Papers that obtained or contributed code in ModelDB

These papers state (in text or supplementary material) they used or contributed code to ModelDB or both
or they mention ModelDB in a neuroinformatics infrastructure context.

1Abbasi S, Hudson AE, Maran SK, Cao Y, Abbasi A, Heck DH, Jaeger D (2017) Robust Transmission of Rate Coding in the Inhibitory Purkinje Cell to Cerebellar Nuclei Pathway in Awake Mice PLOS Computational Biologyboth
2Balbi 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(9):e1005737[PubMed]both
3Ben-Shalom R, Keeshen CM,Berrios KN, An JY, Sanders SJ, Bender KJ (2017) Opposing effects on NaV1.2 function underlie differences between SCN2A variants observed in individuals with autism spectrum disorder or infantile seizures Biological Psychiatry, epub before printsubmitted materials
4Bhalla US (2017) Synaptic input sequence discrimination on behavioral time-scales mediated by reaction-diffusion chemistry in dendrites. Elife[PubMed]submitted materials
5Bono J, Clopath C (2017) Modeling somatic and dendritic spike mediated plasticity at the single neuron and network level Nature Communications 8:706submitted materials
6Brzosko Z, Zannone S, Schultz W, Clopath C, Paulsen O (2017) Sequential neuromodulation of Hebbian plasticity offers mechanism for effective reward-based navigation. Elife[PubMed]submitted materials
7Canakci S, Toy MF, Inci AF, Liu X, Kuzum D (2017) Computational analysis of network activity and spatial reach of sharp wave-ripples PLoS ONE 12(9):e0184542[PubMed]submitted materials
8Chen W, De Schutter E (2017) Parallel STEPS: Large Scale Stochastic Spatial Reaction-Diffusion Simulation with High Performance Computers Front. Neuroinform. 11:13submitted materials
9Danielson NB, Turi GF, Ladow M, Chavlis S, Petrantonakis PC, Poirazi P, Losonczy A (2017) In Vivo Imaging of Dentate Gyrus Mossy Cells in Behaving Mice. Neuron 93:552-559.e4[PubMed]submitted materials
10Diekman CO, Thomas PJ, Wilson CG (2017) Eupnea, tachypnea, and autoresuscitation in a closed-loop respiratory control model J Neurophysiol 118(4):2194-2215[PubMed]submitted materials
11Diwakar S, Medini C, Nair M, Parasuram H, Vijayan A, Nair B (2017) Computational Neuroscience of Timing, Plasticity and Function in Cerebellum Microcircuits (Chapter 12) Computational Neurology and Psychiatry, Springer Series in Bio-/Neuroinformatics, Érdi P:et al, ed. pp.343submitted materials
12Dougalis AG, Matthews GA, Liss B, Ungless MA (2017) Ionic currents influencing spontaneous firing and pacemaker frequency in dopamine neurons of the ventrolateral periaqueductal gray and dorsal raphe nucleus (vlPAG/DRN): A voltage-clamp and computational modelling study. J Comput Neurosci[PubMed]submitted materials
13Droste F, Lindner B (2017) Exact analytical results for integrate-and-fire neurons driven by excitatory shot noise J. Comp. Neurosci.submitted materials
14Dura-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):6:1-6:14submitted materials
15Eglen SJ, Marwick B, Halchenko YO, Hanke M, Sufi S, Gleeson P, Silver RA, Davison AP, Lanyon L, Abrams M, Wachtler T, Willshaw DJ, Pouzat C, Poline JB (2017) Toward standard practices for sharing computer code and programs in neuroscience. Nat Neurosci 20:770-773[PubMed]mentions
16Glabska H, Chintaluri C, Wójcik DK (2017) Collection of Simulated Data from a Thalamocortical Network Model. Neuroinformatics 15:87-99[PubMed]obtained materials
17Gunn BG, Cox CD, Chen Y, Frotscher M, Gall CM, Baram TZ, Lynch G (2017) The Endogenous Stress Hormone CRH Modulates Excitatory Transmission and Network Physiology in Hippocampus. Cereb Cortex :1-17[PubMed]both
18Gutnisky DA, Yu J, Hires SA, To MS, Bale M, Svoboda K, Golomb D (2017) Mechanisms underlying a thalamocortical transformation during active tactile sensation PLoS Comput Biol 13(6):e1005576submitted materials
19Handy G, Taheri M, White JA, Borisyuk A (2017) Mathematical investigation of IP3-dependent calcium dynamics in astrocytes. J Comput Neurosci[PubMed]submitted materials
20Hepburn I, Jain A, Gangal H, Yamamoto Y, Tanaka-Yamamoto K, De Schutter E (2017) A model of induction of cerebellar Long-Term Depression including RKIP inactivation of Raf and MEK Frontiers in Molecular Neurosciencesubmitted materials
21Hummos A, Nair SS (2017) An integrative model of the intrinsic hippocampal theta rhythm. PLoS One 12:e0182648[PubMed]obtained materials
22Jedrzejewska-Szmek J, Luczak V, Abel T, Blackwell KT (2017) ß-adrenergic signaling broadly contributes to LTP induction PLOS Computational Biology 13(7):e1005657[PubMed]submitted materials
23Justus D, Dalügge D, Bothe S, Fuhrmann F, Hannes C, Kaneko H, Friedrichs D, Sosulina L, Schwarz I, Elliott DA, Schoch S, Bradke F, Schwarz MK, Remy S (2017) Glutamatergic synaptic integration of locomotion speed via septoentorhinal projections. Nat Neurosci 20:16-19[PubMed]submitted materials
24Kim CM, Nykamp DQ (2017) The influence of depolarization block on seizure-like activity in networks of excitatory and inhibitory neurons. J Comput Neurosci 43:65-79[PubMed]submitted materials
25Knowlton CJ, Kutterer S, Roeper J, Canavier CC (2017) Calcium dynamics control K-ATP channel mediated bursting in substantia nigra dopamine neurons: a combined experimental and modeling study. J Neurophysiol :jn.00351.2017[PubMed]submitted materials
