Publications

115 publications, 1991–2026

Consciousness Decision & Confidence Dendritic Embodiment Learning & Memory Olfaction Perception Serotonin Space Spike Synaptic Vision Volition & Agency

115 of 115 publications

2026
Serotonin State Prediction Error In preparation
Félix Hubert, Alexandre Pouget, Zachary F. Mainen
2025
DRN serotonin correlates of investigatory behavior In preparation
Stefan Hajduk et al.
2025
Serotonin neurons encode stimulus novelty and predictive structure during associative learning In preparation
Solène Sautory, Leopoldo Petreanu, Z. Mainen
2025
Serotonin modulates neural dynamics in a subspace orthogonal to the choice space Preprint
Guido T. Meijer et al.
bioRxiv
DOI · PDF · Code · Data
2020
Functional MRI of large scale activity in behaving mice Preprint 12 cited
Madalena S. Fonseca et al.
bioRxiv, doi: https://doi.org/10.1101/2020.04.16.044941
DOI · PDF
2019
Data architecture and visualization for a large-scale neuroscience collaboration Preprint 11 cited
International Brain Laboratory et al.
bioRxiv, 827873
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2025
Facial expressions in mice reveal latent cognitive variables and their neural correlates 7 cited
Fanny Cazettes et al.
Nature Neuroscience
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2024
A brain-wide map of neural activity during complex behaviour 115 cited
International Brain Laboratory
Nature
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2024
Brain-wide representations of prior information in mouse decision-making 82 cited
Charles Findling et al.
Nature
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2024
An adaptable, reusable, and light implant for chronic Neuropixels probes
C. Bimbard et al.
eLife 13:RP98522
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2023
A reservoir of foraging decision variables in the mouse brain 39 cited
Fanny Cazettes et al.
https://doi.org/10.1038/s41593-023-01305-8
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2023
Serotonin 20 cited
Romain Ligneul, Z. Mainen
Current Biology 33, R1209–R1221
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2022
Mice alternate between discrete strategies during perceptual decision-making 131 cited
Ashwood ZC et al.
Nat Neurosci 25, 201-212
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2022
Stress-sensitive inference of task controllability 31 cited
R. Ligneul et al.
Nat Hum Behav 6, 812
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2022
Next-generation brain observatories 19 cited
Christof Koch et al.
Neuron 110
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2022
Maturation of prefrontal input to dorsal raphe increases behavioral persistence in mice 2 cited
Nicolas Gutierrez-Castellanos et al.
eLife 13, e93485
DOI · Preprint · PDF · Code
2021
Spatial maps in olfactory cortex during olfactory navigation 95 cited
C. Poo et al.
Nature 601, 595-599
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2021
Metastable attractors explain the variable timing of stable behavioral action sequences 70 cited
Stefano Recanatesi et al.
Neuron 110 (1): 139
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2021
Extracting the dynamics of behavior in sensory decision-making experiments 7 cited
Roy NA et al.
Neuron 109 (4), 597-610
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2021
Phasic activation of dorsal raphe serotonergic neurons increases pupil-linked arousal 6 cited
Fanny Cazettes et al.
Curr Biol 31 (1), 192–197
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2021
A Novel Olfactory Self-Test Effectively Screens for COVID-19 4 cited
K. Snitz et al.
Commun Med 2, 34
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2021
Citric Acid as an alternative to water restrictions for high-yield mouse behavior 3 cited
Anne E. Urai et al.
eNeuro 11 January 2021, ENEURO.0230-20.2020
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2021
A standardized and reproducible method to measure decision-making in mice
The IBL et al.
doi: 10.7554/eLife.63711
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2020
Inference-based decisions in a hidden state foraging task: differential contributions of prefrontal areas 79 cited
Pietro Vertechi et al.
Neuron 106 (1), 166
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2020
The impact of learning on perceptual decisions and its implication for speed-accuracy tradeoffs 55 cited
André G. Mendonça et al.
