Citation Relationships



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 [PubMed]

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

References and models cited by this paper

References and models that cite this paper

Abouzeid A,Kath WL (2014) Fully automated multi-objective fitting of morphologically realistic hippocampal CA1 pyramidal cell models Neuroscience meeting planner 372:14

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

Achard P, De Schutter E (2008) Calcium, synaptic plasticity and intrinsic homeostasis in purkinje neuron models. Front Comput Neurosci 2:8 [PubMed]

Achard P,Van Geit W,LeMasson G (2010) Parameter searching Computational Modeling Methods for Neuroscientists, De Schutter E, ed. pp.31

Ahern CA, Payandeh J, Bosmans F, Chanda B (2016) The hitchhiker's guide to the voltage-gated sodium channel galaxy. J Gen Physiol 147:1-24 [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]

Amatrudo JM, Weaver CM, Crimins JL, Hof PR, Rosene DL, Luebke JI (2012) Influence of highly distinctive structural properties on the excitability of pyramidal neurons in monkey visual and prefrontal cortices J. Neurosci, 32(40):13644-60 [Journal] [PubMed]

   Rhesus Monkey Layer 3 Pyramidal Neurons: V1 vs PFC (Amatrudo, Weaver et al. 2012) [Model]

Amendola J, Woodhouse A, Martin-Eauclaire MF, Goaillard JM (2012) Ca2+/cAMP-sensitive covariation of I(A) and I(H) voltage dependences tunes rebound firing in dopaminergic neurons. J Neurosci 32:2166-81 [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]

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]

Buhry L,Pace M,Saïghi S (2012) Global parameter estimation of an Hodgkin-Huxley formalism using membrane voltage recordings: Application to neuro-mimetic analog integrated circuits Neurocomputing 81:75-85

Burke RE (2004) Comparison of alternative designs for reducing complex neurons to equivalent cables. J Comput Neurosci 9:31-47 [PubMed]

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

Carnevale NT, Hines ML (2006) The NEURON Book [Journal]

Chang YM, Rosene DL, Killiany RJ, Mangiamele LA, Luebke JI (2005) Increased action potential firing rates of layer 2/3 pyramidal cells in the prefrontal cortex are significantly related to cognitive performance in aged monkeys. Cereb Cortex 15:409-18 [Journal] [PubMed]

Coskren PJ, Luebke JI, Kabaso D, Wearne SL, Yadav A, Rumbell T, Hof PR, Weaver CM (2015) Functional consequences of age-related morphologic changes to pyramidal neurons of the rhesus monkey prefrontal cortex. J Comput Neurosci 38:263-83 [Journal] [PubMed]

   Rhesus Monkey Layer 3 Pyramidal Neurons: Young vs aged PFC (Coskren et al. 2015) [Model]

Destexhe A (2001) Simplified models of neocortical pyramidal cells preserving somatodendritic voltage attenuation Neurocomputing 38-40:167-173

Druckmann S, Banitt Y, Gidon A, Schurmann 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 [PubMed]

Druckmann S, Berger TK, Hill S, Schurmann F, Markram H, Segev I (2008) Evaluating automated parameter constraining procedures of neuron models by experimental and surrogate data. Biol Cybern 99:371-9 [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]

Eiben AE,Smith JE () Introduction to Evolutionary Computing

Friedrich P, Vella M, Gulyas AI, Freund TF, Kali S (2014) A flexible, interactive software tool for fitting the parameters of neuronal models. Front Neuroinform 8:63 [Journal] [PubMed]

   Software (called Optimizer) for fitting neuronal models (Friedrich et al. 2014) [Model]

Gilman JP, Medalla M, Luebke JI (2017) Area-Specific Features of Pyramidal Neurons-a Comparative Study in Mouse and Rhesus Monkey. Cereb Cortex 27:2078-2094 [Journal] [PubMed]

Goldman MS, Golowasch J, Marder E, Abbott LF (2001) Global structure, robustness, and modulation of neuronal models. J Neurosci 21:5229-38 [Journal] [PubMed]

   Global structure, robustness, and modulation of neuronal models (Goldman et al. 2001) [Model]

Gunay 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]

   Globus pallidus multi-compartmental model neuron with realistic morphology (Gunay et al. 2008) [Model]

Handl J, Kell DB, Knowles J (2007) Multiobjective optimization in bioinformatics and computational biology. IEEE/ACM Trans Comput Biol Bioinform 4:279-92 [Journal] [PubMed]

Hay E, Hill S, Schurmann 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]
   L5b PC model constrained for BAC firing and perisomatic current step firing (Hay et al., 2011) [Model]
   Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2017) [Model]

Hay E, Schurmann F, Markram H, Segev I (2013) Preserving Axo-somatic Spiking Features Despite Diverse Dendritic Morphology. J Neurophysiol 109(12):2972-81 [Journal] [PubMed]

   Preserving axosomatic spiking features despite diverse dendritic morphology (Hay et al., 2013) [Model]