26Kobayashi T, Shimada Y, Fujiwara K, Ikeguchi T (2017) Reproducing Infra-Slow Oscillations with Dopaminergic Modulation. Sci Rep 7:2411[PubMed]submitted materials
27Mäki-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[PubMed]submitted materials
28Mäki-Marttunen T, Lines GT, Edwards AG, Tveito A, Dale AM, Einevoll GT, Andreassen OA (2017) Pleiotropic effects of schizophrenia-associated genetic variants in neuron firing and cardiac pacemaking revealed by computational modeling Translational Psychiatry, acceptedsubmitted materials
29Manninen T, Havela R, Linne ML (2017) Reproducibility and comparability of computational models for astrocyte calcium excitability Front. Neuroinform.both
30Masquelier T (2017) STDP allows close-to-optimal spatiotemporal spike pattern detection by single coincidence detector neurons Neuroscience, in press, accepted manuscriptsubmitted materials
31McColgan T, Liu J, Kuokkanen PT, Carr CE, Wagner H, Kempter R (2017) Dipolar extracellular potentials generated by axonal projections. Elife[PubMed]obtained materials
32Neymotin 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[PubMed]submitted materials
33Ona-Jodar T, Gerkau NJ, Aghvami SS, Rose CR, Egger V (2017) Two-Photon Na+ Imaging Reports Somatically Evoked Action Potentials in Rat Olfactory Bulb Mitral and Granule Cell Neurites Front. Cell. Neurosci. 11:50submitted materials
34Papoutsi A, Kastellakis G, Poirazi P (2017) Basal tree complexity shapes functional pathways in the prefrontal cortex. J Neurophysiol :jn.00099.2017[PubMed]both
35Pedrosa V, Clopath C (2017) The role of neuromodulators in cortical plasticity. A computational perspective. Front. Synaptic Neurosci. 8:38submitted materials
36Podlaski WF, Seeholzer A, Groschner LN, Miesenböck G, Ranjan R, Vogels TP (2017) Mapping the function of neuronal ion channels in model and experiment. Elife[PubMed]mentions
37Powers AR III, Mathys CH, Corlett PR (2017) Pavlovian conditioning-induced hallucinations result from overweighting of perceptual priors Science 357(6351):20596-600[PubMed]submitted materials
38Tarfa RA, Evans RC, Khaliq ZM (2017) Enhanced sensitivity to hyperpolarizing inhibition in mesoaccumbal relative to nigrostriatal dopamine neuron subpopulations. J Neurosci[PubMed]submitted materials
39Tikidji-Hamburyan RA, Narayana V, Bozkus Z, El-Ghazawi TA (2017) Software for Brain Network Simulations: A Comparative Study Front. Neuroinform.both
40Ueyama Y (2017) Optimal feedback control to describe multiple representations of primary motor cortex neurons. J Comput Neurosci 43:93-106[PubMed]submitted materials
41Urdapilleta E, Si B, Treves A (2017) Self-organization of modular activity of grid cells. Hippocampus[PubMed]submitted materials
42von Reyn CR, Nern A, Williamson WR, Breads P, Wu M, Namiki S, Card GM (2017) Feature Integration Drives Probabilistic Behavior in the Drosophila Escape Response. Neuron 94:1190-1204.e6[PubMed]submitted materials
43Wang Y, Trevelyan AJ, Valentin A, Alarcon G, Taylor PN, Kaiser M (2017) Mechanisms underlying different onset patterns of focal seizures PLoS 13(5):e1005475submitted materials
44Watanabe T, Shimazaki T, Oda Y (2017) Coordinated Expression of Two Types of Low-Threshold K+ Channels Establishes Unique Single-Spiking of Mauthner Cells among Segmentally Homologous Neurons in the Zebrafish Hindbrain eNeurosubmitted materials
45Whittington JCR, Bogacz R (2017) An approximation of the error back-propagation algorithm in a predictive coding network with local Hebbian synaptic plasticity Neural Computation, in press (preprint available)submitted materials
46Zylbertal A, Yarom Y, Wagner S (2017) Synchronous infra-slow bursting in the mouse accessory olfactory bulb emerge from interplay between intrinsic neuronal dynamics and network connectivity. J Neurosci[PubMed]submitted materials
47Zylbertal A, Yarom Y, Wagner S (2017) The Slow Dynamics of Intracellular Sodium Concentration Increase the Time Window of Neuronal Integration: A Simulation Study Front. Comput. Neurosci. 11(85):1-16both
48Alturki A, Feng F, Nair A, Guntu V, Nair SS (2016) Distinct current modules shape cellular dynamics in model neurons. Neuroscience 334:309-331[PubMed]both
49Bezaire MJ, Raikov I, Burk K, Vyas D, Soltesz I (2016) Interneuronal mechanisms of hippocampal theta oscillation in a full-scale model of the rodent CA1 circuit. Elife[PubMed]submitted materials
50Bird AD, Cuntz H (2016) Optimal Current Transfer in Dendrites. PLoS Comput Biol 12:e1004897[PubMed]obtained materials
51Bloss EB, Cembrowski MS, Karsh B, Colonell J, Fetter RD, Spruston N (2016) Structured Dendritic Inhibition Supports Branch-Selective Integration in CA1 Pyramidal Cells. Neuron[PubMed]submitted materials
52Buchin A, Chizhov A, Huberfeld G, Miles R, Gutkin BS (2016) Reduced Efficacy of the KCC2 Cotransporter Promotes Epileptic Oscillations in a Subiculum Network Model. J Neurosci 36:11619-11633[PubMed]submitted materials
53Buchin A, Rieubland S, Häusser M, Gutkin BS, Roth A (2016) Inverse Stochastic Resonance in Cerebellar Purkinje Cells. PLoS Comput Biol 12:e1005000[PubMed]submitted materials
54Cattani A, Solinas S, Canuto C (2016) A Hybrid Model for the Computationally-Efficient Simulation of the Cerebellar Granular Layer. Front Comput Neurosci 10:30[PubMed]submitted materials
