Citation Relationships



Mäki-Marttunen T, Halnes G, Devor A, Metzner C, Dale AM, Andreassen OA, Einevoll GT (2018) A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. J Neurosci Methods 293:264-283 [PubMed]

   Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018)

References and models cited by this paper

References and models that cite this paper

Achard P, De Schutter E (2006) Complex parameter landscape for a complex neuron model. PLoS Comput Biol 2:e94 [Journal] [PubMed]

Acimovic 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. Front Neuroanat 9:76 [Journal] [PubMed]

Acker CD, Hoyos E, Loew LM (2016) EPSPs Measured in Proximal Dendritic Spines of Cortical Pyramidal Neurons. eNeuro [Journal] [PubMed]

Almog M, Korngreen A (2009) Characterization of voltage-gated Ca(2+) conductances in layer 5 neocortical pyramidal neurons from rats. PLoS One 4:e4841 [Journal] [PubMed]

Almog M, Korngreen A (2014) A Quantitative Description of Dendritic Conductances and Its Application to Dendritic Excitation in Layer 5 Pyramidal Neurons J Neurosci 34(1):182-196 [Journal]

   Ionic mechanisms of dendritic spikes (Almog and Korngreen 2014) [Model]

Antic SD, Empson RM, Knöpfel T (2016) Voltage imaging to understand connections and functions of neuronal circuits. J Neurophysiol 116:135-52 [Journal] [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. J Gen Physiol 120:29-37 [PubMed]

Bahl A, Stemmler MB, Herz AV, Roth A (2012) Automated optimization of a reduced layer 5 pyramidal cell model based on experimental data. J Neurosci Methods 210:22-34 [Journal] [PubMed]

   A set of reduced models of layer 5 pyramidal neurons (Bahl et al. 2012) [Model]

Bekkers JM, Häusser M (2007) Targeted dendrotomy reveals active and passive contributions of the dendritic tree to synaptic integration and neuronal output. Proc Natl Acad Sci U S A 104:11447-52 [Journal] [PubMed]

Brinks D, Klein AJ, Cohen AE (2015) Two-Photon Lifetime Imaging of Voltage Indicating Proteins as a Probe of Absolute Membrane Voltage. Biophys J 109:914-21 [Journal] [PubMed]

Brookings T, Goeritz ML, Marder E (2014) Automatic parameter estimation of multicompartmental neuron models via minimization of trace error with control adjustment. J Neurophysiol 112:2332-48 [Journal] [PubMed]

Bush PC, Sejnowski TJ (1993) Reduced compartmental models of neocortical pyramidal cells. J Neurosci Methods 46:159-66 [PubMed]

Cannon RC, Gleeson P, Crook S, Ganapathy G, Marin B, Piasini E, Silver RA (2014) LEMS: a language for expressing complex biological models in concise and hierarchical form and its use in underpinning NeuroML 2. Front Neuroinform 8:79 [Journal] [PubMed]

Christophe E, Doerflinger N, Lavery DJ, Molnár Z, Charpak S, Audinat E (2005) Two populations of layer v pyramidal cells of the mouse neocortex: development and sensitivity to anesthetics. J Neurophysiol 94:3357-67 [Journal] [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 6:182-197

Druckmann S, Banitt Y, Gidon A, Schürmann F, Markram H, Segev I (2007) A novel multiple objective optimization framework for constraining conductance-based neuron models by experimental data. Front Neurosci 1:7-18 [Journal] [PubMed]

Druckmann S, Berger TK, Schürmann F, Hill S, Markram H, Segev I (2011) Effective stimuli for constructing reliable neuron models. PLoS Comput Biol 7:e1002133 [Journal] [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. Cereb Cortex 23:2994-3006 [Journal] [PubMed]

Durstewitz D, Seamans JK, Sejnowski TJ (2000) Dopamine-mediated stabilization of delay-period activity in a network model of prefrontal cortex. J Neurophysiol 83:1733-50 [Journal] [PubMed]

   Neocortical pyramidal neuron: deep; effects of dopamine (Durstewitz et al 2000) [Model]

Göbel W, Helmchen F (2007) New angles on neuronal dendrites in vivo. J Neurophysiol 98:3770-9 [Journal] [PubMed]

