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Identification

Personal identification

Full name
Zachary Frank Mainen

Author identifiers

Ciência ID
351E-CBAF-395B
ORCID iD
0000-0001-7913-9109
Education
Degree Classification
1995
Concluded
 Neurosciences (Doctor of Philosophy)
University of California San Diego, United States
"Spike Generation in Neocortical Neurons" (THESIS/DISSERTATION)
 Excellent
1991
Concluded
 Psychology (Master)
Yale University, United States
"N/a" (THESIS/DISSERTATION)
 Excellent
1990
Concluded
 Psychology (Bachelor)
Yale University, United States
"N/a" (THESIS/DISSERTATION)
 Excellent
Affiliation

Science

Category
Host institution 		Employer
2007 - Current Principal Investigator (Research) Programa Champalimaud de Neurociências, Portugal
2007 - 2012 Principal Investigator (Research) Instituto Gulbenkian de Ciência, Portugal
Centro Champalimaud, Portugal
2007 - 2011 Principal Investigator (Research) Programa Champalimaud de Neurociências, Portugal
Instituto Gulbenkian de Ciência, Portugal
2008 - 2010 Visiting Researcher (Research) Howard Hughes Medical Institute Janelia Farm Research Campus, United States
1997 - 1999 Postdoc (Research) Laboratory of Karel Svoboda, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
1995 - 1997 Postdoc (Research) Laboratory of Roberto Malinow, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States
1992 - 1995 Researcher (Research) Laboratory of Terrence J Sejnowski, The Salk Institute, La Jolla, CA, United States
1989 - 1991 Research Assistant (Research) Laboratory of Thomas H Brown, Yale University, New Haven, CT, United States

Teaching in Higher Education

Category
Host institution 		Employer
2004 - 2008 Associate Professor (University Teacher) Cold Spring Harbor Laboratory, United States
2004 - 2008 Associate Professor (University Teacher) Cold Spring Harbor Laboratory, United States
2002 - 2007 Invited Associate Professor (University Teacher) Stony Brook University Department of Neurobiology and Behavior, United States
1999 - 2003 Assistant Professor (University Teacher) Cold Spring Harbor Laboratory, United States

Positions / Appointments

Category
Host institution 		Employer
2016 - Current Founder and Executive Board Member International Brain Laboratory, Portugal
2014 - 2019 Organic Unit Director Champalimaud Research - Champalimaud Foundation, Portugal
2010/01/01 - 2014/12/31 Organic Unit Director Programa Champalimaud de Neurociências, Portugal
2007 - 2010 Coordinator Programa Champalimaud de Neurociências, Portugal
Outputs

Publications

Book chapter
  1. Rigato, J.; Murakami, M.; Mainen, Z.. "Spontaneous decisions and free will: Empirical results and philosophical considerations". In Cold Spring Harbor Symposia on Quantitative Biology: Cognition, 177-184. 2015.
    10.1101/sqb.2014.79.024810
  2. Kepecs, A.; Mainen, Z.F.. "A computational framework for the study of confidence across species". In The Cognitive Neuroscience of Metacognition, 115-145. Springer Berlin Heidelberg, 2014.
    10.1007/978-3-642-45190-4_6
  3. Mainen, Z.F.; Abbott, L.F.. "Functional plasticity at dendritic synapses". In Dendrites, 465-498. Oxford University Press, 2007.
    10.1093/acprof:oso/9780198566564.003.0018
  4. Mainen, Zachary. "Functional plasticity at dendritic synapses". In Methods in Neuronal Modeling, 310-338. Oxford University Press, 2000.
    10.1093/acprof:oso/9780198566564.003.0018
  5. Maravall, M.; Mainen, Z. F.; Svoboda, K.. "Dendritic [Ca2+] dynamics in the presence of immobile buffers and of dyes". In Foundations and Tools for Neural Modeling, 43-52. Springer Berlin Heidelberg, 1999.
    10.1007/bfb0098159
  6. Mainen, Zachary; Sejnowski, T.J.. "Modeling active dendritic processes in pyramidal neurons". In Methods in Neuronal Modeling. MIT Press, 1998.
  7. Mainen, Zachary. "Synaptic currents, neuromodulation and kinetic models". In The Handbook of Brain Theory and Neural Networks, 956-959. 1995.
  8. Destexhe, Alain; Mainen, Zachary F.; Sejnowski, Terrence J.. "Fast Kinetic Models for Simulating AMPA, NMDA, GABA A and GABA B Receptors". In The Neurobiology of Computation, 9-14. Springer US, 1995.
    10.1007/978-1-4615-2235-5_2
  9. Kairiss, Edward W.; Mainen, Zachary F.; Claiborne, Brenda J.; Brown, Thomas H.. "Dendritic Control of Hebbian Computations". In Analysis and Modeling of Neural Systems, 69-83. Springer US, 1992.
    10.1007/978-1-4615-4010-6_7
  10. CLAIBORNE, BRENDA J.; ZADOR, ANTHONY M.; MAINEN, ZACHARY F.; BROWN, THOMAS H.. "Computational Models of Hippocampal Neurons". In Single Neuron Computation, 61-80. Elsevier, 1992.
    10.1016/b978-0-12-484815-3.50009-8
  11. Mainen, Zachary. "Self-organization and non-linear processing in hippocampal neurons". In Advances in neural information processing systems 3, 39-45. Morgan Kaufmann, 1991.
Conference abstract
  1. Bougrova, Kcenia; Bonacchi, Niccolò; Catarino, Joana A; DeWitt, Eric; Meijer, Guido; Dayan, Peter; Mainen, Zachary; The International Brain Laboratory. "Comparison of neuromodulator signaling in a visual decision-making task". Paper presented in 51st Annual Meeting of the Society for Neuroscience, San Diego, CA, 2022.
    Published
  2. Xuan, F; Tessereau, C; Clopath, C; Jones, M; Mainen, Zachary. "Where did my Cheese Move? Behavioural and Hippocampal Traces of Uncertainties Induced by Changes in Reward Distributions.". Paper presented in FENS Forum 2022, Paris, 2022.
    Published
  3. "Parallel inference in the mouse frontal cortex". Paper presented in Cosyne, 2021.
  4. "A basis set for accumulation of action outcomes in the mouse frontal cortex". Paper presented in European Brain and Behavior Society, 2021.
  5. "State predictions in the primary olfactory cortex". Paper presented in Champalimaud Research Symposium: Dialogues on Neural and Machine Intelligence, 2021.
  6. "Spatial maps in piriform cortex during olfactory navigation". Paper presented in Champalimaud Research Symposium: Dialogues on Neural and Machine Intelligence, 2021.
