMed]
Newman MEJ. (2003). The structure and function of complex networks SIAM Review. 45
Nigam S et al. (2016). Rich-Club Organization in Effective Connectivity among Cortical Neurons. The Journal of neuroscience : the official journal of the Society for Neuroscience. 36 [PubMed]
Perin R, Berger TK, Markram H. (2011). A synaptic organizing principle for cortical neuronal groups. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Pfeffer CK, Xue M, He M, Huang ZJ, Scanziani M. (2013). Inhibition of inhibition in visual cortex: the logic of connections between molecularly distinct interneurons. Nature neuroscience. 16 [PubMed]
Rieubland S, Roth A, Häusser M. (2014). Structured connectivity in cerebellar inhibitory networks. Neuron. 81 [PubMed]
Romand S, Wang Y, Toledo-Rodriguez M, Markram H. (2011). Morphological development of thick-tufted layer v pyramidal cells in the rat somatosensory cortex. Frontiers in neuroanatomy. 5 [PubMed]
Roxin A. (2011). The role of degree distribution in shaping the dynamics in networks of sparsely connected spiking neurons. Frontiers in computational neuroscience. 5 [PubMed]
Rubinov M, Sporns O. (2010). Complex network measures of brain connectivity: uses and interpretations. NeuroImage. 52 [PubMed]
Schröter M, Paulsen O, Bullmore ET. (2017). Micro-connectomics: probing the organization of neuronal networks at the cellular scale. Nature reviews. Neuroscience. 18 [PubMed]
Seung HS. (2009). Reading the book of memory: sparse sampling versus dense mapping of connectomes. Neuron. 62 [PubMed]
Silberberg G, Markram H. (2007). Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron. 53 [PubMed]
Song S, Sjöström PJ, Reigl M, Nelson S, Chklovskii DB. (2005). Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS biology. 3 [PubMed]
Sporns O, Tononi G, Kötter R. (2005). The human connectome: A structural description of the human brain. PLoS computational biology. 1 [PubMed]
Stepanyants A, Martinez LM, Ferecskó AS, Kisvárday ZF. (2009). The fractions of short- and long-range connections in the visual cortex. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]
Thomson AM, Lamy C. (2007). Functional maps of neocortical local circuitry. Frontiers in neuroscience. 1 [PubMed]
Towlson EK, Vértes PE, Ahnert SE, Schafer WR, Bullmore ET. (2013). The rich club of the C. elegans neuronal connectome. The Journal of neuroscience : the official journal of the Society for Neuroscience. 33 [PubMed]
Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB. (2011). Structural properties of the Caenorhabditis elegans neuronal network. PLoS computational biology. 7 [PubMed]
Watts DJ, Strogatz SH. (1998). Collective dynamics of 'small-world' networks. Nature. 393 [PubMed]
White JG, Southgate E, Thomson JN, Brenner S. (1986). The structure of the nervous system of the nematode Caenorhabditis elegans. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 314 [PubMed]
Xue M, Atallah BV, Scanziani M. (2014). Equalizing excitation-inhibition ratios across visual cortical neurons. Nature. 511 [PubMed]
Yu S, Huang D, Singer W, Nikolic D. (2008). A small world of neuronal synchrony. Cerebral cortex (New York, N.Y. : 1991). 18 [PubMed]
van den Heuvel MP, Bullmore ET, Sporns O. (2016). Comparative Connectomics. Trends in cognitive sciences. 20 [PubMed]
van den Heuvel MP, Sporns O. (2011). Rich-club organization of the human connectome. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]
Deitcher Y et al. (2017). Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]
Hiratani N, Fukai T. (2018). Redundancy in synaptic connections enables neurons to learn optimally. Proceedings of the National Academy of Sciences of the United States of America. 115 [PubMed]
Papoutsi A, Kastellakis G, Poirazi P. (2017). Basal tree complexity shapes functional pathways in the prefrontal cortex. Journal of neurophysiology. 118 [PubMed]
Schmidt M et al. (2018). A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque visual cortical areas. PLoS computational biology. 14 [PubMed]
Bannister AP. (2005). Inter- and intra-laminar connections of pyramidal cells in the neocortex. Neuroscience research. 53 [PubMed]
Binzegger T, Douglas RJ, Martin KA. (2004). A quantitative map of the circuit of cat primary visual cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24 [PubMed]