Nat Comm 11 (1): 2757
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2020
Knowledge across networks: how to build a global neuroscience collaboration 13 cited
Wool LE, International Brain Laboratory
Curr Opin Neurobiol 65, 100-107
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2020
Relationship Between Odor Intensity Estimates and COVID-19 Prevalence Prediction in a Swedish Population 9 cited
B. Iravani et al.
Chem Senses 45 (6), 449–456
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2019
Learning optimal decisions with confidence 65 cited
Jan Drugowitsch et al.
PNAS 116 (49), 24872
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2019
The mechanistic foundation of Weber's law 65 cited
Jose L. Pardo-Vazquez et al.
Nat Neurosci 22 (9)
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2019
The overlooked ubiquity of first-person experience in the cognitive sciences 12 cited
Joana Rigato, Scott M. Rennie, Z. Mainen
Synthese 198, 8005–8041
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2018
An effect of serotonergic stimulation on learning rates for rewards apparent after long intertrial intervals 103 cited
K. Iigaya et al.
Nat Commun 9 (1), 2477
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2018
Activation of serotonin neurons promotes active persistence in a probabilistic foraging task 1 cited
Eran Lottem et al.
Nat Commun 9 (1): 1000
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2017
Transient inhibition and long-term facilitation of locomotion by phasic optogenetic activation of serotonin neurons 112 cited
Patrícia A. Correia et al.
eLife pii: e20975
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2017
Distinct sources of deterministic and stochastic components of action timing decisions in rodent frontal cortex 87 cited
M. Murakami et al.
Neuron 94 (4), 908-919.e7
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2017
An International Laboratory for Systems and Computational Neuroscience 79 cited
Larry F. Dora E. Matteo Anne K. Yang Peter Sophie Ila Su Abbott Angelaki Carandini Churchland Dan Dayan Den et al.
Neuron 96 (6):1213-1218
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2017
A probabilistic approach to demixing odors 65 cited
A. Grabska-Barwinska et al.
Nat Neurosci 20, 98–106
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2017
Stereotaxic adeno-associated virus injection and cannula implantation in the dorsal raphe nucleus of mice 17 cited
Patrícia A. Correia, S. Matias, Z. Mainen
Bio-protocol 7 (18), e2549
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2017
Activity patterns of serotonin neurons underlying cognitive flexibility 2 cited
S. Matias et al.
eLife pii: e20552
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2016
Optogenetic activation of dorsal raphe serotonin neurons rapidly inhibits spontaneous but not odor-evoked activity in olfactory cortex 70 cited
Eran Lottem, Magor L Lörincz, Z. Mainen
J Neurosci 36 (1), 7-18
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2016
A better way to crack the brain 20 cited
Z. Mainen, M. Häusser, A. Pouget
Nature 539, 159-161
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2016
Expanding perspectives on cognition in humans, animals, and machines 19 cited
A. Gomez-Marin, Z. Mainen
Curr Opin Neurobiol 37, 85–91
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2016
Demixed principal component analysis of neural population data 10 cited
D. Kobak et al.
eLife (5), e10989
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2015
Confidence as bayesian probability: from neural origins to behavior 270 cited
Florent Meyniel, M. Sigman, Z. Mainen
Neuron 88 (1), 78–92
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2015
Preparing and selecting actions with neural populations: toward cortical circuit mechanisms 38 cited
M. Murakami, Z. Mainen
Curr Opin Neurobiol 33 (C), 40–46
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2015
Spontaneous Decisions and Free Will: Empirical Results and Philosophical Considerations 4 cited
Joana Rigato, M. Murakami, Z. Mainen
Cold Spring Harb Symp Quant Biol
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2015
Columnar architecture improves noise robustness in a model cortical network 3 cited
P. Bush, Z. Mainen
PLoS One 10 (3), e0119072
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2014
Big behavioral data: psychology, ethology and the foundations of neuroscience 281 cited
A. Gomez-Marin et al.
Nat Neurosci (17), 1455–1462
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2014
Neural antecedents of self-initiated actions in secondary motor cortex 268 cited
M. Murakami et al.
Nat Neurosci 11, 1574-82
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2014
Orbitofrontal Cortex Is Required for Optimal Waiting Based on Decision Confidence 217 cited
Armin Lak et al.