  7. "Stimulating serotonergic neurons in the dorsal raphe nucleus during decision making results in stronger priors which are updated more rapidly". Paper presented in Champalimaud Research Symposium: Dialogues on Neural and Machine Intelligence, 2021.
  8. "Multiplexing decision computations in the mouse frontal cortex". Paper presented in Champalimaud Research Symposium: Dialogues on Neural and Machine Intelligence, 2021.
  9. "Multiplexed accumulation of evidence in the mouse brain". Paper presented in Japan Neuroscience Society, 2021.
  10. "Spatial maps in piriform cortex during olfactory navigation". Paper presented in Spanish Society of Neuroscience Meeting, 2021.
  11. "Reproducibility of electrophysiological measurements during decision-making". Paper presented in SfN, 2021.
  12. "State predictions in the primary olfactory cortex,". Paper presented in SfN, 2021.
  13. "A map for odors and place in posterior piriform cortex". Paper presented in Cosyne, Denver, 2020.
  14. "A basis set for accumulation of action outcomes in the mouse frontal cortex.". Paper presented in Simons Collaboration on the Global Brain Postdoc/Student Meeting, 2020.
  15. "Inference-Based Decisions in a Hidden State Foraging Task: Differential Contributions of Prefrontal Cortical Areas.". Paper presented in Neuroplasticity & Neuroimaging in Psychedelics Workshop, 2020.
  16. "A map for odors and place in posterior piriform cortex". Paper presented in Neuromatch 2.0, 2020.
  17. "A map for odors and place in posterior piriform cortex". Paper presented in Annual Meeting of the Japan Neuroscience Society, 2020.
  18. "Increase of pupil-linked arousal by phasic activation of dorsal raphe serotonergic neurons". Paper presented in FENS Virtual Forum, 2020.
  19. Bergomi, M; Soares, Lucas; Mainen, ZF. "Identification of multi-scale fluctuations in behavioral recordings". Paper presented in Cosyne, Lisbon, 2019.
  20. Recanatesi, S; Pereira,U; Murakami, M; Mainen, ZF; Mazzucato, L. "Self-initiated action sequences are driven by low-rank noise to motor cortex during decision making". Paper presented in Cosyne, Lisbon, 2019.
  21. Agarwal, G; Quendera, Tiago; Bergomi, M; Mainen, ZF. "Lingering generalization in humans learning a complex skill". Paper presented in Cosyne, Lisbon, 2019.
  22. Mainen, ZF; Cazettes, F; Murakami, M; Vertechi, Pietro. "Distinct prefrontal neural ensembles contribute to solving the explore/exploit tradeoff". Paper presented in Cosyne, Lisbon, 2019.
  23. Sarra, D; Lottem, E; Vertechi, Pietro; Mainen, ZF. "Serotonin modulation of persistence and flexibility". Paper presented in Cosyne, Lisbon, 2019.
  24. Poo, Cindy; Agarwal, G; Bonacchi, N; Mainen, ZF. "Conjunctive map for odors and space in posterior piriform cortex". Paper presented in Cosyne, Lisbon, 2019.
  25. Fonseca, MS; Shemesh, N; Mainen, ZF. "Impact of serotonin neuron activation on brain-wide activity and sensory processing via mouse fMRI". Paper presented in Cosyne, Lisbon, 2019.
  26. Fonseca, MS; Mainen, ZF; Shemesh, N. "Whole-brain functional magnetic resonance imaging of serotonergic neuron optogenetic activation". Paper presented in 27th ISMRM, Montreal, 2019.
  27. Cazettes, F; Vertechi, Pietro; Murakami, M; Mainen, ZF. "Distinct frontal neural ensembles contributes differentially to the inference of hidden states". Paper presented in NeuroFrance, Marseille, 2019.
  28. Agarwal, G; Quendera, Tiago; Bergomi, M; Mainen, ZF. "Learning complex skills: psychophysics in high dimensions". Paper presented in Conference on Cognitive Computational Neuroscience, Berlin, 2019.
  29. Fonseca, MS; Mainen, ZF; Shemesh, N. "Whole brain imaging of serotonergic neuron activation". Paper presented in Israely SfN, Eliat, 2019.
  30. Agarwal, G; Quendera, Tiago; Bergomi, M; Mainen, ZF. "The emergence of abstraction in human skill learning". Paper presented in Protolang, Lisbon, 2019.
  31. Mainen, ZF; IBL collaboration. "Robust and generalizable tracking of body parts of head-fixed mice". Paper presented in SfN, Chicago, 2019.
  32. Mainen, ZF; Bonacchi, N; Chapuis, GA; Churchland, AK; Harris, KD; Rossant, C; Winter, O; Wells, MJ; IBL collaboration. "The IBL data architecture: tools for storing and accessing divers databases collected at multiple sites". Paper presented in SfN, Chicago, 2019.
  33. Raiser, G; Atallah, Bassam; Lottem, E; Sautory, S; Poo, Cindy; Mainen, ZF. "Mouse olfactory bulb odor responses are negatively modulated by expectation: evidence for predictive coding". Paper presented in Cosyne, Denver, 2018.
  34. Vertechi, Pietro; Lottem, E; Sarra, D; Godinho, BS; Treves, I; Quendera, Tiago; oude Lohuis, M; Mainen, ZF. "A cross-species analysis of accumulation of evidence under non-sensory uncertainty and its modulation by the prefrontal cortex". Paper presented in Cosyne, Denver, 2018.
  35. Godinho, BS; Lottem, E; Sarra, D; Vertechi, Pietro; Mainen, ZF. "Relative contributions of three brain systems to computation of exploration/exploitation tradeoff". Paper presented in Cosyne, Denver, 2018.
  36. Quendera, Tiago; Vertechi, Pietro; Lottem, E; Sarra, D; Godinho, BS; Treves, I; oude Lohuis, M; Mainen, ZF. "A cross-species study of evidence accumulation in a probabilistic foraging task". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  37. Poo, Cindy; Bonacchi, N; Mainen, ZF. "Spatial context modulates odor representations in posterior piriform cortex". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  38. Mainen, ZF; Atallah, Bassam. "Mouse olfactory bulb odor responses are negatively modulated by expectation: evidence for predictive coding". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  39. Agarwal, G; Quendera, Tiago; Mainen, ZF. "A video game-based task to study complex skill learning in an online population". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  40. Cazettes, F; Murakami, M; Vertechi, Pietro; Lottem, E; Mainen, ZF. "Prefrontal neural ensembles dynamics underlying foraging decisions". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  41. Sautory, S; Ligneul, R; Correia, PA; Lottem, E; Mainen, ZF. "Monitoring behavioral changes induced by long-term phasic optogenetic activation of serotonergic neurons". Paper presented in 11th FENS Forum of Neuroscience, Berlin, 2018.
