Legends: | Link to a Model | Reference cited by multiple papers |
References and models cited by this paper | References and models that cite this paper | |||||||||||||||||||||||||||||||||||||||||||||
Ainsworth M, Lee S, Cunningham MO, Roopun AK, Traub RD, Kopell NJ, Whittington MA (2011) Dual ? rhythm generators control interlaminar synchrony in auditory cortex. J Neurosci 31:17040-51 [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] [PubMed]
Almog M, Korngreen A (2016) Is realistic neuronal modeling realistic? J Neurophysiol 116:2180-2209 [Journal] [PubMed] Anderson CT, Sheets PL, Kiritani T, Shepherd GM (2010) Sublayer-specific microcircuits of corticospinal and corticostriatal neurons in motor cortex. Nat Neurosci 13:739-44 [Journal] [PubMed] Apicella AJ, Wickersham IR, Seung HS, Shepherd GM (2012) Laminarly orthogonal excitation of fast-spiking and low-threshold-spiking interneurons in mouse motor cortex. J Neurosci 32:7021-33 [Journal] [PubMed] Ascoli GA, Donohue DE, Halavi M (2007) NeuroMorpho.Org: a central resource for neuronal morphologies. J Neurosci 27:9247-51 [Journal] [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]
Brent RP (1973) Algorithms For Minimization Without Derivatives Carnevale NT, Hines ML (2006) The NEURON Book [Journal] Deb K (2001) Multi-objective optimization using evolutionary algorithms xix:1-497 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 Doloc-Mihu A, Calabrese RL (2011) A database of computational models of a half-center oscillator for analyzing how neuronal parameters influence network activity. J Biol Phys 37:263-83 [Journal] [PubMed]
Dura-Bernal S, Neymotin SA, Kerr CC, Sivagnanam S, Majumdar A, Francis JT, Lytton WW (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):6:1-6:14 [Journal]
Edelman GM, Gally JA (2001) Degeneracy and complexity in biological systems. Proc Natl Acad Sci U S A 98:13763-8 [Journal] [PubMed] Garrett A (2014) inspyred: Bio-inspired Algorithms in Python Garrett A (2014) Python libraries for evolutionary computation inspired.jsu.edu/docs/Inspyred_Report_2012.pdf Golowasch J, Goldman MS, Abbott LF, Marder E (2002) Failure of averaging in the construction of a conductance-based neuron model. J Neurophysiol 87:1129-31 [Journal] [PubMed] Günay C, Edgerton JR, Jaeger D (2008) Channel density distributions explain spiking variability in the globus pallidus: a combined physiology and computer simulation database approach. J Neurosci 28:7476-91 [Journal] [PubMed]
Günay C, Edgerton JR, Li S, Sangrey T, Prinz AA, Jaeger D (2009) Database analysis of simulated and recorded electrophysiological datasets with PANDORA's toolbox. Neuroinformatics 7:93-111 [Journal] [PubMed] Harnett MT, Magee JC, Williams SR (2015) Distribution and function of HCN channels in the apical dendritic tuft of neocortical pyramidal neurons. J Neurosci 35:1024-37 [Journal] [PubMed] Harnett MT, Xu NL, Magee JC, Williams SR (2013) Potassium channels control the interaction between active dendritic integration compartments in layer 5 cortical pyramidal neurons. Neuron 79:516-29 [Journal] [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] Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci 17:7-11 [Journal] [PubMed] Holmes WR, Ambros-Ingerson J, Grover LM (2006) Fitting experimental data to models that use morphological data from public databases. J Comput Neurosci 20:349-65 [Journal] [PubMed] Hu W, Tian C, Li T, Yang M, Hou H, Shu Y (2009) Distinct contributions of Na(v)1.6 and Na(v)1.2 in action potential initiation and backpropagation. Nat Neurosci 12:996-1002 [Journal] [PubMed]
Iftinca M, McKay BE, Snutch TP, McRory JE, Turner RW, Zamponi GW (2006) Temperature dependence of T-type calcium channel gating. Neuroscience 142:1031-42 [Journal] [PubMed] Jolivet R, Kobayashi R, Rauch A, Naud R, Shinomoto S, Gerstner W (2008) A benchmark test for a quantitative assessment of simple neuron models. J Neurosci Methods 169:417-24 [Journal] [PubMed]
Jolivet R, Lewis TJ, Gerstner W (2004) Generalized integrate-and-fire models of neuronal activity approximate spike trains of a detailed model to a high degree of accuracy. J Neurophysiol 92:959-76 [Journal] [PubMed]