Neuron 84, 190-201
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2014
Balanced activity in basal ganglia projection pathways is critical for contraversive movements 190 cited
F. Tecuapetla et al.
Nat Comm 5, 4315
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2014
Optogenetic recruitment of dorsal raphe serotonergic neurons acutely decreases mechanosensory responsivity in behaving mice 61 cited
G. Dugué et al.
PLoS ONE 9 (8), e105941
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2014
Put brain project back on course 14 cited
Z. Mainen, Alexandre Pouget
Nature, 511,534
DOI
2014
A Computational Framework for the Study of Confidence Across Species 9 cited
Adam Kepecs, Z. Mainen
Springer Berlin Heidelberg
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2014
Activation of dorsal raphe serotonergic neurons promotes persistent waiting independently of reinforcing effects 1 cited
Madalena S. Fonseca, M. Murakami, Z. Mainen
Curr Biol 25 (3), 306-15
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2013
The limits of deliberation in a perceptual decision task 80 cited
Hatim A. Zariwala et al.
Neuron 78 (2), 339-51
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2013
Social cognition in the rodent: nothing to be sniffed at 15 cited
Scott M. Rennie, Marta M. Moita, Z. Mainen
Trends Cogn Sci 17 (7), 306-7
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2013
BRAIN Initiative and Human Brain Project: Hopes and Reservations 3 cited
Arber S et al.
Cell 155(2): 265-266
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2012
A computational framework for the study of confidence in humans and animals 273 cited
Adam Kepecs, Z. Mainen
367 (1594), 1322-37
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2012
Odor Representations in Olfactory Cortex: Distributed Rate Coding and Decorrelated Population Activity 221 cited
K. Miura, Z. Mainen, N. Uchida
Neuron 74 (6), 1087-98
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2012
Midbrain contributions to sensorimotor decision-making 55 cited
Gidon Felsen, Z. Mainen
J Neurophysiol 108 (1), 135-47
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2011
Convergence in the piriform cortex 3 cited
M. I. Vicente, Z. Mainen
Neuron 70 (1), 1-2
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2010
Listening to the crowd: neuronal ensembles rule 1 cited
C. Feierstein, Z. Mainen
Neuron 66 (3), 334-6
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2010
Electrophysiological Monitoring of the Interactions Between Neurons
Zachary F. Mainen
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2009
A defined network of fast-spiking interneurons in orbitofrontal cortex: responses to behavioral contingencies and ketamine administration 271 cited
C. Feierstein et al.
Front Syst Neurosci Nov09 (3), 13
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2009
Transient firing of dorsal raphe neurons encodes diverse and specific sensory, motor, and reward events 185 cited
S. Ranade, Z. Mainen
J Neurophysiol 102, 3026-37
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2009
Neural representation of behavioral outcomes in the orbitofrontal cortex 77 cited
Z. Mainen, Adam Kepecs
Curr Opin Neurobiol 19 , 84-91
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2009
How serotonin gates olfactory information flow 28 cited
G. Dugué, Z. Mainen
Nat Neurosci 12, 673-5
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2008
Neural correlates, computation and behavioral impact of decision confidence 810 cited
Adam Kepecs et al.
Nature 455, 227-31
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2008
Sparse optical microstimulation in barrel cortex drives learned behavior in freely moving mice 542 cited
D. Huber et al.
Nature 451, 61-4
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2008
Neural substrates of sensory-guided locomotor decisions in the rat superior colliculus 155 cited
Gidon Felsen, Z. Mainen
Neuron 60, 137-48
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2008
Odor concentration invariance by chemical ratio coding 68 cited
N. Uchida, Z. Mainen
Apr 08 (1), 3
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2008
Towards an image of a memory trace 1 cited
M. Ines et al.
Front Sys Neurosci Dec 08 (2), 131
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2008
A Low-Power Low-Data-Rate Neural Recording System with Adaptive Compression
Donghwi Kim et al.