Hendrickson EB, Edgerton JR, Jaeger D (2011) The use of automated parameter searches to improve ion channel kinetics for neural modeling. J Comput Neurosci [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. J. Comp. Neurosci. 30(2):301-321 [Journal] [PubMed]

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

Hollander M,Wolfe DA,Chicken E (2014) Nonparametric statistical methods, 3rd

Huys QJ, Ahrens MB, Paninski L (2006) Efficient estimation of detailed single-neuron models. J Neurophysiol 96:872-90 [Journal] [PubMed]

   Efficient estimation of detailed single-neuron models (Huys et al. 2006) [Model]

Huys QJ, Paninski L (2009) Smoothing of, and parameter estimation from, noisy biophysical recordings. PLoS Comput Biol 5:e1000379-80 [Journal] [PubMed]

   Smoothing of, and parameter estimation from, noisy biophysical recordings (Huys & Paninski 2009) [Model]

Jan LY, Jan YN (2012) Voltage-gated potassium channels and the diversity of electrical signalling. J Physiol 590:2591-9 [Journal] [PubMed]

Johnson ME,Moore LM,Ylvisaker D (1990) Minimax and maximin distance designs Journal of Statistical Planning and Inference 26(2):131-148

Jolliffe IT (2002) Principal component analysis (2nd ed)

Kabaso D, Coskren PJ, Henry BI, Hof PR, Wearne SL (2009) The electrotonic structure of pyramidal neurons contributing to prefrontal cortical circuits in macaque monkeys is significantly altered in aging. Cereb Cortex 19:2248-68 [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]

Kostuk M, Toth BA, Meliza CD, Margoliash D, Abarbanel HD (2012) Dynamical estimation of neuron and network properties II: Path integral Monte Carlo methods. Biol Cybern 106:155-67 [Journal] [PubMed]

Lemasson G, Maex R (2001) Introduction to equation solving and parameter fitting. Computational neuroscience: Realistic modelling for experimentalists 125:125

Loeppky JL,Sacks J,Welch WJ (2009) Choosing the sample size of a computer experiment: A practical guide Technometrics 51(4):366-376

Malik A,Shim K,Prinz AA,Smolinski TG (2013) Multi-objective evolutionary algorithms for analysis of conductance correlations involved in recovery of bursting after neuromodulator deprivation in lobster stomatogastric neuron models BMC Neuroscience 14(suppl 1):P370

Marder E, Goaillard JM (2006) Variability, compensation and homeostasis in neuron and network function. Nat Rev Neurosci 7:563-74 [PubMed]

Martina M, Jonas P (1997) Functional differences in Na+ channel gating between fast-spiking interneurones and principal neurones of rat hippocampus. J Physiol 505 ( Pt 3):593-603 [PubMed]

Meliza CD, Kostuk M, Huang H, Nogaret A, Margoliash D, Abarbanel HD (2014) Estimating parameters and predicting membrane voltages with conductance-based neuron models. Biol Cybern 108:495-516 [Journal] [PubMed]

Mensi S, Naud R, Pozzorini C, Avermann M, Petersen CC, Gerstner W (2012) Parameter Extraction and Classification of Three Cortical Neuron Types Reveals Two Distinct Adaptation Mechanisms J Neurophysiol 107(6):1756-1775 [Journal] [PubMed]

   Extraction and classification of three cortical neuron types (Mensi et al. 2012) [Model]

Mezura-Montes E,Reyes-Sierra M,Coello Coello CA (2008) Multi-objective optimization using differential evolution: a survey of the state-of-the-art Advances in differential evolution, Chakraborty U, ed. pp.173

Morris MD,Mitchell TJ (1995) Exploratory designs for computational experiments Journal of Statistical Planning and Inference 43(3):381-402

O'Leary T, Williams AH, Franci A, Marder E (2014) Cell types, network homeostasis, and pathological compensation from a biologically plausible ion channel expression model. Neuron 82:809-21 [Journal] [PubMed]

Pospischil M, Toledo-Rodriguez M, Monier C, Piwkowska Z, Bal T, Fregnac Y, Markram A, Destexhe A (2008) Minimal Hodgkin-Huxley type models for different classes of cortical and thalamic neurons. Biol Cybern 99:427-41 [Journal] [PubMed]

   Hodgkin-Huxley models of different classes of cortical neurons (Pospischil et al. 2008) [Model]

Price KV (2008) Eliminating drift bias from the differential evoluation algorithm Advances in differential evolution, 1st edn 2:33-88

Price KV,Storn RM,Lampinen JA (2005) Differential Evolution

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]

Rodriguez A, Ehlenberger DB, Dickstein DL, Hof PR, Wearne SL (2008) Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images. PLoS One 3:e1997-61 [PubMed]

Rodriguez A, Ehlenberger DB, Hof PR, Wearne SL (2009) Three-dimensional neuron tracing by voxel scooping. J Neurosci Methods 184:169-75 [Journal] [PubMed]