  42. Agarwal, G; Quendera, Tiago; Ferreira, M; Mainen, ZF. "A planning game reveals individual differences in strategy that are highly constrained". Paper presented in Cosyne, Denver, 2017.
  43. Lottem, E; Vertechi, Pietro; oude Lohuis, M; Sarra, D; Mainen, ZF. "Efficient inference of hidden states by mice in a probabilistic foraging task". Paper presented in Cosyne, Denver, 2017.
  44. Lottem, E; Mainen, ZF. "Activation of dorsal raphe serotonergic neurons delays leaving in a probabilistic foraging task". Paper presented in 47th European Brain and Behaviour Society meeting, Bilbao, 2017.
  45. Murakami, M; Shteingart, H; Loewenstein, Y; Mainen, ZF. "Dissociation of deterministic and stochastic components in the timing of voluntary actions in rodent frontal cortex". Paper presented in SfN, San Diego, 2016.
  46. Fonseca, MS; Murakami, M; Lottem, E; Mainen, ZF. "Serotonin stimulation modulates waiting through direct effects and associative learning". Paper presented in SfN, San Diego, 2016.
  47. Bonacchi, N; Poo, Cindy; Cruz, AS; Mainen, ZF. "Orbitofrontal cortex, reversals and locations". Paper presented in SfN, San Diego, 2016.
  48. Vertechi, Pietro; Lottem, E; oude Lohuis, M; Banerjee, D; Sarra, D; Mainen, ZF. "A computational account of foraging in probabilistic environments and its modulation by dorsal raphe serotonergic neurons". Paper presented in SfN, San Diego, 2016.
  49. Sarra, D; Lottem, E; Vertechi, Pietro; Banerjee, D; oude Lohuis, M; Mainen, ZF. "Serotonergic modulation of decision making in a foraging task". Paper presented in SfN, San Diego, 2016.
  50. Lottem, E; Vertechi, Pietro; oude Lohuis, M; Banerjee, D; Mainen, ZF. "Serotonin delays switching by promoting reward seeking in a probabilistic foraging task". Paper presented in SfN, San Diego, 2016.
  51. Poo, Cindy; Bonacchi, N; Cruz, A; Mainen, ZF. "Posterior piriform cortex in an odor-guided spatial navigation task". Paper presented in SfN, San Diego, 2016.
  52. Correia, PA; Lottem, E; Banerjee, D; Mainen, ZF. "Photostimulation of dorsal raphe serotonin neurons biases action selection". Paper presented in FENS, Copenhagen, 2016.
  53. Agarwal, G; Mainen, ZF. "Dissecting dynamical components of decision-making using a computer game-based approach". Paper presented in FENS, Copenhagen, 2016.
  54. Matias, S; Lottem, E; Dugué, GP; Mainen, ZF. "Serotonin and dopamine neurons signal distinct prediction error during reversal learning". Paper presented in Cosyne, Salt Lake City, 2016.
  55. Bonacchi, N; Poo, Cindy; Cruz, AS; Mainen, ZF. "Orbitofrontal cortex and outcome locations". Paper presented in Cosyne, Salt Lake City, 2016.
  56. Murakami, M; Shteingart, H; Loewenstein, Y; Mainen, ZF. "Distinct neural dynamics in two frontal areas contribute to multi-scale temporal control of decision timing". Paper presented in Cosyne, Salt Lake City, 2016.
  57. Fonseca, MS; Murakami, M; Lottem, E; Mainen, ZF. "Serotonin stimulation modulates waiting through direct and associative learning effects". Paper presented in Cosyne, Salt Lake City, 2016.
  58. Lottem, E; Vertechi, Pietro; oude Lohuis, M; Banerjee, D; Mainen, ZF. "Serotonin delays switching by promoting reward seeking in a probabilistic foraging task". Paper presented in Cosyne, Salt Lake City, 2016.
  59. Poo, Cindy; Bonacchi, N; Cruz, AS; Mainen, ZF. "Encoding of odor context in posterior piriform cortex". Paper presented in Cosyne, Salt Lake City, 2016.
  60. Agarwal, G; Medina, R; Mainen, ZF; Renart, A. "Movement trajectories encode stimulus dynamics in a decision-making task". Paper presented in FENS Bridging Neural Mechanisms and Cognition, Copenhagen, 2015.
  61. Matias, S; Lottem, E; Dugué, GP; Mainen, ZF. "Encoding of reward prediction errors by serotonin neurons revealed by bulk fluorescence recordings". Paper presented in Cosyne, Salt Lake City, 2015.
  62. Matias, S; Lottem, E; Dugué, GP; Mainen, ZF. "Encoding of reward prediction errors by serotonin neurons revealed by bulk fluorescence recordings". Paper presented in Motivational Circuits in Natural and Learned Behaviors, Virginia, 2015.
  63. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "Reinforcement learning limits performance in categorical decision-making". Paper presented in Cosyne, Salt Lake City, 2015.
  64. Murakami, M; Mainen, ZF. "Contrasting roles of medial prefrontal cortex and secondary motor cortex in waiting decisions". Paper presented in Cosyne, Salt Lake City, 2015.
  65. Correia, PA; Valente, SS; Lima, SQ; Mainen, ZF. "Neuromodulation of sexual behavior: a role for serotonin?". Paper presented in 9th FENS Forum of Neuroscience, Milan, 2014.
  66. Correia, PA; Valente, SS; Lima, SQ; Mainen, ZF. "Neuromodulation of sexual behavior: a role for serotonin?". Paper presented in Controlling Neurons, Circuits and Behaviour, FENS Spring Brain Conference, Copenhagen, 2014.
  67. DeWitt, EJ; Costa, GM; Gouvea, TS; Mendonça, AG; Vicente, MI; Mainen, ZF. "The story of ongoing learning in a stationary world". Paper presented in Champalimaud Neuroscience Programme Retreat, Beja, 2014.
  68. Brendel, W; Kobak, D; Romo, R; Feierstein, CE; Mainen, ZF; Machens, C. "Orthogonal representation of tasks parameters in higher cortical areas". Paper presented in Cosyne, Salt Lake City, 2014.
  69. Mainen, ZF; Hobbiss, A; Afonso,B; Rennie, S; Marques,T; Ramos, C. "Ar | Respire connosco: sharing scientific knowledge and promoting dialogue in an interactive and critical way". Paper presented in SciCom PT, Porto, 2014.