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2007
The functional microarchitecture of the mouse barrel cortex 233 cited
Takashi R. Sato et al.
PLoS Biol 5 (7), e189
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2007
Rapid and precise control of sniffing during olfactory discrimination in rats 190 cited
Adam Kepecs, N. Uchida, Z. Mainen
J Neurophysiol 98, 205-13
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2007
Low-power high-resolution 32-channel neural recording system 13 cited
X. Yun et al.
Conf Proc IEEE Eng Med Biol Soc, 2373-2376
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2007
The main olfactory bulb and innate behavior: different perspectives on an olfactory scene 8 cited
Z. Mainen
Nat Neurosci 10, 1511-2
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2007
Functional plasticity at dendritic synapses 6 cited
Z. Mainen, L. Abbott
Oxford: Oxford University Press
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2006
Early events in olfactory processing 408 cited
Rachel I. Wilson, Z. Mainen
Annu Rev Neurosci 29, 163-201
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2006
The sniff as a unit of olfactory processing 331 cited
Adam Kepecs, N. Uchida, Z. Mainen
Chem Senses 31, 167-79
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2006
Representation of spatial goals in rat orbitofrontal cortex 271 cited
C. Feierstein et al.
Neuron 51, 495-507
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2006
Seeing at a glance: Limits on temporal integration in perception 243 cited
N. Uchida, Adam Kepecs, Z. Mainen
Nature Rev Neurosci 7, 485-91
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2006
Sensory-evoked intrinsic optical signals in the olfactory bulb are coupled to glutamate release and uptake 115 cited
H. Gurden, N. Uchida, Z. Mainen
Neuron 52, 335-45
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2006
Behavioral analysis of olfactory coding and computation in rodents 28 cited
Z. Mainen
Curr Opin Neurobiol 16, 429-34
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2005
Dendrodendritic synaptic signals in olfactory bulb granule cells: local spine boost and global low-threshold spike 166 cited
Veronica Egger, K. Svoboda, Z. Mainen
J Neurosci 25, 3521-30
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2003
Speed and accuracy of olfactory discrimination in the rat 714 cited
N. Uchida, Z. Mainen
Nat Neurosci 6, 1224-9
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2003
Mechanisms of lateral inhibition in the olfactory bulb: efficiency and modulation of spike-evoked calcium influx into granule cells 183 cited
Veronica Egger, K. Svoboda, Z. Mainen
J Neurosci 23, 7551-8
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2000
Estimating intracellular calcium concentrations and buffering without wavelength rationing 429 cited
M. Maravall et al.
Biophys J 78, 2655-67
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2000
LTP mechanisms: from silence to four-lane traffic 397 cited
R. Malinow, Z. Mainen, Y. Hayashi
Curr Opin Neurobiol 10, 352-7
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2000
Thinking about feeling 76 cited
Z. Mainen
Nat Neurosci 3, 857
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2000
2-Photon Excitation Laser Scanning Microscopy for High Resolution Imaging
K. Svoboda et al.
Microscopy and Microanalysis
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1999
Synaptic calcium transients in single spines indicate that NMDA receptors are not saturated 332 cited
