Achard P, De Schutter E. (2006). Complex parameter landscape for a complex neuron model. PLoS computational biology. 2 [PubMed]
Acker CD, Hoyos E, Loew LM. (2016). EPSPs Measured in Proximal Dendritic Spines of Cortical Pyramidal Neurons. eNeuro. 3 [PubMed]
Almog M, Korngreen A. (2009). Characterization of voltage-gated Ca(2+) conductances in layer 5 neocortical pyramidal neurons from rats. PloS one. 4 [PubMed]
Almog M, Korngreen A. (2014). A Quantitative Description of Dendritic Conductances and Its Application to Dendritic Excitation in Layer 5 Pyramidal Neurons The Journal of neuroscience : the official journal of the Society for Neuroscience. 34 [PubMed]
Antic SD, Empson RM, Knöpfel T. (2016). Voltage imaging to understand connections and functions of neuronal circuits. Journal of neurophysiology. 116 [PubMed]
Artym VV, Petty HR. (2002). Molecular proximity of Kv1.3 voltage-gated potassium channels and beta(1)-integrins on the plasma membrane of melanoma cells: effects of cell adherence and channel blockers. The Journal of general physiology. 120 [PubMed]
Aćimović J, Mäki-Marttunen T, Linne ML. (2015). The effects of neuron morphology on graph theoretic measures of network connectivity: the analysis of a two-level statistical model. Frontiers in neuroanatomy. 9 [PubMed]
Bahl A, Stemmler MB, Herz AV, Roth A. (2012). Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. Journal of neuroscience methods. 210 [PubMed]
Bekkers JM, Häusser M. (2007). Targeted dendrotomy reveals active and passive contributions of the dendritic tree to synaptic integration and neuronal output. Proceedings of the National Academy of Sciences of the United States of America. 104 [PubMed]
Brinks D, Klein AJ, Cohen AE. (2015). Two-Photon Lifetime Imaging of Voltage Indicating Proteins as a Probe of Absolute Membrane Voltage. Biophysical journal. 109 [PubMed]
Brookings T, Goeritz ML, Marder E. (2014). Automatic parameter estimation of multicompartmental neuron models via minimization of trace error with control adjustment. Journal of neurophysiology. 112 [PubMed]
Bush PC, Sejnowski TJ. (1993). Reduced compartmental models of neocortical pyramidal cells. Journal of neuroscience methods. 46 [PubMed]
Cannon RC et al. (2014). LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Frontiers in neuroinformatics. 8 [PubMed]
Christophe E et al. (2005). Two populations of layer v pyramidal cells of the mouse neocortex: development and sensitivity to anesthetics. Journal of neurophysiology. 94 [PubMed]
Deb K, Pratap A, Agarwal S, Meyarivan T. (2002). A fast and elitist multiobjective genetic algorithm: NSGA-II Nsga-ii Ieee Transactions On Evolutionary Computation. 6
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]
Durstewitz D, Seamans JK, Sejnowski TJ. (2000). Dopamine-mediated stabilization of delay-period activity in a network model of prefrontal cortex. Journal of neurophysiology. 83 [PubMed]
Gong Y et al. (2015). High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor. Science (New York, N.Y.). 350 [PubMed]
Grewe BF, Langer D, Kasper H, Kampa BM, Helmchen F. (2010). High-speed in vivo calcium imaging reveals neuronal network activity with near-millisecond precision. Nature methods. 7 [PubMed]
Grienberger C, Chen X, Konnerth A. (2015). Dendritic function in vivo. Trends in neurosciences. 38 [PubMed]
Göbel W, Helmchen F. (2007). New angles on neuronal dendrites in vivo. Journal of neurophysiology. 98 [PubMed]
Harmony T. (2013). The functional significance of delta oscillations in cognitive processing. Frontiers in integrative neuroscience. 7 [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]
Hay E, Segev I. (2015). Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. Cerebral cortex (New York, N.Y. : 1991). 25 [PubMed]
Hendrickson EB, Edgerton JR, Jaeger D. (2011). The capabilities and limitations of conductance-based compartmental neuron models with reduced branched or unbranched morphologies and active dendrites. Journal of computational neuroscience. 30 [PubMed]
Hines ML, Carnevale NT. (1997). The NEURON simulation environment. Neural computation. 9 [PubMed]
Hochbaum DR et al. (2014). All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nature methods. 11 [PubMed]
Häusser M, Spruston N, Stuart GJ. (2000). Diversity and dynamics of dendritic signaling. Science (New York, N.Y.). 290 [PubMed]
Insel TR, Landis SC, Collins FS. (2013). Research priorities. The NIH BRAIN Initiative. Science (New York, N.Y.). 340 [PubMed]
Jahr CE, Stevens CF. (1990). Voltage dependence of NMDA-activated macroscopic conductances predicted by single-channel kinetics. The Journal of neuroscience : the official journal of the Society for Neuroscience. 10 [PubMed]
Jones KA, Zhang H, Large CH, Garbati N. (2009). Automated patch clamping using the qpatch High Throughput Screening: Methods and Protocols, Second Edition.