55Cavarretta F, Marasco A, Hines ML, Shepherd GM, Migliore M (2016) Glomerular and Mitral-Granule Cell Microcircuits Coordinate Temporal and Spatial Information Processing in the Olfactory Bulb. Front Comput Neurosci 10:67[PubMed]submitted materials
56Ceballos CC, Li S, Roque AC, Tzounopoulos T, Leao RM (2016) Ih equalizes membrane input resistance in a heterogeneous population of fusiform neurons in the dorsal cochlear nucleus Front. Cell. Neurosci. 10:249[PubMed]submitted materials
57Chay A, Zamparo I, Koschinski A, Zaccolo M, Blackwell KT (2016) Control of betaAR- and N-methyl-D-aspartate (NMDA) Receptor-Dependent cAMP Dynamics in Hippocampal Neurons PLoS Computational Biology 12(2):e1004735[PubMed]submitted materials
58Cui Y, Prokin I, Xu H, Delord B, Genet S, Venance L, Berry H (2016) Endocannabinoid dynamics gate spike-timing dependent depression and potentiation. Elife[PubMed]submitted materials
59Dover K, Marra C, Solinas S, Popovic M, Subramaniyam S, Zecevic D, D'Angelo E, Goldfarb M (2016) FHF-independent conduction of action potentials along the leak-resistant cerebellar granule cell axon. Nat Commun 7:12895[PubMed]submitted materials
60Dura-Bernal S, Li K, Neymotin SA, Francis JT, Principe JC, Lytton WW (2016) Restoring behavior via inverse neurocontroller in a lesioned cortical spiking model driving a virtual arm. Front. Neurosci. Neuroprosthetics 10:28submitted materials
61Ehling P, Meuth P, Eichinger P, Herrmann AM, Bittner S, Pawlowski M, Pankratz S, Herty M, Budde T, Meuth SG (2016) Human T cells in silico: Modelling their electrophysiological behaviour in health and disease. J Theor Biol 404:236-50[PubMed]obtained materials
62Enrico P, Migliore M, Spiga S, Mulas G, Caboni F, Diana M (2016) Morphofunctional alterations in ventral tegmental area dopamine neurons in acute and prolonged opiates withdrawal. A computational perspective. Neuroscience 322:195-207[PubMed]both
63Fietkiewicz C, Loparo KA (2016) Analysis and Enhancements of a Prolific Macroscopic Model of Epilepsy. Scientifica (Cairo) 2016:3628247[PubMed]both
64Fietkiewicz C, Shafer GO, Platt EA, Wilson CG (2016) Variability in respiratory rhythm generation: In vitro and in silico models Communications in Nonlinear Science and Numerical Simulation 32:158-168submitted materials
65Fribance S, Wang J, Roppolo JR, de Groat WC, Tai C (2016) Axonal model for temperature stimulation. J Comput Neurosci[PubMed]submitted materials
66Goldwyn JH, Rinzel J (2016) Neuronal coupling by endogenous electric fields: Cable theory and applications to coincidence detector neurons in the auditory brainstem. J Neurophysiol :jn.00780.2015[PubMed]submitted materials
67Guet-McCreight A, Camire O, Topolnik L, Skinner FK (2016) Using a Semi-Automated Strategy to Develop Multi-Compartment Models That Predict Biophysical Properties of Interneuron-Specific 3 (IS3) Cells in Hippocampus. eNeuro[PubMed]submitted materials
68Gupta R, Reneaux M, Karmeshu (2016) Role of Heterogeneous Macromolecular Crowding and Geometrical Irregularity at Central Excitatory Synapses in Shaping Synaptic Transmission. PLoS One 11:e0167505[PubMed]submitted materials
69Halnes G, Mäki-Marttunen T, Keller D, Pettersen KH, Andreassen OA, Einevoll GT (2016) Effect of Ionic Diffusion on Extracellular Potentials in Neural Tissue PLoS Comput Biol 12:e1005193[PubMed]submitted materials
70Hass J, Hertag L, Durstewitz D (2016) A detailed data-driven network model of prefrontal cortex reproduces key features of in vivo activity PLoS Comput Biol 12(5):e1004930[PubMed]submitted materials
71Ho ECY, Truccolo W (2016) Interaction between Synaptic Inhibition and Glial-Potassium Dynamics leads to Diverse Seizure Transition Modes in Biophysical Models of Human Focal Seizures J Comput Neuroscisubmitted materials
72Hubel N, Andrew RD, Ullah G (2016) Large extracellular space leads to neuronal susceptibility to ischemic injury in a Na(+)/K (+) pumps-dependent manner. J Comput Neurosci 40:177-92[PubMed]submitted materials
73Hubel N, Ullah G (2016) Anions Govern Cell Volume: A Case Study of Relative Astrocytic and Neuronal Swelling in Spreading Depolarization. PLoS One 11:e0147060[PubMed]submitted materials
74Jedrzejewska-Szmek J, Damodaran S, Dorman DB, Blackwell KT (2016) Calcium dynamics predict direction of synaptic plasticity in striatal spiny projection neurons. Eur J Neurosci[PubMed]submitted materials
75Ji Y, Zhang YH, Zheng WM (2016) Modelling Spiking Neural Network from the Architecture Evaluation Perspective Journal of Computer Science and Technology 31:50-59obtained materials
75Ji Y, Zhang YH, Zheng WM (2016) Modelling Spiking Neural Network from the Architecture Evaluation Perspective Journal of Computer Science and Technology 31:50-59mentions
76Kastellakis G, Silva AJ, Poirazi P (2016) Linking Memories across Time via Neuronal and Dendritic Overlaps in Model Neurons with Active Dendrites. Cell Rep 17:1491-1504[PubMed]submitted materials
77Kato A, Morita K (2016) Forgetting in Reinforcement Learning Links Sustained Dopamine Signals to Motivation. PLoS Comput Biol 12:e1005145[PubMed]submitted materials
78Lombardo J, Harrington MA (2016) Non-reciprocal mechanisms of up- and down-regulation of spinal motoneuron excitability by modulators of KCNQ/Kv7 channels. J Neurophysiol :jn.00446.2016[PubMed]both