Z. Mainen, R. Malinow, K. Svoboda
Nature 399, 151-5
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1999
Two-photon imaging in brain slices 182 cited
Z. Mainen et al.
Methods 18, 231-9
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1999
Synaptic calcium: Intracellular stores spill their guts 106 cited
K. Svoboda, Z. Mainen
Neuron 22, 427-30
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1999
Functional plasticity at dendritic synapses 6 cited
Z. Mainen, L. Abbott
Oxford: Oxford University Press, pp 310-338
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1998
Kinetic models of synaptic transmission 554 cited
A. Destexhe, Z. Mainen, T. Sejnowski
(Koch C, Segev I, eds), Cambridge, MA: MIT Press, pp 1-26
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1998
Use-dependent AMPA receptor block in mice lacking GluR2 suggests postsynaptic site for LTP expression 70 cited
Z. Mainen et al.
Nat Neurosci 1, 579-86
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1998
Kinetic Models of Synaptic Transmission
Alain Destexhe, Zachary F. Mainen, Terrence J. Sejnowski
PDF
1998
Modeling Active Dendritic Processes in Pyramidal Neurons
Zachary F. Mainen, Terrence J. Sejnowski
PDF
1996
Influence of dendritic structure on firing pattern in model neocortical neurons 526 cited
Z. Mainen, T. Sejnowski
Nature 382, 363-6
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1996
Electrotonic architecture of hippocampal CA1 pyramidal neurons based on three-dimensional reconstructions 105 cited
Z. Mainen et al.
J Neurophysiol 76, 1904-23
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1996
Long-term potentiation in the CA1 hippocampus [technical comment] 14 cited
R. Malinow et al.
Science 271, 1604-6
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1995
Reliability of spike timing in neocortical neurons 1893 cited
Z. Mainen, T. Sejnowski
Science 268, 1503-6
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1995
Elementary kinetics provide efficient models of synaptic transmission and neuromodulation 554 cited
A. Destexhe, Z. Mainen, T. Sejnowski
In: The Neurobiology of Computation (Bower J, ed) Norwell, MA: Kluwer Academic Press, pp 9-14
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1995
Synaptic currents, neuromodulation and kinetic models 554 cited
A. Destexhe, Z. Mainen, T. Sejnowski
In: The Handbook of Brain Theory and Neural Networks (Arbib M, ed) Cambridge, MA: MIT Press, pp 956-959
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1995
A model of spike initiation in neocortical pyramidal neurons 455 cited
Z. Mainen et al.
Neuron 15, 1427-39
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1995
Fast Kinetic Models for Simulating AMPA, NMDA, GABA-A and GABA-B Receptors
Alain Destexhe, Zachary F. Mainen, Terrence J. Sejnowski
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1995
Synaptic Currents, Neuromodulation, and Kinetic Models
Alain Destexhe, Zachary F. Mainen, Terrence J. Sejnowski
PDF
1995
Synaptic Interactions
Alain Destexhe, Zachary F. Mainen, Terrence J. Sejnowski
PDF
1994
Synthesis of models for excitable membranes, synaptic transmission, and neuromodulation using a common kinetic framework 554 cited
A. Destexhe, Z. Mainen, T. Sejnowski
J Computational Neurosci 1, 195-230
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1994
An efficient method for computing synaptic conductances based on a kinetic model of receptor binding 507 cited
A. Destexhe, Z. Mainen, T. Sejnowski
Neural Computation 6, 14-8
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1993
Self-organization of Hebbian Synapses in Hippocampal Neurons
Thomas H. Brown, Zachary F. Mainen, Anthony M. Zador, Brenda J. Claiborne
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1992
Computational models of the principal classes of hippocampal neurons 30 cited
B. Claiborne et al.
In: Single Neuron Computation (McKenna T, Davis J, Zornetzer SF, eds) New York: Academic Press, pp 61-80
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1992
Dendritic control of hebbian computations 7 cited
E. W. Kairiss et al.
In: Analysis and Modeling of Neural Systems (Eeckman FH, ed) Boston: Kluwer Academic Publishers
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1991
Self-organization and non-linear processing in hippocampal neurons 30 cited
B. Claiborne et al.
In: Advances in neural information processing systems 3 (Lippman RP, Moody JE, Touretzky DS, eds) San Mateo, CA: Morgan Kaufmann, pp 39-45
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