  70. Vicente, AM; Pereira, A; Abril de Abreu, R; Ferreira, PG; Li Chen, Tânia; Carlos, T; Vieira, C; et al. "Sciencecalifragilistic – Critical Thinking and Science: a Journey through the Scientific Method". Paper presented in SciCom PT, Porto, 2014.
  71. Vicente, MI; Mendonça, AG; Mainen, ZF. "Task-dependent speed-accuracy tradeoffs in olfaction". Paper presented in SfN, 2014.
  72. Matias, S; Lottem, E; Dugué, GP; Mainen, ZF. "Dorsal Raphe Serotonergic Activity Correlates with Value". Paper presented in MIT Portugal Conference, Coimbra, 2014.
  73. Matias, S; Lottem, E; Dugué, GP; Mainen, ZF. "Long-term monitoring of serotonergic neuronal activity in behaving mice through an optical fiber". Paper presented in 9th FENS Forum, Milan, 2014.
  74. Fonseca, MS; Murakami, M; Mainen, ZF. "Optical activation of dorsal raphe serotonin neurons is sufficient to facilitate waiting for delayed rewards". Paper presented in SfN, Washington DC, 2014.
  75. Matias, S; Dugué, GP; Lottem, E; Audero, E; Vassilevskaia, T; Mainen, ZF. "Long-term monitoring of genetically defined neuronal populations in freely behaving rodents through an optical fiber". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  76. Fonseca, M; Murakami, M; Mainen, ZF. "Serotonergic modulation of waiting behaviour". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  77. Costa, GM; Mainen, ZF. "Interplay between value and uncertainty in the olfactory striatum". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  78. Vicente, MI; Mendonça, AG; Mainen, ZF. "Task-dependent speed accuracy-tradeoffs in olfaction". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  79. Lottem, E; Lörincz, ML; Dugué, GP; Mainen, ZF. "Serotonergic modulation of sensory information processing in the piriform cortex". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  80. Correia, PA; Valente, SS; Lima, SQ; Mainen, ZF. "Serotonergic modulation of sexual behaviour". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  81. Murakami, M; Vicente, MI; Costa, GM; Mainen, ZF. "Neural dynamics of waiting and giving up in the rat secondary motor cortex". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  82. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "Crystalized learning as a suboptimal strategy that degrades odor categorization performance". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  83. Venturini, R; Johnson, H; Mainen, ZF. "Feedback manipulation affects confidence in decision-making". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2013.
  84. Mendonça, AG; Vicente, MI; DeWitt, E; Pouget, A; Mainen, ZF. "Uncertainty in the brain as a two-step problem: how continuous learning may generate errors". Paper presented in Annual Meeting for Gulbenkian Students, Seia, 2013.
  85. Correia, PA; Valente, SS; Lima, SQ; Mainen, ZF. "Serotonergic modulation of sexual behavior". Paper presented in Sociedade Portuguesa de Etologia, Lisbon, 2013.
  86. Costa, GM; Mainen, ZF. "Interplay between value and confidence in a olfactory guided decision". Paper presented in Sociedade Portuguesa de Etologia, Lisbon, 2013.
  87. Fonseca, AR; Mainen, ZF. "Planning and selecting between multiple action sequences in a multiple alternative non-forced choice task". Paper presented in EPFL SV- Life Science Symposium, Lausanne, 2013.
  88. Costa, GM; Mainen, ZF. "Interplay of confidence and value in the transformation of olfaction to action". Paper presented in Cosyne, Arizona, 2013.
  89. DeWitt, E; Mendonça, AG; Kepecs, A; Mainen, ZF. "Confidence based learning in a perceptual task: How uncertainty and outcome influence choice". Paper presented in Cosyne, Arizona, 2013.
  90. Murakami, M; Vicente, MI; Costa, GM; Mainen, ZF. "Neural dynamics of waiting and giving up in the rat secondary motor cortex". Paper presented in Cosyne, Arizona, 2013.
  91. Murakami, M; Vicente, MI; Costa, GM; Mainen, ZF. "Neural dynamics of waiting and giving up in the rat secondary motor cortex". Paper presented in Janelia Conference, Virginia, 2013.
  92. DeWitt, EJ; Mendonça, AG; Gouvea, TS; Kepecs, A; Mainen, ZF. "Trial-by-trial perceptual learning during odor category decisions: Reinforcement learning, uncertainty and modeling choice". Paper presented in SfN, New Orleans, 2012.
  93. Vicente, MI; Mendonça, AG; Mainen, ZF. "Perceptual decision-making and interval timing: two sides of the same coin?". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2012.
  94. Correia, PA; Dugué, GP; Lottem, E; Lörincz, ML; Matias, S; DeWitt, E; Audero, E; Lima, SQ; Mainen, ZF. "Serotonin’s role in behavior: using an optogenetic strategy to understand it". Paper presented in FENS-IBRO-SfN School Causal Neuroscience II, FENS Satellite Symposium, Barcelona, 2012.
  95. Correia, PA; Dugué, GP; Lottem, E; Lörincz, ML; Matias, S; DeWitt, E; Audero, E; Mainen, ZF. "Serotonin’s role in behavior: using an optogenetic strategy to understand it". Paper presented in Cell Symposia - Neuromodulatory Mechanisms, New Orleans, 2012.
  96. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "A computational dissection: contributions of sensory and category uncertainty in perceptual decision-making". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2012.
  97. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "Detecting is different from categorizing: how uncertainty affects perceptual decision-making". Paper presented in Annual Meeting of Gulbenkian Students, Foz do Arelho, 2012.
  98. Bonacchi, N; Mainen, ZF. "Context dependent modulation of value". Paper presented in Annual Meeting of Gulbenkian Students, Foz do Arelho, 2012.
  99. Bonacchi, N; Poo, Cindy; Mainen, ZF. "Spatial goals and actions in the orbitofrontal cortex". Paper presented in SfN, New Orleans, 2012.
  100. Gouvea, TS; Costa, GM; DeWitt, EJ; Mainen, ZF. "Trial-by-trial perceptual learning during odor category decisions: Value, uncertainty and dopamine". Paper presented in Cosyne, Salt Lake City, 2012.
  101. Matias, S; Dugué, GP; Lottem, E; Mainen, ZF. "Long-term monitoring of genetically defined neuronal populations in freely behaving rodents through an optical fiber". Paper presented in SfN, New Orleans, 2012.
  102. Vicente, MI; Mendonça, AG; Pouget, A; Mainen, ZF. "Odor detection vs. odor categorization: crucial differences in behavioral and learning strategies". Paper presented in Cosyne, Salt Lake City, 2012.