79Lytton WW, Seidenstein AH, Dura-Bernal S, McDougal RA, Schurmann F, Hines ML (2016) Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON. Neural Comput :1-28[PubMed]submitted materials
80Maki-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[PubMed]submitted materials
81Masquelier T, Portelli G, Kornprobst P (2016) Microsaccades enable efficient synchrony-based coding in the retina: a simulation study Scientific Reports 6:24086[PubMed]submitted materials
82Matsubara T, Torikai H (2016) An Asynchronous Recurrent Network of Cellular Automaton-Based Neurons and Its Reproduction of Spiking Neural Network Activities. IEEE Trans Neural Netw Learn Syst 27:836-52[PubMed]obtained materials
83McDougal RA, Bulanova AS, Lytton WW (2016) Reproducibility in computational neuroscience models and simulations IEEE Trans Biomed Eng 63(10):2021-2035[PubMed]mentions
84McDougal RA, Morse TM, Carnevale T, Marenco L, Wang R, Migliore M, Miller PL, Shepherd GM, Hi (2016) Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. J Comput Neurosci 42(1):1-10[PubMed]mentions
85McIntyre AB, Cleland TA (2016) Biophysical constraints on lateral inhibition in the olfactory bulb. J Neurophysiol :jn.00671.2015[PubMed]obtained materials
86Migliore R, De Simone G, Leinekugel X, Migliore M (2016) The possible consequences for cognitive functions of external electric fields at power line frequency on hippocampal CA1 pyramidal neurons. Eur J Neurosci[PubMed]both
87Ness TV, Remme MW, Einevoll GT (2016) Active subthreshold dendritic conductances shape the local field potential. J Physiol 594:3809-25[PubMed]obtained materials
88Neymotin 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[PubMed]both
89Neymotin 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 316:344-366[PubMed]both
90Osinski BL, Kay LM (2016) Granule cell excitability regulates gamma and beta oscillations in a model of the olfactory bulb dendrodendritic microcircuit. J Neurophysiol 116:522-539[PubMed]submitted materials
91Parasuram H, Nair B, D`Angelo E, Hines M, Naldi G, Diwakar S (2016) Computational modeling of single neuron extracellular electric potentials and network Local Field Potentials using LFPsim Front. Comput. Neurosci. 10:65both
92Salazar-Gatzimas E, Chen J, Creamer MS, Mano O, Mandel HB, Matulis CA, Pottackal J, Clark DA (2016) Direct Measurement of Correlation Responses in Drosophila Elementary Motion Detectors Reveals Fast Timescale Tuning. Neuron 92:227-239[PubMed]submitted materials
93Short SM, Morse TM, McTavish TS, Shepherd GM, Verhagen JV (2016) Respiration gates sensory input responses in the Mitral Cell layer of the Olfactory Bulb PLOS ONE 11(12):e0168356[PubMed]both
94Spera E, Migliore M, Unsworth N, Tegolo D (2016) On the cellular mechanisms underlying working memory capacity in humans Neural Network World 4:335-359submitted materials
95Sweeney Y, Clopath C (2016) Emergent spatial synaptic structure from diffusive plasticity. Eur J Neurosci :1-11[PubMed]submitted materials
96Teka W, Stockton D, Santamaria F (2016) Power-law dynamics of membrane conductances increase spiking diversity in a Hodgkin-Huxley model PLoS Comput Biol 12(3):e1004776submitted materials
97Tikidji-Hamburyan RA, El-Ghazawi TA, Triplett JW (2016) Novel Models of Visual Topographic Map Alignment in the Superior Colliculus PLoS Computational Biology 12(12):e1005315[PubMed]submitted materials
98Waltemath D, Wolkenhauer O (2016) How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine. IEEE Trans Biomed Eng 63:1999-2006[PubMed]mentions
99Williams AH, O'Donnell C, Sejnowski TJ, O'Leary T (2016) Dendritic trafficking faces physiologically critical speed-precision tradeoffs. Elife[PubMed]obtained materials
100Wilmes KA, Sprekeler H, Schreiber S (2016) Inhibition as a Binary Switch for Excitatory Plasticity in Pyramidal Neurons. PLoS Comput Biol 12:e1004768[PubMed]submitted materials
101Zhang Y, Smolen P, Alberini CM, Baxter DA, Byrne JH (2016) Computational model of a positive BDNF feedback loop in hippocampal neurons following inhibitory avoidance training. Learn Mem 23:714-722[PubMed]submitted materials
102Allam SL, Bouteiller JM, Hu EY, Ambert N, Greget R, Bischoff S, Baudry M, Berger TW (2015) Synaptic Efficacy as a Function of Ionotropic Receptor Distribution: A Computational Study. PLoS One 10:e0140333[PubMed]submitted materials
103Anderson WD, Makadia HK, Greenhalgh AD, Schwaber JS, David S, Vadigepalli R (2015) Computational modeling of cytokine signaling in microglia. Mol Biosyst 11:3332-46[PubMed]submitted materials
104Anderson WD, Makadia HK, Vadigepalli R (2015) Molecular variability elicits a tunable switch with discrete neuromodulatory response phenotypes. J Comput Neurosci[PubMed]submitted materials
105Aumentado-Armstrong T, Metzen MG, Sproule MKJ, Chacron MJ (2015) Electrosensory midbrain neurons display feature invariant responses to natural communication stimuli PLoS Computational Biology 11(10):e1004430[PubMed]submitted materials
106Balbi P, Martinoia S, Massobrio P (2015) Axon-somatic back-propagation in detailed models of spinal alpha motoneurons Front. Comput. Neurosci. 9:15submitted materials
107Bartol TM, Keller DX, Kinney JP, Bajaj CL, Harris KM, Sejnowski TJ, Kennedy MB (2015) Computational reconstitution of spine calcium transients from individual proteins. Front Synaptic Neurosci 7:17[PubMed]obtained materials