Kiritani T, Wickersham IR, Seung HS, Shepherd GM (2012) Hierarchical connectivity and connection-specific dynamics in the corticospinal-corticostriatal microcircuit in mouse motor cortex. J Neurosci 32:4992-5001 [Journal] [PubMed] Kole MH, Hallermann S, Stuart GJ (2006) Single Ih channels in pyramidal neuron dendrites: properties, distribution, and impact on action potential output. J Neurosci 26:1677-87 [Journal] [PubMed]
Konak A,Coit D,Smith A (2006) Multi-objective optimization using genetic algorithms: A tutorial Reliability Engineering & System Safety 91(9):992-1007 Lakatos P, Barczak A, Neymotin SA, McGinnis T, Ross D, Javitt DC, O'Connell MN (2016) Global dynamics of selective attention and its lapses in primary auditory cortex. Nat Neurosci 19:1707-1717 [Journal] [PubMed] Lakatos P, Karmos G, Mehta AD, Ulbert I, Schroeder CE (2008) Entrainment of neuronal oscillations as a mechanism of attentional selection. Science 320:110-3 [Journal] [PubMed] Lakatos P, Musacchia G, O'Connel MN, Falchier AY, Javitt DC, Schroeder CE (2013) The spectrotemporal filter mechanism of auditory selective attention. Neuron 77:750-61 [Journal] [PubMed] Lakatos P., Barczak, A., Neymotin S,Lytton W,McGinnis T,Javitt D,O'Connell N (2014) Thalamocortical dynamics of rhythmic selective and tonic suppressive modes in the auditory system Society for Neuroscience Abstracts Laudanski J, Torben-Nielsen B, Segev I, Shamma S (2014) Spatially distributed dendritic resonance selectively filters synaptic input. PLoS Comput Biol 10:e1003775 [Journal] [PubMed] Lundqvist M, Rehn M, Djurfeldt M, Lansner A (2006) Attractor dynamics in a modular network model of neocortex. Network 17:253-76 [Journal] [PubMed] Mainen ZF, Sejnowski TJ (1995) Reliability of spike timing in neocortical neurons. Science 268:1503-6 [PubMed] Marin B, Barnett WH, Doloc-Mihu A, Calabrese RL, Cymbalyuk GS (2013) High prevalence of multistability of rest states and bursting in a database of a model neuron. PLoS Comput Biol 9:e1002930 [Journal] [PubMed] Migliore M, Morse TM, Davison AP, Marenco L, Shepherd GM, Hines ML (2003) ModelDB: making models publicly accessible to support computational neuroscience. Neuroinformatics 1:135-9 [Journal] [PubMed] Migliore M, Shepherd GM (2002) Emerging rules for the distributions of active dendritic conductances. Nat Rev Neurosci 3:362-70 [Journal] [PubMed]
Mo J, Schroeder CE, Ding M (2011) Attentional modulation of alpha oscillations in macaque inferotemporal cortex. J Neurosci 31:878-82 [Journal] [PubMed] Neymotin S,Lytton W,O'Connell M,Lakatos P (2013) Dynamical microstates in primary auditory cortex Society for Neuroscience Abstracts Neymotin S,McDougal R,Hines M,Lytton W (2014) Calcium regulation of HCN supports persistent activity associated with working memory: a multiscale model of prefrontal cortex. BMC Neuroscience 15:108 Neymotin SA, Dura-Bernal S, Lakatos P, Sanger TD, Lytton WW (2016) Multitarget Multiscale Simulation for Pharmacological Treatment of Dystonia in Motor Cortex. Front Pharmacol 7:157 [Journal] [PubMed]
Neymotin SA, Hilscher MM, Moulin TC, Skolnick Y, Lazarewicz MT, Lytton WW (2013) Ih tunes theta/gamma oscillations and cross-frequency coupling in an in silico CA3 model. PLoS One 8:e76285 [Journal] [PubMed]
Neymotin SA, McDougal RA, Bulanova AS, Zeki M, Lakatos P, Terman D, Hines ML, Lytton WW (2016) Calcium regulation of HCN channels supports persistent activity in a multiscale model of neocortex. Neuroscience 316:344-66 [Journal] [PubMed]
Neymotin SA, McDougal RA, Sherif MA, Fall CP, Hines ML, Lytton WW (2015) Neuronal calcium wave propagation varies with changes in endoplasmic reticulum parameters: a computer model. Neural Comput 27:898-924 [Journal] [PubMed]