  103. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "Dissecting the Contributions of Sensory and Category Uncertainty in Perceptual Decision-Making". Paper presented in Cosyne, Salt Lake City, 2012.
  104. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "A computational dissection of rodent behavior: Contributions of sensory and category uncertainty in olfactory decision-making". Paper presented in Nanosymposium “Neural Mechanisms of Decision-Making”, SfN, New Orleans, 2012.
  105. DeWitt, E; Mainen, ZF; Glimcher, PW. "Comparing reinforcement learning in humans and animals to a normative model". Paper presented in XII Meeting of the Portuguese Society for Neuroscience, Lisbon, 2011.
  106. Mendonça, AG; Vicente, MI; Mainen, ZF. "Different tasks, different tradeoffs: speed and accuracy in odor detection vs. odor categorization". Paper presented in XII Meeting of the Portuguese Society for Neuroscience, Lisbon, 2011.
  107. Mendonça, AG; Vicente, MI; Pouget, A; Mainen, ZF. "Odor detection vs. odor categorization: links between speed-accuracy tradeoff and noise sources". Paper presented in Champalimaud Neuroscience Symposium, Lisbon, 2011.
  108. Correia, PA; Dugué, GP; Lottem, E; Lörincz, ML; Matias, S; DeWitt, E; Audero, E; Lima, SQ; Mainen, ZF. "Serotonin’s role in behavior: using an optogenetic strategy to understand it". Paper presented in FENS-IBRO-SfN School Causal Neuroscience, Bertinoro, 2011.
  109. Dugué, GP; Lörincz, ML; Matias, S; Vinhas, M; Garcia Da Silva, P; Lima, SQ; Mainen, ZF. "Optogenetic control of serotonergic neurons in rats". Paper presented in Genetic Manipulation of Neuronal Activity II, Virginia, 2011.
  110. Correia, PA; Dugué, GP; Matias, S; Lörincz, ML; Bonacchi, N; Audero, E; Lottem, E; Mainen, ZF. "Testing the link between serotonin and aversive behaviors using optogenetics". Paper presented in CNP-CRICM Meeting, Lisbon, 2011.
  111. Matias, S; Dugué, GP; Lima, SQ; Mainen, ZF. "Monitoring Serotonergic Neuronal Activity in Behaving Rats". Paper presented in XII Meeting of the Portuguese Neuroscience Society, Lisbon, 2011.
  112. Vicente, MI; Mendonça, AG; Mainen, ZF. "Different tasks, different tradeoffs: speed and accuracy in odor detection vs. odor categorization". Paper presented in Cosyne, Salt Lake City, 2011.
  113. Lottem, E; Dugué, GP; Lörincz, ML; Correia, PA; DeWitt, EJ; Mainen, ZF. "Serotonergic modulation of sensory information processing". Paper presented in Cosyne, Salt Lake City, 2011.
  114. Murakami, M; Vicente, MI; Costa, GM; Mainen, ZF. "Neural substrates of withholding impulsive actions in rat frontal cortex". Paper presented in 7th FENS Forum of European Neuroscience, Amsterdam, 2010.
  115. Dugué, DP; Lörincz, ML; Matias, S; Vinhas, M; Garcia Da Silva, P; Lima, SQ; Mainen, ZF. "Optogenetic control of serotonergic neurons in rats". Paper presented in 7th FENS Forum of European Neuroscience, Amsterdam, 2010.
  116. Murakami, M; Mainen, ZF. "Role of Medial Prefrontal Cortex and Secondary Motor Cortex in Withholding Impulsive Action". Paper presented in Cosyne, 2009.
  117. Kepecs, A; Uchida, N; Mainen, ZF. "Active learning using uncertainty: behavioral evidence and neural correlates in rats". Paper presented in Cosyne, Salt Lake City, 2009.
  118. Miura, K; Mainen, ZF; Uchida, N. "Fast and dynamic odor encoding in rat olfactory cortex during odor discrimination task". Paper presented in Cosyne, 2009.
  119. Felsen, G; Mainen, ZF. "Motor planning in the rat superior colliculus". Paper presented in Cosyne, 2009.
  120. Mainen, ZF. "Neural mechanisms for odor-guided decisions in the rat". Paper presented in Okinawa Computer Neuroscience Course, Okinawa, 2009.
  121. Costa, GM; Lak, A; Mainen, ZF; Kepecs, A. "Role of orbitofrontal cortex in confidence judgments in rats". Paper presented in SfN, 2009.
  122. Costa, GM; Lak, A; Mainen, ZF; Kepecs, A. "Role of orbitofrontal cortex in confidence judgments in rats". Paper presented in Pan-Iberian System Neuroscience Meeting, Lisbon, 2009.
  123. Bonacchi, N; Dugué, G; Mainen, ZF. "Behavioral suppression in a modified conflict paradigm". Paper presented in Associação Portuguesa de Psicologia Experimental, 2009.
  124. Murakami, M; Vicente, MI; Costa, GM; Mainen, ZF. "Role of Medial Prefrontal Cortex and Secondary Motor Cortex in Withholding Impulsive Action". Paper presented in SfN, Chicago, 2009.
  125. Mainen, ZF; Kepecs, A; Zariwala, H; Uchida, N. "Uncertainty representation in the orbitofrontal cortex during decision making in rats". Paper presented in FENS, 2008.
  126. Felsen, G; Klein, R; Mainen, ZF. "Movement selection and initiation in the rat superior colliculus". Paper presented in Cosyne, 2008.
  127. Khan, AG; Bhalla, US; Mainen, ZF. "Odour mixture processing in the rat olfactory cortex". Paper presented in FENS, 2008.
  128. Felsen, G; Mainen, ZF. "The role of the superior colliculus in sensory-guided spatial decisions in rats". Paper presented in SfN, 2008.
  129. Kepecs, A; Mainen, ZF; Uchida, N. "How uncertainty boosts learning: Dynamic updating of decision strategies". Paper presented in SfN, 2008.
  130. Miura, K; Mainen, ZF; Uchida, N. "Dynamic odor representation in rat piriform cortex during active sensation". Paper presented in SfN, 2008.
  131. Kepecs, A; Uchida, N; Mainen, ZF. "Graded prediction error signal drives behavioral choice biases in rats". Paper presented in Cosyne, 2008.
  132. Murakami, M; Mainen, ZF. "Role of medial prefrontal cortex and secondary motor cortex in withholding impulsive action". Paper presented in Cosyne, 2008.
  133. Mainen, ZF. "Single unit correlates of decision-making in the dorsal raphe of the rat". Paper presented in SfN, 2007.