108Briant LJ, Paton JF, Pickering AE, Champneys AR (2015) Modelling the vascular response to sympathetic postganglionic nerve activity. J Theor Biol 371:102-16[PubMed]obtained materials
109Bush D, Barry C, Manson D, Burgess N (2015) Using Grid Cells for Navigation Neuron 87:507-520submitted materials
110Carey RM, Sherwood WE, Shipley MT, Borisyuk A, Wachowiak M (2015) Role of intraglomerular circuits in shaping temporally structured responses to naturalistic inhalation-driven sensory input to the olfactory bulb. J Neurophysiol :jn.00394.2014[PubMed]submitted materials
111Chung B, Bacque-Cazenave J, Cofer DW, Cattaert D, Edwards DH (2015) The effect of sensory feedback on crayfish posture and locomotion: I. Experimental analysis of closing the loop. J Neurophysiol 113(6):1763-71[PubMed]submitted materials
112Coskren 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[PubMed]both
113Costa RP, Froemke RC, Sjöström PJ, van Rossum MCW (2015) Unified pre- and postsynaptic long-term plasticity enables reliable and flexible learning eLifesubmitted materials
114Couto J, Linaro D, De Schutter E, Giugliano M (2015) On the Firing Rate Dependency Of the Phase Response Curves of rat Purkinje Neurons In Vitro PLOS Comp Biol[PubMed]both
115Damodaran S, Cressman JR, Jedrzejewski-Szmek Z, Blackwell KT (2015) Desynchronization of Fast-Spiking Interneurons Reduces beta-Band Oscillations and Imbalance in Firing in the Dopamine-Depleted Striatum. J Neurosci 35:1149-59[PubMed]submitted materials
116David F, Courtiol E, Buonviso N, Fourcaud-Trocmé N (2015) Competing Mechanisms of Gamma and Beta Oscillations in the Olfactory Bulb Based on Multimodal Inhibition of Mitral Cells Over a Respiratory Cycle. eNeuro[PubMed]submitted materials
117de Wiljes OO, van Elburg RA, Biehl M, Keijzer FA (2015) Modeling spontaneous activity across an excitable epithelium: Support for a coordination scenario of early neural evolution. Front Comput Neurosci 9:110[PubMed]obtained materials
118Dura-Bernal S, Zhou X, Neymotin SA, Przekwas A, Francis JT, Lytton WW (2015) Cortical Spiking Network Interfaced with Virtual Musculoskeletal Arm and Robotic Arm. Front Neurorobot 9:13[PubMed]submitted materials
119Egger R, Schmitt AC, Wallace DJ, Sakmann B, Oberlaender M, Kerr JND (2015) Robustness of sensory-evoked excitation is increased by inhibitory inputs to distal apical tuft dendrites PNAS 112(45):14072-7[PubMed]submitted materials
120Esposito U, Giugliano M, Vasilaki E (2015) Adaptation of short-term plasticity parameters via error-driven learning may explain the correlation between activity-dependent synaptic properties, connectivity motifs and target specificity. Front Comput Neurosci 8:175[PubMed]submitted materials
121Ferguson KA, Huh CY, Amilhon B, Manseau F, Williams S, Skinner FK (2015) Network models provide insights into how oriens-lacunosum-moleculare and bistratified cell interactions influence the power of local hippocampal CA1 theta oscillations. Front Syst Neurosci 9:110[PubMed]submitted materials
122Ferrante M, Ascoli GA (2015) Distinct and synergistic feedforward inhibition of pyramidal cells by basket and bistratified interneurons. Front Cell Neurosci 9:439[PubMed]submitted materials
123Fink CG, Gliske S, Catoni N, Stacey WC (2015) Network Mechanisms Generating Abnormal and Normal Hippocampal High-Frequency Oscillations: A Computational Analysis eNeuro 2(3):ENEURO.0024-15.2015[PubMed]submitted materials
124Forrest MD (2015) Simulation of alcohol action upon a detailed Purkinje neuron model and a simpler surrogate model that runs >400 times faster BMC Neuroscience 16:27[PubMed]submitted materials
125Garci­a-Grajales JA, Rucabado G, Garci­a-Dopico A, Pena JM, Jerusalem A (2015) Neurite, a Finite Difference Large Scale Parallel Program for the Simulation of Electrical Signal Propagation in Neurites under Mechanical Loading. PLoS One 10(2):e0116532[PubMed]submitted materials
126Gehring TV, Luksys G, Sandi C, Vasilaki E (2015) Detailed classification of swimming paths in the Morris Water Maze: multiple strategies within one trial Scientific Reports 5:14562[PubMed]submitted materials
127Gilra A, Bhalla US (2015) Bulbar microcircuit model predicts connectivity and roles of interneurons in odor coding. PLoS One 10:e0098045[PubMed]submitted materials
128Gunay C, Sieling FH, Dharmar L, Lin WH, Wolfram V, Marley R, Baines RA, Prinz AA (2015) Distal spike initiation zone location estimation by morphological simulation of ionic current filtering demonstrated in a novel model of an identified Drosophila motoneuron. PLoS Comput Biol 11:e1004189[PubMed]submitted materials
129Hay E, Segev I (2015) Dendritic excitability and gain control in recurrent cortical microcircuits Cerebral Cortex 25(10):3561-3571[PubMed]submitted materials
130Hyun JH, Eom K, Lee KH, Bae JY, Bae YC, Kim MH, Kim S, Ho WK, Lee SH (2015) Kv1.2 mediates heterosynaptic modulation of direct cortical synaptic inputs in CA3 pyramidal cells. J Physiol 593:3617-43[PubMed]both
131Jedlicka P, Benuskova L, Abraham WC (2015) A Voltage-Based STDP Rule Combined with Fast BCM-Like Metaplasticity Accounts for LTP and Concurrent “Heterosynaptic” LTD in the Dentate Gyrus In Vivo PLoS Computational Biology 11(11):e1004588[PubMed]submitted materials