Gong Y, Huang C, Li JZ, Grewe BF, Zhang Y, Eismann S, Schnitzer MJ (2015) High-speed recording of neural spikes in awake mice and flies with a fluorescent voltage sensor. Science 350:1361-6 [Journal] [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. Nat Methods 7:399-405 [Journal] [PubMed]

Grienberger C, Chen X, Konnerth A (2015) Dendritic function in vivo. Trends Neurosci 38:45-54 [Journal] [PubMed]

Harmony T (2013) The functional significance of delta oscillations in cognitive processing. Front Integr Neurosci 7:83 [Journal] [PubMed]

Häusser M, Spruston N, Stuart GJ (2000) Diversity and dynamics of dendritic signaling. Science 290:739-44 [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 Comput Biol 7:e1002107 [Journal] [PubMed]

   Cortical Layer 5b pyr. cell with [Na+]i mechanisms, from Hay et al 2011 (Zylbertal et al 2017) [Model]
   Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018) [Model]
   L5b PC model constrained for BAC firing and perisomatic current step firing (Hay et al., 2011) [Model]

Hay E, Segev I (2015) Dendritic Excitability and Gain Control in Recurrent Cortical Microcircuits. Cereb Cortex 25:3561-71 [Journal] [PubMed]

   Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2018) [Model]
   Microcircuits of L5 thick tufted pyramidal cells (Hay & Segev 2015) [Model]

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. J Comput Neurosci 30:301-21 [Journal] [PubMed]

   Comparison of full and reduced globus pallidus models (Hendrickson 2010) [Model]

Hines ML, Carnevale NT (1997) The NEURON simulation environment. Neural Comput 9:1179-209 [PubMed]

Hochbaum DR, Zhao Y, Farhi SL, Klapoetke N, Werley CA, Kapoor V, Zou P, Kralj JM, Maclaurin D, Smedemark-Margulies N, Saulnier JL, Boulting GL, Straub C, Cho YK, Melkonian M, Wong GK, Harrison DJ, Murthy VN, Sabatini BL, Boyden ES, Campbell RE, Cohen AE (2014) All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins. Nat Methods 11:825-33 [Journal] [PubMed]

Insel TR, Landis SC, Collins FS (2013) Research priorities. The NIH BRAIN Initiative. Science 340:687-8 [Journal] [PubMed]

Jahr CE, Stevens CF (1990) Voltage dependence of NMDA-activated macroscopic conductances predicted by single-channel kinetics. J Neurosci 10:3178-82 [PubMed]

Jones KA,Garbati N,Zhang H,Large CH (2009) Automated patch clamping using the qpatch High Throughput Screening: Methods and Protocols, Second Edition :209-223

Keren N, Bar-Yehuda D, Korngreen A (2009) Experimentally guided modelling of dendritic excitability in rat neocortical pyramidal neurones. J Physiol 587:1413-37 [Journal] [PubMed]

Keren N, Peled N, Korngreen A (2005) Constraining compartmental models using multiple voltage recordings and genetic algorithms. J Neurophysiol 94:3730-42 [Journal] [PubMed]

Kodandaramaiah SB, Franzesi GT, Chow BY, Boyden ES, Forest CR (2012) Automated whole-cell patch-clamp electrophysiology of neurons in vivo. Nat Methods 9:585-7 [Journal] [PubMed]

Korngreen A, Sakmann B (2000) Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats: subtypes and gradients. J Physiol 525 Pt 3:621-39 [PubMed]

   Pyramidal Neuron Deep: K+ kinetics (Korngreen, Sakmann 2000) [Model]

Larkum M (2013) A cellular mechanism for cortical associations: an organizing principle for the cerebral cortex. Trends Neurosci 36:141-51 [Journal] [PubMed]

Lou S, Adam Y, Weinstein EN, Williams E, Williams K, Parot V, Kavokine N, Liberles S, Madisen L, Zeng H, Cohen AE (2016) Genetically Targeted All-Optical Electrophysiology with a Transgenic Cre-Dependent Optopatch Mouse. J Neurosci 36:11059-11073 [Journal] [PubMed]

Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382:363-6 [Journal] [PubMed]

   Influence of dendritic structure on neocortical neuron firing patterns (Mainen and Sejnowski 1996) [Model]