  134. Murakami, M; Mainen, ZF. "Involvement of medial prefrontal cortex in withholding impulsive action". Paper presented in SfN, 2007.
  135. Kepecs, A; Uchida, N; Zariwala, H; Mainen, ZF. "Uncertainty representation in orbitofrontal cortex during decision making in rats". Paper presented in SfN, 2007.
  136. Mainen, ZF; Xu, N. "Expectation of forthcoming stimulus affects odor discrimination in rodents". Paper presented in SfN, 2007.
  137. Smear, M; Mainen, ZF. "Using rat chemotaxis to study the "where" problem of olfaction". Paper presented in SfN, 2007.
  138. Uchida, N; Mainen, ZF. "Rapid formation of dense odor representations in the piriform cortex of behaving rats". Paper presented in SfN, 2006.
  139. Kepecs, A; Uchida, N; Zariwala, H; Mainen, ZF. "Neural encoding and behavioral impact of uncertainty in category decisions". Paper presented in SfN, 2006.
  140. Felsen, G; Mainen, ZF. "Activity of orbitofrontal neurons during task learning". Paper presented in SfN, 2006.
  141. Feierstein, CE; Quirk, MC; Mainen, ZF. "Orbitofrontal cortex responses during acquisition of novel stimulus--response associations". Paper presented in SfN, 2005.
  142. Gurden, H; Pain, F; Desbree, A; Mastrippolito, R; Bonventom, G; Hantraye, P; Uchida, N; Mainen, ZF; Laniece, P. "Odor-evoked activation of olfactory glomeruli: An attractive model to probe neurometabolic and neurovascular coupling mechanisms by optical and radioisotopic techniques". Paper presented in SfN, 2005.
  143. Kepecs, A; Uchida, N; Mainen, ZF. "Sniffing patterns in rats performing an olfactory discrimination task". Paper presented in SfN, 2005.
  144. Sosulski, D; Quirk, MC; Mainen, ZF. "Ketamine inhibits interneuron firing in prefrontal cortex of behaving rats". Paper presented in SfN, 2005.
  145. Sato, T; Yasuda, R; Mainen, ZF; Svoboda, K. "Using [Ca2+] imaging to detect single action potentials in multiple neurons in the mouse somatosensory cortex in vivo". Paper presented in SfN, 2005.
  146. Zariwala, HA; Uchida, N; Mainen, ZF. "A study of speed and performance accuracy in an olfactory discrimination task". Paper presented in SfN, 2005.
  147. Egger, V; Svoboda, K; Mainen, ZF. "Glomerular input results in distinct modes of calcium signaling in olfactory bulb granule cell dendrites". Paper presented in SfN, 2004.
  148. Ranade, SP; Mainen, ZF. "Serotonin modulates odor-evoked sensory input in the rat main olfactory bulb". Paper presented in SfN, 2004.
  149. Uchida, N; Mainen, ZF. "Psychophysical characterization of concentration invariant olfactory recognition". Paper presented in SfN, 2004.
  150. Feierstein, C.E.; Quirk, M.C.; Mainen, ZF. "Spatial coding in piriform and orbitofrontal cortex during olfactory discrimination". Paper presented in SfN, 2004.
  151. Kepecs, A; Mainen, ZF. "Inter-areal interactions during olfactory discrimination in rats". Paper presented in SfN, 2004.
  152. Zariwala, HA; Kepecs, A; Mainen, ZF. "Contextual adaptation in rat olfactory discrimination". Paper presented in SfN, 2004.
  153. Gurden, H; Uchida, N.; Mainen, ZF. "Presynaptic origin of odor-evoked intrinsic optical signal in olfactory glomeruli". Paper presented in SfN, 2003.
  154. Quirk, M.C.; Feierstein, C.E.; Mainen, ZF. "Local network interactions within rodent frontal cortex during olfactory discrimination". Paper presented in SfN, 2003.
  155. Uchida, N.; Mainen, ZF. "Fine olfactory discrimination in a single sniff". Paper presented in SfN, 2003.
  156. Zariwala, H; Uchida, N; Kepecs, A; Mainen, ZF. "Context-dependent changes in olfactory discrimination performance in rodents". Paper presented in SfN, 2003.
  157. Uchida, N.; Mainen, ZF. "Concentration-invariant odor quality perception: ratio coding and behavioral discrimination". Paper presented in SfN, 2002.
  158. Egger, V; Svoboda, K.; Mainen, ZF. "Regulation of action potential evoked calcium signals in rat olfactory bulb granule cells: contribution of low – threshold Ca2+ channel inactivation by sustained depolarization". Paper presented in FENS, 2002.
  159. Uchida, N.; Macknik, SL; Mainen, ZF. "Psychophysical measurement of odor quality perception in rodents using a two-alternative choice task with odor mixtures". Paper presented in SfN, 2001.
  160. Oertner, TG; Sabatini, BS; Mainen, ZF; Svoboda, K.. "Dissecting mechanisms of paired-pulse facilitation at single synapses in rat hippocampal slices". Paper presented in SfN, 2001.
  161. Egger, V; Mainen, ZF. "Action potential-evoked calcium transients in rat olfactory bulb granule cell dendrites in vitro". Paper presented in SfN, 2001.
  162. Caporale, N; Mehta, N; Mainen, ZF. "Natural and non-natural volatile olfactory cues mediating social discrimination and recognition". Paper presented in SfN, 2001.
  163. Mainen, ZF; Macknik, SL; Gasperini, R. "Odor-evoked optical signals in rat and mouse olfactory bulb: relating neural activity and perception". Paper presented in SfN, 2000.
  164. Mainen, ZF; Malinow, R.; Svoboda, K.. "Optical quantal analysis". Paper presented in SfN, 1998.
  165. Mainen, ZF; Roder, J.; Malinow, R.. "Measurement of release probability by use-dependent block of AMPA-R mediated synaptic transmission in GluR2 knockout mice". Paper presented in SfN, 1997.
  166. Mainen, ZF; Malinow, R.. "Kinetics of NMDA receptor activation by caged glutamate in the hippocampal slice: Constraining functional synaptic geometry". Paper presented in SfN, 1996.
  167. Mainen, ZF; Sejnowski, T.J.. "Minimal models of spike encoding by neocortical neurons". Paper presented in SfN, 1995.
  168. Tsodyks M; Bell AJ; Mainen, ZF; Sejnowski TJ. "Why do cortical neurons spike irregularly?". Paper presented in SfN, 1994.
  169. Mainen, ZF; Sejnowski, T. J.. "Reliability of spike initiation in neocortex". Paper presented in SfN, 1994.
  170. Huguenard, JR; Joerges, J; Mainen, ZF; Sejnowski, T.J.. "Functional role of axon hillock and initial segment in cortical spike initiation". Paper presented in SfN, 1994.