132Keller D, Babai N, Kochubey O, Han Y, Markram H, Schürmann F, Schneggenburger R (2015) An Exclusion Zone for Ca2+ Channels around Docked Vesicles Explains Release Control by Multiple Channels at a CNS Synapse. PLoS Comput Biol 11:e1004253[PubMed]submitted materials
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548Cornelisse LN, van Elburg RAJ, Meredith RM, Yuste R, Mansvelder HD (2007) High Speed Two-Photon Imaging of Calcium Dynamics in Dendritic Spines: Consequences for Spine Calcium Kinetics and Buffer Capacity. PLoS ONE 2(10):e1073[PubMed]submitted materials
549Crasto CJ, Marenco LN, Liu N, Morse TM, Cheung KH, Lai PC, Bahl G, Masiar P, Lam HY, Lim E, C (2007) SenseLab: new developments in disseminating neuroscience information. Brief Bioinform 8:150-62[PubMed]mentions
550Crasto CJ, Shepherd GM (2007) Managing knowledge in neuroscience. Methods Mol Biol 401:3-21[PubMed]mentions
551Dyhrfjeld-Johnsen J, Santhakumar V, Morgan RJ, Huerta R, Tsimring L, Soltesz I (2007) Topological determinants of epileptogenesis in large-scale structural and functional models of the dentate gyrus derived from experimental data. J Neurophysiol 97:1566-87[PubMed]submitted materials
552Garcia-Lazaro JA, Ho SS, Nair A, Schnupp JW (2007) Shifting and scaling adaptation to dynamic stimuli in somatosensory cortex. Eur J Neurosci 26:2359-68[PubMed]obtained materials
553Gleeson P, Steuber V, Silver RA (2007) neuroConstruct: a tool for modeling networks of neurons in 3D space. Neuron 54:219-35[PubMed]obtained materials
554Gold C, Henze DA, Koch C (2007) Using Extracellular Action Potential Recordings to Tune Compartmental Models. Journal of Computational Neuroscience 23:39-58[PubMed]submitted materials
555Hines ML, Morse TM, Carnevale NT (2007) Book chapter, Model structure analysis in NEURON : toward interoperability among neural simulators. Methods Mol Biol 401:91-102[PubMed]mentions
556Jones SR, Pritchett DL, Stufflebeam SM, Hamalainen M, Moore CI (2007) Neural correlates of tactile detection: a combined magnetoencephalography and biophysically based computational modeling study. J Neurosci 27:10751-64[PubMed]both
557Karbowski J, Schindelman G, Cronin CJ, Seah A, Sternberg PW (2007) Systems level circuit model of C. elegans undulatory locomotion: mathematical modeling and molecular genetics. J Comput Neurosci[PubMed]submitted materials
558Kole MH, Brauer AU, Stuart GJ (2007) Inherited cortical HCN1 channel loss amplifies dendritic calcium electrogenesis and burst firing in a rat absence epilepsy model. J Physiol 578:507-25[PubMed]submitted materials
559Kretzberg J, Kretschmer F, Marin-Burgin A (2007) Effects of multiple spike-initiation zones in touch sensory cells of the leech , Volume 70, Issues 10-12, June 2007, Pages 1645-1651 Neurocomputing 70:1645-1651submitted materials
560Kulagina IB, Korogod SM, Horcholle-Bossavitt G, Batini C, Tyc-Dumont S (2007) The electro-dynamics of the dendritic space in Purkinje cells of the cerebellum. Arch Ital Biol 145:211-33[PubMed]obtained materials
561Liu N, Marenco L, Miller PL (2007) ResourceLog: an embeddable tool for dynamically monitoring the usage of web-based bioscience resources. J Am Med Inform Assoc 13:432-7[PubMed]mentions
562Matveev V, Bose A, Nadim F (2007) Capturing the bursting dynamics of a two-cell inhibitory network using a one-dimensional map. J Comput Neurosci 23:169-87[PubMed]mentions
563Migliore M, Inzirillo C, Shepherd GM (2007) Learning mechanism for column formation in the olfactory bulb. Front Integr Neurosci 1:12[PubMed]submitted materials
564Morgan RJ, Santhakumar V, Soltesz I (2007) Modeling the dentate gyrus. Prog Brain Res 163:639-58[PubMed]mentions
565Postlethwaite M, Hennig MH, Steinert JR, Graham BP, Forsythe ID (2007) Acceleration of AMPA receptor kinetics underlies temperature-dependent changes in synaptic strength at the rat calyx of Held. J Physiol 579:69-84[PubMed]submitted materials
566Ramasamy L, Sperelakis N (2007) Cable properties and propagation velocity in a long single chain of simulated myocardial cells. Theor Biol Med Model 4:36[PubMed]submitted materials
567Sakurai A, Calin-Jageman RJ, Katz PS (2007) Potentiation phase of spike timing-dependent neuromodulation by a serotonergic interneuron involves an increase in the fraction of transmitter release. J Neurophysiol 98:1975-87[PubMed]obtained materials
568Scuri R, Lombardo P, Cataldo E, Ristori C, Brunelli M (2007) Inhibition of Na+-K+ ATPase potentiates synaptic transmission in tactile sensory neurons of the leech. Eur J Neurosci 25:159-67[PubMed]submitted materials
569Stiefel KM, Sejnowski TJ (2007) Mapping Function onto Neuronal Morphology. J Neurophysiol 98:513-526[PubMed]submitted materials
570Wada K, Sakaguchi Y (2007) Repetitive firing of a model motoneuron: inhibitory effect of a Ca2+-activated potassium conductance on the slope of the frequency-current relationship. Neurosci Res 57:259-67[PubMed]obtained materials
571Zaika O, Tolstykh GP, Jaffe DB, Shapiro MS (2007) Inositol triphosphate-mediated Ca2+ signals direct purinergic P2Y receptor regulation of neuronal ion channels. J Neurosci 27:8914-26[PubMed]obtained materials
572Akemann W, Knopfel T (2006) Interaction of Kv3 potassium channels and resurgent sodium current influences the rate of spontaneous firing of Purkinje neurons. J Neurosci 26:4602-12[PubMed]both