Peterson BE, Healy MD, Nadkarni PM, Miller PL, Shepherd GM (1996) ModelDB: an environment for running and storing computational models and their results applied to neuroscience. J Am Med Inform Assoc 3:389-98 [Journal] [PubMed] Preibisch S, Saalfeld S, Tomancak P (2009) Globally optimal stitching of tiled 3D microscopic image acquisitions. Bioinformatics 25:1463-5 [Journal] [PubMed] Prinz AA, Billimoria CP, Marder E (2003) Alternative to hand-tuning conductance-based models: construction and analysis of databases of model neurons. J Neurophysiol 90:3998-4015 [Journal] [PubMed] Prinz AA, Bucher D, Marder E (2004) Similar network activity from disparate circuit parameters. Nat Neurosci 7:1345-52 [Journal] [PubMed]
Reetz O, Stadler K, Strauss U (2014) Protein kinase C activation mediates interferon-ß-induced neuronal excitability changes in neocortical pyramidal neurons. J Neuroinflammation 11:185 [Journal] [PubMed]
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]
Schroeder CE, Lakatos P (2009) Low-frequency neuronal oscillations as instruments of sensory selection. Trends Neurosci 32:9-18 [Journal] [PubMed] Sekulic V, Chen TC, Lawrence JJ, Skinner FK (2015) Dendritic distributions of I h channels in experimentally-derived multi-compartment models of oriens-lacunosum/moleculare (O-LM) hippocampal interneurons. Front Synaptic Neurosci 7:2 [Journal] [PubMed]
Sekulic V, Lawrence JJ, Skinner FK (2014) Using multi-compartment ensemble modeling as an investigative tool of spatially distributed biophysical balances: application to hippocampal oriens-lacunosum/moleculare (O-LM) cells. PLoS One 9:e106567 [Journal] [PubMed] Sheets PL, Suter BA, Kiritani T, Chan CS, Surmeier DJ, Shepherd GM (2011) Corticospinal-specific HCN expression in mouse motor cortex: I(h)-dependent synaptic integration as a candidate microcircuit mechanism involved in motor control. J Neurophysiol 106:2216-31 [Journal] [PubMed] Silva LR, Amitai Y, Connors BW (1991) Intrinsic oscillations of neocortex generated by layer 5 pyramidal neurons. Science 251:432-5 [PubMed] Sivagnanam S,Majumdar A, Yoshimoto K, Astakhov V, Bandrowski A, Martone ME, Carnevale NT (2013) Introducing the Neuroscience Gateway 2013 IWSG, volume 993 of CEUR Workshop Proceedings, CEUR-WS.org, [Journal] Stadler K, Bierwirth C, Stoenica L, Battefeld A, Reetz O, Mix E, Schuchmann S, Velmans T, Rosenberger K, Bräuer AU, Lehnardt S, Nitsch R, Budt M, Wolff T, Kole MH, Strauss U (2014) Elevation in type I interferons inhibits HCN1 and slows cortical neuronal oscillations. Cereb Cortex 24:199-210 [Journal] [PubMed]
Suter BA, Migliore M, Shepherd GM (2013) Intrinsic electrophysiology of mouse corticospinal neurons: a class-specific triad of spike-related properties. Cereb Cortex 23:1965-77 [Journal] [PubMed] Suter BA, O'Connor T, Iyer V, Petreanu LT, Hooks BM, Kiritani T, Svoboda K, Shepherd GM (2010) Ephus: multipurpose data acquisition software for neuroscience experiments. Front Neural Circuits 4:100 [Journal] [PubMed] Suter BA, Shepherd GM (2015) Reciprocal interareal connections to corticospinal neurons in mouse M1 and S2. J Neurosci 35:2959-74 [Journal] [PubMed] Tripathy SJ, Burton SD, Geramita M, Gerkin RC, Urban NN (2015) Brain-wide analysis of electrophysiological diversity yields novel categorization of mammalian neuron types. J Neurophysiol 113:3474-89 [Journal] [PubMed] Van Geit W, Achard P, De Schutter E (2007) Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models. Front Neuroinform 1:1 [Journal] [PubMed] 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] Yamawaki N, Shepherd GM (2015) Synaptic circuit organization of motor corticothalamic neurons. J Neurosci 35:2293-307 [Journal] [PubMed] | Iavarone E, Yi J, Shi Y, Zandt BJ, O'Reilly C, Van Geit W, Rössert C, Markram H, Hill SL (2019) Experimentally-constrained biophysical models of tonic and burst firing modes in thalamocortical neurons. PLoS Comput Biol 15:e1006753 [Journal] [PubMed]
Jedrzejewski-Szmek Z, Abrahao KP, Jedrzejewska-Szmek J, Lovinger DM, Blackwell KT (2018) Parameter Optimization Using Covariance Matrix Adaptation-Evolutionary Strategy (CMA-ES), an Approach to Investigate Differences in Channel Properties Between Neuron Subtypes. Front Neuroinform 12:47 [Journal] [PubMed]
Rumbell T, Kozloski J (2019) Dimensions of control for subthreshold oscillations and spontaneous firing in dopamine neurons PLOS Computational Biology 15:1-34 [Journal]
|