Brown SP, Hestrin S. (2009). Intracortical circuits of pyramidal neurons reflect their long-range axonal targets. Nature. 457 [PubMed]
Callaway EM. (2002). Cell type specificity of local cortical connections. Journal of neurocytology. 31 [PubMed]
Chklovskii DB, Mel BW, Svoboda K. (2004). Cortical rewiring and information storage. Nature. 431 [PubMed]
Delattre V, Keller D, Perich M, Markram H, Muller EB. (2015). Network-timing-dependent plasticity. Frontiers in cellular neuroscience. 9 [PubMed]
Feldmeyer D, Lübke 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. The Journal of physiology. 538 [PubMed]
Felleman DJ, Van Essen DC. (1991). Distributed hierarchical processing in the primate cerebral cortex. Cerebral cortex (New York, N.Y. : 1991). 1 [PubMed]
Fino E, Yuste R. (2011). Dense inhibitory connectivity in neocortex. Neuron. 69 [PubMed]
Helmstaedter M, Staiger JF, Sakmann B, Feldmeyer D. (2008). Efficient recruitment of layer 2/3 interneurons by layer 4 input in single columns of rat somatosensory cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]
Hill SL, Wang Y, Riachi I, Schürmann F, Markram H. (2012). Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits. Proceedings of the National Academy of Sciences of the United States of America. 109 [PubMed]
Hofer SB, Mrsic-Flogel TD, Bonhoeffer T, Hübener M. (2009). Experience leaves a lasting structural trace in cortical circuits. Nature. 457 [PubMed]
Holmgren C, Harkany T, Svennenfors B, Zilberter Y. (2003). Pyramidal cell communication within local networks in layer 2/3 of rat neocortex. The Journal of physiology. 551 [PubMed]
Holtmaat A, Svoboda K. (2009). Experience-dependent structural synaptic plasticity in the mammalian brain. Nature reviews. Neuroscience. 10 [PubMed]
Honey CJ et al. (2009). Predicting human resting-state functional connectivity from structural connectivity. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]
Jiang X et al. (2015). Principles of connectivity among morphologically defined cell types in adult neocortex. Science (New York, N.Y.). 350 [PubMed]
Kasthuri N et al. (2015). Saturated Reconstruction of a Volume of Neocortex. Cell. 162 [PubMed]
Kuan L et al. (2015). Neuroinformatics of the Allen Mouse Brain Connectivity Atlas. Methods (San Diego, Calif.). 73 [PubMed]
LUCE RD, PERRY AD. (1949). A method of matrix analysis of group structure. Psychometrika. 14 [PubMed]
Larimer P, Strowbridge BW. (2008). Nonrandom local circuits in the dentate gyrus. The Journal of neuroscience : the official journal of the Society for Neuroscience. 28 [PubMed]
Le Bé JV, Markram H. (2006). Spontaneous and evoked synaptic rewiring in the neonatal neocortex. Proceedings of the National Academy of Sciences of the United States of America. 103 [PubMed]
Le Bé JV, Silberberg G, Wang Y, Markram H. (2007). Morphological, electrophysiological, and synaptic properties of corticocallosal pyramidal cells in the neonatal rat neocortex. Cerebral cortex (New York, N.Y. : 1991). 17 [PubMed]
Lefort S, Tomm C, Floyd Sarria JC, Petersen CC. (2009). The excitatory neuronal network of the C2 barrel column in mouse primary somatosensory cortex. Neuron. 61 [PubMed]
Markram H, Lübke J, Frotscher M, Roth A, Sakmann B. (1997). Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. The Journal of physiology. 500 ( Pt 2) [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Mishchenko Y et al. (2010). Ultrastructural analysis of hippocampal neuropil from the connectomics perspective. Neuron. 67 [PubMed]
Perin R, Berger TK, Markram H. (2011). A synaptic organizing principle for cortical neuronal groups. Proceedings of the National Academy of Sciences of the United States of America. 108 [PubMed]
Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]
Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H. (2015). An algorithm to predict the connectome of neural microcircuits. Frontiers in computational neuroscience. 9 [PubMed]
Renart A, Song P, Wang XJ. (2003). Robust spatial working memory through homeostatic synaptic scaling in heterogeneous cortical networks. Neuron. 38 [PubMed]
Shepherd GM, Stepanyants A, Bureau I, Chklovskii D, Svoboda K. (2005). Geometric and functional organization of cortical circuits. Nature neuroscience. 8 [PubMed]
Silberberg G, Markram H. (2007). Disynaptic inhibition between neocortical pyramidal cells mediated by Martinotti cells. Neuron. 53 [PubMed]