573Ascoli GA, Scorcioni R (2006) Neuron and Network Modeling Neuroanatomical Tract-Tracing 3, Zaborszky L, Wouterlood FG, Lanciego JL, ed. pp.604mentions
574Bathellier B, Lagier S, Faure P, Lledo PM (2006) Circuit properties generating gamma oscillations in a network model of the olfactory bulb. J Neurophysiol 95:2678-91[PubMed]obtained materials
575Baxter DA, Byrne JH (2007) Short-term plasticity in a computational model of the tail-withdrawal circuit in Aplysia Neurocomputing 70(10-12):1993-1999submitted materials
576Cataldo E, Byrne JH, Baxter DA (2006) Computational Model of a Central Pattern Generator CMSB 2006, Lecture Notes in Bioinformatics LNBI 4210, Priami C, ed. pp.242submitted materials
577Davison AP, Fregnac Y (2006) Learning Cross-Modal Spatial Transformations through Spike Timing-Dependent Plasticity J Neurosci 26:5604-5615[PubMed]submitted materials
578Eberhard JP, Wanner A, Wittum G (2006) NeuGen: a tool for the generation of realistic morphology of cortical neurons and neural networks in 3D Neurocomputing 70:327-342obtained materials
579Graham BP, Lauchlan K, McLean DR (2006) Dynamics of outgrowth in a continuum model of neurite elongation. J Comput Neurosci 20:43-60[PubMed]submitted materials
580Kole 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[PubMed]both
581Kuba H, Ishii TM, Ohmori H (2006) Axonal site of spike initiation enhances auditory coincidence detection. Nature 444:1069-72[PubMed]obtained materials
582Li X, Ascoli GA (2006) Computational simulation of the input-output relationship in hippocampal pyramidal cells J of Comput Neurosci 21(2):191-209[PubMed]both
583Lytton WW (2006) Neural Query System: Data-mining from within the NEURON simulator. Neuroinformatics 4:163-76[PubMed]obtained materials
584Migliore M, Cannia C, Lytton WW, Markram H, Hines ML (2006) Parallel Network Simulations with NEURON. J Comp Neurosci 21:110-119[PubMed]both
585Murakami S, Okada Y (2006) Contributions of principal neocortical neurons to magnetoencephalography and electroencephalography signals. J Physiol 575:925-36[PubMed]obtained materials
586Saftenku EE (2006) Presumed Mechanisms of a Long-Term Increase in the Intrinsic Excitability of Cerebellar Granule Cells: a Model Study Neirofiziologiya/Neurophysiology 38(2):101-110obtained materials
587van Welie I, Remme MW, van Hooft JA, Wadman WJ (2006) Different levels of Ih determine distinct temporal integration in bursting and regular-spiking neurons in rat subiculum. J Physiol 576:203-214[PubMed]submitted materials
588Wang YJ, Sung RJ, Lin MW, Wu SN (2006) Contribution of BK(Ca)-channel activity in human cardiac fibroblasts to electrical coupling of cardiomyocytes-fibroblasts. J Membr Biol 213:175-85[PubMed]obtained materials
589Weaver CM, Wearne SL (2006) The role of action potential shape and parameter constraints in optimization of compartment models Neurocomputing 69:1053-1057obtained materials
590Yokawa K,Nishimura T (2006) Book Chapter, An electrical stimulation on retinal ganglion cell for retinal prosthesis based on CMOS image sensor: A study of electrophysiological simulation IFMBE Proceedings, World Congress on Medical Physics and Biomedical Engineering 2006 Part 23mentions
591Zaika O, Lara L, Gamper N, Hilgemann DW, Jaffe DB, Shapiro MS (2006) Angiotensin II regulates neuronal excitability via phosphatidylinositol 4,5-bisphosphate-dependent modulation of Kv7 (M-type) K+ channels. J. Physiol. 575:49-67[PubMed]obtained materials
592Brette R, Gerstner W (2005) Adaptive exponential integrate-and-fire model as an effective description of neuronal activity. J Neurophysiol 94:3637-42[PubMed]obtained materials
593Bug W (2005) The impact of the NIH public access policy on literature informatics: What role can the neuroinformaticists play? Neuroinformatics 3:81-91[PubMed]mentions
594Cataldo E, Brunelli M, Byrne JH, Av-Ron E, Cai Y, Baxter DA (2005) Computational Model of Touch Sensory Cells (T Cells) of the Leech: Role of the Afterhyperpolarization (AHP) in Activity-Dependent Conduction Failure Journal of Computational Neuroscience 18:5-24[PubMed]submitted materials
595Dyhrfjeld-Johnsen J, Maier J, Schubert D, Staiger J, Luhmann HJ, Stephan KE, Kotter R (2005) CoCoDat: a database system for organizing and selecting quantitative data on single neurons and neuronal microcircuitry. J Neurosci Methods 141:291-308[PubMed]mentions
596Hossain WA, Antic SD, Yang Y, Rasband MN, Morest DK (2005) Where is the spike generator of the cochlear nerve? Voltage-gated sodium channels in the mouse cochlea. J Neurosci 25:6857-68[PubMed]obtained materials
597Lazarewicz M, Das S, Finkel LH (2005) Recognition of temporal event sequences by a network of cortical neurons Neurocomputing 65-66:143-151obtained materials
598Lytton WW, Hines ML (2005) Independent variable time-step integration of individual neurons for network simulations. Neural Comput 17:903-21[PubMed]both
599Migliore M, Ferrante M, Ascoli GA (2005) Signal propagation in oblique dendrites of CA1 pyramidal cells. J Neurophysiol 94:4145-4155[PubMed]submitted materials
600Migliore M, Hines ML, Shepherd GM (2005) The role of distal dendritic gap junctions in synchronization of mitral cell axonal output. J Comp Neurosci 18:151-161[PubMed]submitted materials