Schulz DJ, Goaillard JM, Marder E (2006) Variable channel expression in identified single and electrically coupled neurons in different animals. Nat Neurosci 9:356-62 [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]

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]

Smolinski TG, Prinz AA (2009) Computational intelligence in modeling of biological neurons: A case study of an invertebrate pacemaker neuron Neural Networks, 2009. IJCNN 2009:2964-2970

Swensen AM, Bean BP (2005) Robustness of burst firing in dissociated purkinje neurons with acute or long-term reductions in sodium conductance. J Neurosci 25:3509-20 [PubMed]

Tobin AE, Van Hooser SD, Calabrese RL (2006) Creation and reduction of a morphologically detailed model of a leech heart interneuron. J Neurophysiol 96:2107-20 [Journal] [PubMed]

Toth BA, Kostuk M, Meliza CD, Margoliash D, Abarbanel HD (2011) Dynamical estimation of neuron and network properties I: variational methods. Biol Cybern 105:217-37 [Journal] [PubMed]

Traub RD, Buhl EH, Gloveli T, Whittington MA (2003) Fast Rhythmic Bursting Can Be Induced in Layer 2/3 Cortical Neurons by Enhancing Persistent Na(+) Conductance or by Blocking BK Channels. J Neurophysiol 89:909-21 [Journal] [PubMed]

   Mechanisms of fast rhythmic bursting in a layer 2/3 cortical neuron (Traub et al 2003) [Model]

Traub RD, Jefferys JG, Miles R, Whittington MA, Toth K (1994) A branching dendritic model of a rodent CA3 pyramidal neurone. J Physiol 481 ( Pt 1):79-95 [PubMed]

Van Geit W, Achard P, De Schutter E (2007) Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models. Front Neuroinformatics 1:1-42 [PubMed]

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

Vanier MC, Bower JM (1999) A comparative survey of automated parameter-search methods for compartmental neural models. J Comput Neurosci 7:149-71 [Journal] [PubMed]

Weaver CM, Wearne SL (2006) The role of action potential shape and parameter constraints in optimization of compartment models Neurocomputing 69:1053-1057 [Journal]

   AP shape and parameter constraints in optimization of compartment models (Weaver and Wearne 2006) [Model]

Weaver CM, Wearne SL (2008) Neuronal Firing Sensitivity to Morphologic and Active Membrane Parameters. PLoS Comput Biol 4:e11 [Journal] [PubMed]

Yadav A,Weaver CM,Gao YZ,Luebke JI,Hof PR (2010) Age-related morphologic changes alter robustness of neuronal function BMC Neuroscience 11(Suppl 1):P140

Yadav A,Weaver CM,Gao YZ,Luebke JI,Wearne SL (2008) Why are pyramidal cell firing rates increased with aging, and what can we do about it? BMC Neuroscience 9(Suppl 1):P51

Zielinski K,Laur R (2008) Stopping criteria for differential evolution in constrained single-objective optimization Advances in Differential Evolution 4:111-138

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]

   Motor system model with reinforcement learning drives virtual arm (Dura-Bernal et al 2017) [Model]

Eyal G, Verhoog MB, Testa-Silva G, Deitcher Y, Lodder JC, Benavides-Piccione R, Morales J, DeFelipe J, de Kock CP, Mansvelder HD, Segev I (2016) Unique membrane properties and enhanced signal processing in human neocortical neurons. Elife [Journal] [PubMed]

   Human L2/3 pyramidal cells with low Cm values (Eyal et al. 2016) [Model]

Goodliffe JW, Song H, Rubakovic A, Chang W, Medalla M, Weaver CM, Luebke JI (2018) Differential changes to D1 and D2 medium spiny neurons in the 12-month-old Q175+/- mouse model of Huntington's Disease. PLoS One 13:e0200626 [Journal] [PubMed]

   Electrotonic transform and EPSCs for WT and Q175+/- spiny projection neurons (Goodliffe et al 2018) [Model]

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]

   Parameter optimization using CMA-ES (Jedrzejewski-Szmek et al 2018) [Model]

Mäki-Marttunen T, Halnes G, Devor A, Metzner C, Dale AM, Andreassen OA, Einevoll GT (2017) A stepwise neuron model fitting procedure designed for recordings with high spatial resolution: Application to layer 5 pyramidal cells. J Neurosci Methods [Journal] [PubMed]

   Layer V pyramidal cell model with reduced morphology (Mäki-Marttunen et al 2017) [Model]

Neymotin SA, Suter BA, Dura-Bernal S, Shepherd GM, Migliore M, Lytton WW (2017) Optimizing computer models of corticospinal neurons to replicate in vitro dynamics. J Neurophysiol 117(1):148-162 [Journal] [PubMed]

   Computer models of corticospinal neurons replicate in vitro dynamics (Neymotin et al. 2017) [Model]

(78 refs)