Somogyi P. (1977). A specific 'axo-axonal' interneuron in the visual cortex of the rat. Brain research. 136 [PubMed]
Somogyi P, Tamás G, Lujan R, Buhl EH. (1998). Salient features of synaptic organisation in the cerebral cortex. Brain research. Brain research reviews. 26 [PubMed]
Song S, Sjöström PJ, Reigl M, Nelson S, Chklovskii DB. (2005). Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS biology. 3 [PubMed]
Sporns O, Tononi G, Edelman GM. (2000). Theoretical neuroanatomy: relating anatomical and functional connectivity in graphs and cortical connection matrices. Cerebral cortex (New York, N.Y. : 1991). 10 [PubMed]
Stepanyants A, Chklovskii DB. (2005). Neurogeometry and potential synaptic connectivity. Trends in neurosciences. 28 [PubMed]
Stepanyants A, Martinez LM, Ferecskó AS, Kisvárday ZF. (2009). The fractions of short- and long-range connections in the visual cortex. Proceedings of the National Academy of Sciences of the United States of America. 106 [PubMed]
Thomson AM, West DC, Wang Y, Bannister AP. (2002). Synaptic connections and small circuits involving excitatory and inhibitory neurons in layers 2-5 of adult rat and cat neocortex: triple intracellular recordings and biocytin labelling in vitro. Cerebral cortex (New York, N.Y. : 1991). 12 [PubMed]
Turrigiano GG, Nelson SB. (2004). Homeostatic plasticity in the developing nervous system. Nature reviews. Neuroscience. 5 [PubMed]
Varshney LR, Chen BL, Paniagua E, Hall DH, Chklovskii DB. (2011). Structural properties of the Caenorhabditis elegans neuronal network. PLoS computational biology. 7 [PubMed]
Wang Y, Gupta A, Toledo-Rodriguez M, Wu CZ, Markram H. (2002). Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 12 [PubMed]
Watts DJ, Strogatz SH. (1998). Collective dynamics of 'small-world' networks. Nature. 393 [PubMed]
Watts J, Thomson AM. (2005). Excitatory and inhibitory connections show selectivity in the neocortex. The Journal of physiology. 562 [PubMed]
White JG, Southgate E, Thomson JN, Brenner S. (1986). The structure of the nervous system of the nematode Caenorhabditis elegans. Philosophical transactions of the Royal Society of London. Series B, Biological sciences. 314 [PubMed]
Wozny C, Williams SR. (2011). Specificity of synaptic connectivity between layer 1 inhibitory interneurons and layer 2/3 pyramidal neurons in the rat neocortex. Cerebral cortex (New York, N.Y. : 1991). 21 [PubMed]
Yoshimura Y, Callaway EM. (2005). Fine-scale specificity of cortical networks depends on inhibitory cell type and connectivity. Nature neuroscience. 8 [PubMed]
Deitcher Y et al. (2017). Comprehensive Morpho-Electrotonic Analysis Shows 2 Distinct Classes of L2 and L3 Pyramidal Neurons in Human Temporal Cortex. Cerebral cortex (New York, N.Y. : 1991). 27 [PubMed]
Maass W, Markram H. (2002). Synapses as dynamic memory buffers. Neural networks : the official journal of the International Neural Network Society. 15 [PubMed]
Mackenzie PJ, Kenner GS, Prange O, Murphy TH. (2000). Vesicle number does not predict postsynaptic measures of miniature synaptic activity frequency in cultured cortical neurons. Neuroscience. 98 [PubMed]
Markram H, Lübke J, Frotscher M, Roth A, Sakmann B. (1997). Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex. The Journal of physiology. 500 ( Pt 2) [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Markram H, Wang Y, Tsodyks M. (1998). Differential signaling via the same axon of neocortical pyramidal neurons. Proceedings of the National Academy of Sciences of the United States of America. 95 [PubMed]
Mason A, Nicoll A, Stratford K. (1991). Synaptic transmission between individual pyramidal neurons of the rat visual cortex in vitro. The Journal of neuroscience : the official journal of the Society for Neuroscience. 11 [PubMed]
Molnár G et al. (2016). Human pyramidal to interneuron synapses are mediated by multi-vesicular release and multiple docked vesicles. eLife. 5 [PubMed]
Murphy GJ, Glickfeld LL, Balsen Z, Isaacson JS. (2004). Sensory neuron signaling to the brain: properties of transmitter release from olfactory nerve terminals. The Journal of neuroscience : the official journal of the Society for Neuroscience. 24 [PubMed]
Nadkarni S, Bartol TM, Sejnowski TJ, Levine H. (2010). Modelling vesicular release at hippocampal synapses. PLoS computational biology. 6 [PubMed]