  171. Mainen, ZF; Claiborne, B.J.; Brown, T.H.. "Evolution of feature clusters in hippocampal dendrites". Paper presented in American Inst. Physics: Neural Networks for Computing, Snowbird, Utah, 1991.
  172. Mainen, ZF; Claiborne, B.J.; Brown, T.H.. "A novel role for synaptic competition in the development of cortical lamination". Paper presented in SfN, 1991.
  173. Mainen, ZF; Zador AM; Claiborne, B.J.; Brown, T.H.. "Hebbian synapses induce feature mosaics in hippocampal dendrites". Paper presented in SfN, 1990.
Conference paper
  1. Kim, D.; Stanacevic, M.; Kamoua, R.; Mainen, Z.. "A low-power low-data-rate neural recording system with adaptive spike detection". 2008.
    10.1109/MWSCAS.2008.4616926
  2. Xiao, Y.; Donghwi, K.; Stanacevic, M.; Mainen, Z.. "Low-power high-resolution 32-channel neural recording system". 2007.
    10.1109/IEMBS.2007.4352804
Journal article
  1. Ligneul, Romain; Mainen, ZF. Corresponding author: Mainen, ZF. "Serotonin". Current Biology 33 23 (2023): R1216-R1221. http://dx.doi.org/10.1016/j.cub.2023.09.068.
    10.1016/j.cub.2023.09.068
  2. Cazettes, Fanny; Mazzucato, Luca; Murakami, Masayoshi; Morais, Joao P.; Augusto, Elisabete; Renart, Alfonso; Mainen, ZF. Corresponding author: Mainen, ZF. "A reservoir of foraging decision variables in the mouse brain". Nature Neuroscience 26 5 (2023): 840-849. http://dx.doi.org/10.1038/s41593-023-01305-8.
    10.1038/s41593-023-01305-8
  3. Balci, Fuat; Ben Hamed, Suliann; Boraud, Thomas; Bouret, Sébastien; Brochier, Thomas; Brun, Cédric; Cohen, Jeremiah Y.; et al. "A response to claims of emergent intelligence and sentience in a dish". Neuron 111 5 (2023): 604-605. http://dx.doi.org/10.1016/j.neuron.2023.02.009.
    Published • 10.1016/j.neuron.2023.02.009
  4. Koch, Christof; Svoboda, Karel; Bernard, Amy; Basso, Michele A.; Churchland, Anne K.; Fairhall, Adrienne L.; Groblewski, Peter A.; et al. "Next-generation brain observatories". Neuron 110 22 (2022): 3661-3666. http://dx.doi.org/10.1016/j.neuron.2022.09.033.
    10.1016/j.neuron.2022.09.033
  5. Snitz, Kobi; Honigstein, Danielle; Weissgross, Reut; Ravia, Aharon; Mishor, Eva; Perl, Ofer; Karagach, Shiri; et al. "An olfactory self-test effectively screens for COVID-19". Communications Medicine 2 1 (2022): http://dx.doi.org/10.1038/s43856-022-00095-7.
    10.1038/s43856-022-00095-7
  6. Ligneul, Romain; Mainen, Zachary F.; Ly, Verena; Cools, Roshan. "Stress-sensitive inference of task controllability". Nature Human Behaviour 6 6 (2022): 812-822. http://dx.doi.org/10.1038/s41562-022-01306-w.
    Published • 10.1038/s41562-022-01306-w
  7. Recanatesi, Stefano; Pereira-Obilinovic, Ulises; Murakami, Masayoshi; Mainen, Zachary; Mazzucato, Luca. "Metastable attractors explain the variable timing of stable behavioral action sequences". Neuron 110 1 (2022): 139-153.e9. http://dx.doi.org/10.1016/j.neuron.2021.10.011.
    10.1016/j.neuron.2021.10.011
  8. Poo, Cindy; Agarwal, Gautam; Bonacchi, Niccolò; Mainen, Zachary F.. "Spatial maps in piriform cortex during olfactory navigation". Nature 601 7894 (2021): 595-599. http://dx.doi.org/10.1038/s41586-021-04242-3.
    10.1038/s41586-021-04242-3
  9. Aguillon-Rodriguez, Valeria; Angelaki, Dora; Bayer, Hannah; Bonacchi, Niccolo; Carandini, Matteo; Cazettes, Fanny; Chapuis, Gaelle; et al. "Standardized and reproducible measurement of decision-making in mice". eLife 10 (2021): http://dx.doi.org/10.7554/elife.63711.
    10.7554/elife.63711
  10. Urai, Anne E; Aguillon-Rodriguez, Valeria; Laranjeira, Inês C; Cazettes, Fanny; The International Brain Laboratory; Mainen, Zachary F; Churchland, Anne K. "Citric Acid Water as an Alternative to Water Restriction for High-Yield Mouse Behavior". eneuro (2021): ENEURO.0230-20.2020. http://dx.doi.org/10.1523/eneuro.0230-20.2020.
    Open access • Published • 10.1523/eneuro.0230-20.2020
  11. Cazettes, Fanny; Reato, Davide; Morais, João P.; Renart, Alfonso; Mainen, Zachary F.. "Phasic Activation of Dorsal Raphe Serotonergic Neurons Increases Pupil Size". Current Biology 31 1 (2021): 192-197.e4. http://dx.doi.org/10.1016/j.cub.2020.09.090.
    Open access • Published • 10.1016/j.cub.2020.09.090
  12. Iravani B; Arshamian A; Ravia A; Mishor E; Snitz K; Shushan S; Roth Y; et al. "Corrigendum to: Relationship Between Odor Intensity Estimates and COVID-19 Prevalence Prediction in a Swedish Population". Chemical senses (2020): http://europepmc.org/abstract/PMC/PMC7339068.
  13. Mendonça, AG; Drugowitsch, Jan; Vicente, MI; DeWitt, EEJ; Pouget, A; Mainen, ZF. "The impact of learning on perceptual decisions and its implication for speed-accuracy tradeoffs". Nature Communications 11 1 (2020): http://dx.doi.org/10.1038/s41467-020-16196-7.
    Open access • Published • 10.1038/s41467-020-16196-7
  14. Iravani, Behzad; Arshamian, Artin; Ravia, Aharon; Mishor, Eva; Snitz, Kobi; Shushan, Sagit; Roth, Yehudah; et al. "Relationship Between Odor Intensity Estimates and COVID-19 Prevalence Prediction in a Swedish Population". Chemical Senses 45 6 (2020): 449-456. http://dx.doi.org/10.1093/chemse/bjaa034.