Keren N, Bar-Yehuda D, Korngreen A. (2009). Experimentally guided modelling of dendritic excitability in rat neocortical pyramidal neurones. The Journal of physiology. 587 [PubMed]
Keren N, Peled N, Korngreen A. (2005). Constraining compartmental models using multiple voltage recordings and genetic algorithms. Journal of neurophysiology. 94 [PubMed]
Kodandaramaiah SB, Franzesi GT, Chow BY, Boyden ES, Forest CR. (2012). Automated whole-cell patch-clamp electrophysiology of neurons in vivo. Nature methods. 9 [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]
Larkum M. (2013). A cellular mechanism for cortical associations: an organizing principle for the cerebral cortex. Trends in neurosciences. 36 [PubMed]
Lou S et al. (2016). Genetically Targeted All-Optical Electrophysiology with a Transgenic Cre-Dependent Optopatch Mouse. The Journal of neuroscience : the official journal of the Society for Neuroscience. 36 [PubMed]
Mainen ZF, Sejnowski TJ. (1996). Influence of dendritic structure on firing pattern in model neocortical neurons. Nature. 382 [PubMed]
Markram H et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell. 163 [PubMed]
Markram H, Roth A, Helmchen F. (1998). Competitive calcium binding: implications for dendritic calcium signaling. Journal of computational neuroscience. 5 [PubMed]
Migliore M, Shepherd GM. (2002). Emerging rules for the distributions of active dendritic conductances. Nature reviews. Neuroscience. 3 [PubMed]
Muki-Marttunen T. (2017). An Algorithm for Motif-Based Network Design. IEEE/ACM transactions on computational biology and bioinformatics. 14 [PubMed]
Mäki-Marttunen T, Aćimović J, Ruohonen K, Linne ML. (2013). Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework. PloS one. 8 [PubMed]
Mäki-Marttunen T et al. (2016). Functional Effects of Schizophrenia-Linked Genetic Variants on Intrinsic Single-Neuron Excitability: A Modeling Study. Biological psychiatry. Cognitive neuroscience and neuroimaging. 1 [PubMed]
Neske GT. (2015). The Slow Oscillation in Cortical and Thalamic Networks: Mechanisms and Functions. Frontiers in neural circuits. 9 [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]
Oertner TG, Sabatini BL, Nimchinsky EA, Svoboda K. (2002). Facilitation at single synapses probed with optical quantal analysis. Nature neuroscience. 5 [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]
Peterka DS, Takahashi H, Yuste R. (2011). Imaging voltage in neurons. Neuron. 69 [PubMed]
Popovic M, Gao X, Zecevic D. (2012). Voltage-sensitive dye recording from axons, dendrites and dendritic spines of individual neurons in brain slices. Journal of visualized experiments : JoVE. [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]
Roth A, Bahl A. (2009). Divide et impera: optimizing compartmental models of neurons step by step. The Journal of physiology. 587 [PubMed]
Rudolph S, Thanawala MS. (2015). Location matters: somatic and dendritic SK channels answer to distinct calcium signals. Journal of neurophysiology. 114 [PubMed]
Rudy B, Iverson LE. (1997). Ion channels. 207
Rumbell TH et al. (2016). Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons. Journal of computational neuroscience. 41 [PubMed]
Schiller J, Schiller Y, Stuart G, Sakmann B. (1997). Calcium action potentials restricted to distal apical dendrites of rat neocortical pyramidal neurons. The Journal of physiology. 505 ( Pt 3) [PubMed]
Smith SL, Smith IT, Branco T, Häusser M. (2013). Dendritic spikes enhance stimulus selectivity in cortical neurons in vivo. Nature. 503 [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]
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]
Timofeev I, Chauvette S. (2011). Thalamocortical oscillations: local control of EEG slow waves. Current topics in medicinal chemistry. 11 [PubMed]
Traub RD et al. (2005). Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. Journal of neurophysiology. 93 [PubMed]
Van Geit W, De Schutter E, Achard P. (2008). Automated neuron model optimization techniques: a review. Biological cybernetics. 99 [PubMed]
Van Geit W et al. (2016). BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience. Frontiers in neuroinformatics. 10 [PubMed]
Wang G et al. (2015). An optogenetics- and imaging-assisted simultaneous multiple patch-clamp recording system for decoding complex neural circuits. Nature protocols. 10 [PubMed]
Watts DJ, Strogatz SH. (1998). Collective dynamics of 'small-world' networks. Nature. 393 [PubMed]
Wu X et al. (2012). Is ZD7288 a selective blocker of hyperpolarization-activated cyclic nucleotide-gated channel currents? Channels (Austin, Tex.). 6 [PubMed]
Zhao L, Beverlin B, Netoff T, Nykamp DQ. (2011). Synchronization from second order network connectivity statistics. Frontiers in computational neuroscience. 5 [PubMed]
Zitzler E, Kunzli S. (2004). Indicator-based selection in multiobjective search Parallel Problem Solving From Nature-ppsn Viii. 3242
Ben-Shalom R et al. (2022). NeuroGPU: Accelerating multi-compartment, biophysically detailed neuron simulations on GPUs Journal of neuroscience methods. 366 [PubMed]
Mäki-Marttunen T et al. (2019). Computational modeling of genetic contributions to excitability and neural coding in layer V pyramidal cells: applications to schizophrenia pathology Front. Comput. Neurosci.. 13
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]
Sætra MJ, Einevoll GT, Halnes G. (2021). An electrodiffusive neuron-extracellular-glia model for exploring the genesis of slow potentials in the brain PLoS computational biology. 17 [PubMed]