Mäki-Marttunen T, Acimovic J, Ruohonen K, Linne ML (2013) Structure-dynamics relationships in bursting neuronal networks revealed using a prediction framework. PLoS One 8:e69373 [Journal] [PubMed]

   Structure-dynamics relationships in bursting neuronal networks revealed (Mäki-Marttunen et al. 2013) [Model]

Mäki-Marttunen T, Halnes G, Devor A, Witoelar A, Bettella F, Djurovic S, Wang Y, Einevoll GT, Andreassen OA, Dale AM (2016) Functional Effects of Schizophrenia-Linked Genetic Variants on Intrinsic Single-Neuron Excitability: A Modeling Study. Biol Psychiatry Cogn Neurosci Neuroimaging 1:49-59 [Journal] [PubMed]

   Schiz.-linked gene effects on intrinsic single-neuron excitability (Maki-Marttunen et al. 2016) [Model]

Markram H, Muller E, Ramaswamy S, Reimann MW, Abdellah M, Sanchez CA, Ailamaki A, Alonso-Nanclares L, Antille N, Arsever S, Kahou GA, Berger TK, Bilgili A, Buncic N, Chalimourda A, Chindemi G, Courcol JD, Delalondre F, Delattre V, Druckmann S, Dumusc R, Dynes J, Eilemann S, Gal E, Gevaert ME, Ghobril JP, Gidon A, Graham JW, Gupta A, Haenel V, Hay E, Heinis T, Hernando JB, Hines M, Kanari L, Keller D, Kenyon J, Khazen G, Kim Y, King JG, Kisvarday Z, Kumbhar P, Lasserre S, Le Bé JV, Magalhães BR, Merchán-Pérez A, Meystre J, Morrice BR, Muller J, Muñoz-Céspedes A, Muralidhar S, Muthurasa K, Nachbaur D, Newton TH, Nolte M, Ovcharenko A, Palacios J, Pastor L, Perin R, Ranjan R, Riachi I, Rodríguez JR, Riquelme JL, Rössert C, Sfyrakis K, Shi Y, Shillcock JC, Silberberg G, Silva R, Tauheed F, Telefont M, Toledo-Rodriguez M, Tränkler T, Van Geit W, Díaz JV, Walker R, Wang Y, Zaninetta SM (2015) Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163:456-92 [Journal] [PubMed]

   The neocortical microcircuit collaboration portal (Markram et al. 2015) [Model]

Markram H, Roth A, Helmchen F (1998) Competitive calcium binding: implications for dendritic calcium signaling. J Comput Neurosci 5:331-48 [PubMed]

Migliore M, Shepherd GM (2002) Emerging rules for the distributions of active dendritic conductances. Nat Rev Neurosci 3:362-70 [Journal] [PubMed]

   Modulation of temporal integration window (Migliore, Shepherd 2002) [Model]

Muki-Marttunen T (2017) An Algorithm for Motif-Based Network Design. IEEE/ACM Trans Comput Biol Bioinform 14:1181-1186 [Journal] [PubMed]

Neske GT (2015) The Slow Oscillation in Cortical and Thalamic Networks: Mechanisms and Functions. Front Neural Circuits 9:88 [Journal] [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. Nat Neurosci 10:206-14 [Journal] [PubMed]

   Dendritic Na+ spike initiation and backpropagation of APs in active dendrites (Nevian et al. 2007) [Model]

Oertner TG, Sabatini BL, Nimchinsky EA, Svoboda K (2002) Facilitation at single synapses probed with optical quantal analysis. Nat Neurosci 5:657-64 [Journal] [PubMed]

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

Peterka DS, Takahashi H, Yuste R (2011) Imaging voltage in neurons. Neuron 69:9-21 [Journal] [PubMed]

Popovic M, Gao X, Zecevic D (2012) Voltage-sensitive dye recording from axons, dendrites and dendritic spines of individual neurons in brain slices. J Vis Exp :e4261 [Journal] [PubMed]

Ramaswamy S, Hill SL, King JG, Schürmann F, Wang Y, Markram H (2012) Intrinsic morphological diversity of thick-tufted layer 5 pyramidal neurons ensures robust and invariant properties of in silico synaptic connections. J Physiol 590:737-52 [Journal] [PubMed]