601Migliore M, Shepherd GM (2005) Opinion: an integrated approach to classifying neuronal phenotypes. Nat Rev Neurosci 6:810-8[PubMed]obtained materials
602Moss BL, Fuller AD, Sahley CL, Burrell BD (2005) Serotonin modulates axo-axonal coupling between neurons critical for learning in the leech J Neurophysiol 94(4):2575-89[PubMed]submitted materials
603Otake M, Takagi T (2005) Reassembly and interfacing neural models registered on biological model databases. Genome Inform 16:76-85[PubMed]obtained materials
604Saghatelyan A,Roux P,Migliore M,Rochefort C,Desmaisons D,Charneau P,Shepherd GM, Lledo PM (2005) Activity-dependent adjustments of the inhibitory network in the olfactory bulb following early postnatal deprivation. Neuron 46:103-116[PubMed]submitted materials
605Santhakumar V, Aradi I, Soltesz I (2005) Role of mossy fiber sprouting and mossy cell loss in hyperexcitability: a network model of the dentate gyrus incorporating cell types and axonal topography. J Neurophysiol 93:437-53[PubMed]obtained materials
606Sengupta B (2005) Book Chapter, Modeling of Short-Term Synaptic Plasticity Using Dynamic Synapses Lecture Notes in Computer Science, Advances in Natural Computationobtained materials
607Shapshak P, Minagar A, Duran EM, Ziegler F, Davis W, Seth R, Kazic T (2005) Chapter 16, Gene Expression in HIV-Associated Dementia Current Clinical Neurology, Inflammatory Disorders of the Nervous System, Minagar A, Alexander JS, ed. mentions
608Sikora MA, Gottesman J, Miller RF (2005) A computational model of the ribbon synapse. J Neurosci Methods 145:47-61[PubMed]submitted materials
609Trevelyan AJ, Watkinson O (2005) Does inhibition balance excitation in neocortex? Prog Biophys Mol Biol 87:109-43[PubMed]obtained materials
610Wu SN, Chang HD (2005) Diethyl pyrocarbonate, a histidine-modifying agent, directly stimulates activity of ATP-sensitive potassium channels in pituitary GH(3) cells. Biochem Pharmacol[PubMed]submitted materials
611Aradi I, Maccaferri G (2004) Cell type-specific synaptic dynamics of synchronized bursting in the juvenile CA3 rat hippocampus. J Neurosci 24:9681-92[PubMed]obtained materials
612Davison A (2004) Biologically-detailed network modelling (Chapter 10) Computation Neuroscience: A Comprehensive Approach, Feng J, ed. pp.287mentions
613Djurisic M, Antic S, Chen WR, Zecevic D (2004) Voltage imaging from dendrites of mitral cells: EPSP attenuation and spike trigger zones. J Neurosci 24:6703-14[PubMed]submitted materials
614Gasparini S, Migliore M, Magee JC (2004) On the initiation and propagation of dendritic spikes in CA1 pyramidal neurons. J Neurosci 24:11046-11056[PubMed]both
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616Hines ML, Carnevale NT (2004) Discrete event simulation in the NEURON environment. Neurocomputing 58-60:1117-1122mentions
617Hines ML, Morse T, Migliore M, Carnevale NT, Shepherd GM (2004) ModelDB: A Database to Support Computational Neuroscience. J Comput Neurosci 17:7-11[PubMed]mentions
618Maurice N, Mercer J, Chan CS, Hernandez-Lopez S, Held J, Tkatch T, Surmeier DJ (2004) D2 dopamine receptor-mediated modulation of voltage-dependent Na+ channels reduces autonomous activity in striatal cholinergic interneurons. J Neurosci 24:10289-301[PubMed]both
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620Sterratt DC, van Ooyen A (2004) Does a dendritic democracy need a ruler? Neurocomputing 58:437-442obtained materials
621Crasto CJ, Marenco LN, Migliore M, Mao B, Nadkarni PM, Miller P, Shepherd GM (2003) Text mining neuroscience journal articles to populate neuroscience databases. Neuroinformatics 1:215-37[PubMed]mentions
622D'Alessandro G (2003) Axiope: data sharing using distributed catalogs. Neuroinformatics 1:285-8[PubMed]mentions
623Davison AP, Feng J, Brown D (2003) Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. J Neurophysiol 90:1921-1935[PubMed]submitted materials
624Graham LJ (2003) ModelDB, neuroinformatics, and computational neuroscience. Neuroinformatics 1:141-4[PubMed]mentions
625Marenco L, Tosches N, Crasto C, Shepherd G, Miller PL, Nadkarni PM (2003) Achieving evolvable Web-database bioscience applications using the EAV-CR framework: recent advances. J Am Med Inform Assoc 10:444-53[PubMed]mentions
626Migliore M (2003) On the Integration of Subthreshold Inputs from Perforant Path and Schaffer Collaterals in Hippocampal CA1 Pyramidal Neurons. J Comput Neurosci 14:185-192[PubMed]submitted materials
627Migliore 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[PubMed]mentions
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631Migliore M, Messineo L, Cardaci M, Ayala GF (2001) Quantitative modeling of perception and production of time intervals. J Neurophysiol 86:2754-60[PubMed]submitted materials
632Mirsky JS, Nadkarni PM, Healy MD, Miller PL, Shepherd GM (1998) Database tools for integrating and searching membrane property data correlated with neuronal morphology. J Neurosci Methods 82:105-21[PubMed]mentions
633Shepherd GM, Mirsky JS, Healy MD, Singer MS, Skoufos E, Hines MS, Nadkarni PM, Miller PL (1998) The Human Brain Project: neuroinformatics tools for integrating, searching and modeling multidisciplinary neuroscience data. Trends Neurosci 21:460-8[PubMed]mentions
634Peterson 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[PubMed]mentions