Neher E, Sakaba T. (2008). Multiple roles of calcium ions in the regulation of neurotransmitter release. Neuron. 59 [PubMed]
Neishabouri A, Faisal AA. (2014). Axonal noise as a source of synaptic variability. PLoS computational biology. 10 [PubMed]
Oertner TG, Sabatini BL, Nimchinsky EA, Svoboda K. (2002). Facilitation at single synapses probed with optical quantal analysis. Nature neuroscience. 5 [PubMed]
Press WH, Teukolsky SA. (1988). Kolmogorov-Smirnov test for two dimensional data Comput Phys. 2
Pulido C, Marty A. (2017). Quantal Fluctuations in Central Mammalian Synapses: Functional Role of Vesicular Docking Sites. Physiological reviews. 97 [PubMed]
Ramaswamy S et al. (2015). The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex. Frontiers in neural circuits. 9 [PubMed]
Ramaswamy S, Markram H. (2015). Anatomy and physiology of the thick-tufted layer 5 pyramidal neuron. Frontiers in cellular neuroscience. 9 [PubMed]
Redman S. (1990). Quantal analysis of synaptic potentials in neurons of the central nervous system. Physiological reviews. 70 [PubMed]
Reimann MW, King JG, Muller EB, Ramaswamy S, Markram H. (2015). An algorithm to predict the connectome of neural microcircuits. Frontiers in computational neuroscience. 9 [PubMed]
Ren HP, Bai C, Baptista MS, Grebogi C. (2017). Weak connections form an infinite number of patterns in the brain. Scientific reports. 7 [PubMed]
Richardson MJ, Silberberg G. (2008). Measurement and analysis of postsynaptic potentials using a novel voltage-deconvolution method. Journal of neurophysiology. 99 [PubMed]
Rizo J, Xu J. (2015). The Synaptic Vesicle Release Machinery. Annual review of biophysics. 44 [PubMed]
Rollenhagen A, Lübke JH. (2006). The morphology of excitatory central synapses: from structure to function. Cell and tissue research. 326 [PubMed]
Rollenhagen A et al. (2018). Structural Properties of Synaptic Transmission and Temporal Dynamics at Excitatory Layer 5B Synapses in the Adult Rat Somatosensory Cortex. Frontiers in synaptic neuroscience. 10 [PubMed]
Rudolph S, Tsai MC, von Gersdorff H, Wadiche JI. (2015). The ubiquitous nature of multivesicular release. Trends in neurosciences. 38 [PubMed]
Ruiz R et al. (2011). Active zones and the readily releasable pool of synaptic vesicles at the neuromuscular junction of the mouse. The Journal of neuroscience : the official journal of the Society for Neuroscience. 31 [PubMed]
Sakaba T. (2018). Kinetics of transmitter release at the calyx of Held synapse. Proceedings of the Japan Academy. Series B, Physical and biological sciences. 94 [PubMed]
Silver RA, Lubke J, Sakmann B, Feldmeyer D. (2003). High-probability uniquantal transmission at excitatory synapses in barrel cortex. Science (New York, N.Y.). 302 [PubMed]
Stevens CF. (2003). Neurotransmitter release at central synapses. Neuron. 40 [PubMed]
Südhof TC. (2000). The synaptic vesicle cycle revisited. Neuron. 28 [PubMed]
Tang CM, Margulis M, Shi QY, Fielding A. (1994). Saturation of postsynaptic glutamate receptors after quantal release of transmitter. Neuron. 13 [PubMed]
Tong G, Jahr CE. (1994). Multivesicular release from excitatory synapses of cultured hippocampal neurons. Neuron. 12 [PubMed]
Tsodyks MV, Markram H. (1997). The neural code between neocortical pyramidal neurons depends on neurotransmitter release probability. Proceedings of the National Academy of Sciences of the United States of America. 94 [PubMed]
Varela JA et al. (1997). A quantitative description of short-term plasticity at excitatory synapses in layer 2/3 of rat primary visual cortex. The Journal of neuroscience : the official journal of the Society for Neuroscience. 17 [PubMed]
Waites CL, Garner CC. (2011). Presynaptic function in health and disease. Trends in neurosciences. 34 [PubMed]
Wang Y, Gupta A, Toledo-Rodriguez M, Wu CZ, Markram H. (2002). Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex. Cerebral cortex (New York, N.Y. : 1991). 12 [PubMed]
Wang Y et al. (2006). Heterogeneity in the pyramidal network of the medial prefrontal cortex. Nature neuroscience. 9 [PubMed]
Watanabe S et al. (2013). Ultrafast endocytosis at mouse hippocampal synapses. Nature. 504 [PubMed]
Zhang C, Peskin CS. (2015). Improved signaling as a result of randomness in synaptic vesicle release. Proceedings of the National Academy of Sciences of the United States of America. 112 [PubMed]