Roth A, Bahl A (2009) Divide et impera: optimizing compartmental models of neurons step by step. J Physiol 587:1369-70 [Journal] [PubMed]

Rudolph S, Thanawala MS (2015) Location matters: somatic and dendritic SK channels answer to distinct calcium signals. J Neurophysiol 114:1-5 [Journal] [PubMed]

Rudy B,Iverson LE (1997) Ion channels

Rumbell TH, Draguljic D, Yadav A, Hof PR, Luebke JI, Weaver CM (2016) Automated evolutionary optimization of ion channel conductances and kinetics in models of young and aged rhesus monkey pyramidal neurons. J Comput Neurosci 41:65-90 [Journal] [PubMed]

   Rhesus Monkey Young and Aged L3 PFC Pyramidal Neurons (Rumbell et al. 2016) [Model]

Schiller J, Schiller Y, Stuart G, Sakmann B (1997) Calcium action potentials restricted to distal apical dendrites of rat neocortical pyramidal neurons. J Physiol 505 ( Pt 3):605-16 [PubMed]

Smith SL, Smith IT, Branco T, Häusser M (2013) Dendritic spikes enhance stimulus selectivity in cortical neurons in vivo. Nature 503:115-20 [Journal] [PubMed]

   Dendritic spikes enhance stimulus selectivity in cortical neurons in vivo (Smith et al 2013) [Model]

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

Steriade M, Nuñez A, Amzica F (1993) A novel slow (< 1 Hz) oscillation of neocortical neurons in vivo: depolarizing and hyperpolarizing components. J Neurosci 13:3252-65 [PubMed]

Timofeev I, Chauvette S (2011) Thalamocortical oscillations: local control of EEG slow waves. Curr Top Med Chem 11:2457-71 [PubMed]

Traub RD, Contreras D, Cunningham MO, Murray H, LeBeau FE, Roopun A, Bibbig A, Wilent WB, Higley MJ, Whittington MA (2005) Single-column thalamocortical network model exhibiting gamma oscillations, sleep spindles, and epileptogenic bursts. J Neurophysiol 93:2194-232 [Journal] [PubMed]

   Collection of simulated data from a thalamocortical network model (Glabska, Chintaluri, Wojcik 2017) [Model]
   A single column thalamocortical network model (Traub et al 2005) [Model]

Van Geit W, De Schutter E, Achard P (2008) Automated neuron model optimization techniques: a review. Biol Cybern 99:241-51 [Journal] [PubMed]

Van Geit W, Gevaert M, Chindemi G, Rössert C, Courcol JD, Muller EB, Schürmann F, Segev I, Markram H (2016) BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience. Front Neuroinform 10:17 [Journal] [PubMed]

Wang G, Wyskiel DR, Yang W, Wang Y, Milbern LC, Lalanne T, Jiang X, Shen Y, Sun QQ, Zhu JJ (2015) An optogenetics- and imaging-assisted simultaneous multiple patch-clamp recording system for decoding complex neural circuits. Nat Protoc 10:397-412 [Journal] [PubMed]

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

Wu X, Liao L, Liu X, Luo F, Yang T, Li C (2012) Is ZD7288 a selective blocker of hyperpolarization-activated cyclic nucleotide-gated channel currents? Channels (Austin) 6:438-42 [Journal] [PubMed]

Zhao L, Beverlin B, Netoff T, Nykamp DQ (2011) Synchronization from second order network connectivity statistics. Front Comput Neurosci 5:28 [Journal] [PubMed]

Zitzler E, Kunzli S (2004) Indicator-based selection in multiobjective search Parallel Problem Solving From Nature-ppsn Viii 3242:832-842

Mäki-Marttunen T, Krull F, Bettella F, Hagen E, Næss S, Ness TV, Moberget T, Elvsåshagen T, Metzner C, Devor A, Edwards AG, Fyhn M, Djurovic S, Dale AM, Andreassen OA, Einevoll GT (2019) Alterations in Schizophrenia-Associated Genes Can Lead to Increased Power in Delta Oscillations. Cereb Cortex 29:875-891 [Journal] [PubMed]

   SCZ-associated variant effects on L5 pyr cell NN activity and delta osc. (Maki-Marttunen et al 2018) [Model]

(71 refs)