    Published • 10.1093/chemse/bjaa034
  15. Vertechi, Pietro; Lottem, Eran; Sarra, Dario; Godinho, Beatriz; Treves, Isaac; Quendera, Tiago; Oude Lohuis, Matthijs Nicolai; Mainen, Zachary F.. "Inference-Based Decisions in a Hidden State Foraging Task: Differential Contributions of Prefrontal Cortical Areas". Neuron 106 1 (2020): 166-176.e6. http://dx.doi.org/10.1016/j.neuron.2020.01.017.
    Published • 10.1016/j.neuron.2020.01.017
  16. Drugowitsch, Jan; Mendonça, André G.; Mainen, Zachary F.; Pouget, Alexandre. "Learning optimal decisions with confidence". Proceedings of the National Academy of Sciences (2019): 201906787. http://dx.doi.org/10.1073/pnas.1906787116.
    10.1073/pnas.1906787116
  17. Pardo-Vazquez, Jose L.; Castiñeiras-de Saa, Juan R.; Valente, Mafalda; Damião, Iris; Costa, Tiago; Vicente, M. Inês; Mendonça, André G.; Mainen, ZF; Renart, Alfonso. "The mechanistic foundation of Weber’s law". Nature Neuroscience 22 9 (2019): 1493-1502. http://dx.doi.org/10.1038/s41593-019-0439-7.
    10.1038/s41593-019-0439-7
  18. Rigato, Joana; Rennie, Scott M.; Mainen, Zachary F.. "The overlooked ubiquity of first-person experience in the cognitive sciences". Synthese (2019): http://dx.doi.org/10.1007/s11229-019-02136-6.
    10.1007/s11229-019-02136-6
  19. Iigaya, Kiyohito; Fonseca, Madalena S.; Murakami, Masayoshi; Mainen, Zachary F.; Dayan, Peter. "An effect of serotonergic stimulation on learning rates for rewards apparent after long intertrial intervals". Nature Communications 9 1 (2018): http://dx.doi.org/10.1038/s41467-018-04840-2.
    10.1038/s41467-018-04840-2
  20. Lottem, Eran; Banerjee, Dhruba; Vertechi, Pietro; Sarra, Dario; Lohuis, Matthijs oude; Mainen, Zachary F.. "Activation of serotonin neurons promotes active persistence in a probabilistic foraging task". Nature Communications 9 1 (2018): http://dx.doi.org/10.1038/s41467-018-03438-y.
    10.1038/s41467-018-03438-y
  21. Abbott, Larry F.; Angelaki, Dora E.; Carandini, Matteo; Churchland, Anne K.; Dan, Yang; Dayan, Peter; Deneve, Sophie; et al. "An International Laboratory for Systems and Computational Neuroscience". Neuron 96 6 (2017): 1213-1218. http://dx.doi.org/10.1016/j.neuron.2017.12.013.
    10.1016/j.neuron.2017.12.013
  22. Murakami, M.; Shteingart, H.; Loewenstein, Y.; Mainen, Z.F.; Murakami, Masayoshi; Shteingart, Hanan; Loewenstein, Yonatan; Mainen, Zachary F.. "Distinct Sources of Deterministic and Stochastic Components of Action Timing Decisions in Rodent Frontal Cortex". Neuron 94 4 (2017): 908-919.e7. http://www.scopus.com/inward/record.url?eid=2-s2.0-85020081011&partnerID=MN8TOARS.
    10.1016/j.neuron.2017.04.040
  23. Correia, P.A.; Lottem, E.; Banerjee, D.; Machado, A.S.; Carey, M.R.; Mainen, Z.F.; Correia, Patrícia A; et al. "Transient inhibition and long-term facilitation of locomotion by phasic optogenetic activation of serotonin neurons". eLife 6 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85013441075&partnerID=MN8TOARS.
    10.7554/eLife.20975
  24. Matias, S.; Lottem, E.; Dugué, G.P.; Mainen, Z.F.; Matias, Sara; Lottem, Eran; Dugué, Guillaume P; Mainen, Zachary F. "Activity patterns of serotonin neurons underlying cognitive flexibility". eLife 6 (2017): http://www.scopus.com/inward/record.url?eid=2-s2.0-85015831758&partnerID=MN8TOARS.
    10.7554/eLife.20552
  25. Grabska-Barwinska, A.; Barthelmé, S.; Beck, J.; Mainen, Z.F.; Pouget, A.; Latham, P.E.. "A probabilistic approach to demixing odors". Nature Neuroscience 20 1 (2017): 98-106. http://www.scopus.com/inward/record.url?eid=2-s2.0-85002498895&partnerID=MN8TOARS.
    10.1038/nn.4444
  26. Correia, Patrícia; Matias, Sara; Mainen, Zachary. "Stereotaxic Adeno-associated Virus Injection and Cannula Implantation in the Dorsal Raphe Nucleus of Mice". BIO-PROTOCOL 7 18 (2017): http://dx.doi.org/10.21769/bioprotoc.2549.
    10.21769/bioprotoc.2549
  27. Kobak, D.; Brendel, W.; Constantinidis, C.; Feierstein, C.E.; Kepecs, A.; Mainen, Z.F.; Qi, X.-L.; et al. "Demixed principal component analysis of neural population data". eLife 5 APRIL2016 (2016): http://www.scopus.com/inward/record.url?eid=2-s2.0-84971572886&partnerID=MN8TOARS.
    10.7554/eLife.10989
  28. Mainen, Z.F.; Haüsser, M.; Pouget, A.. "A better way to crack the brain". Nature 539 7628 (2016): 159-161. http://www.scopus.com/inward/record.url?eid=2-s2.0-85014859264&partnerID=MN8TOARS.
    10.1038/539159a
  29. Lottem, E.; Lörincz, M.L.; Mainen, Z.F.. "Optogenetic activation of dorsal raphe serotonin neurons rapidly inhibits spontaneous but not odor-evoked activity in olfactory cortex". Journal of Neuroscience 36 1 (2016): 7-18. http://www.scopus.com/inward/record.url?eid=2-s2.0-84953736069&partnerID=MN8TOARS.
    10.1523/JNEUROSCI.3008-15.2016
  30. Gomez-Marin, A.; Mainen, Z.F.. "Expanding perspectives on cognition in humans, animals, and machines". Current Opinion in Neurobiology 37 (2016): 85-91. http://www.scopus.com/inward/record.url?eid=2-s2.0-84957599108&partnerID=MN8TOARS.
    10.1016/j.conb.2016.01.011
  31. Meyniel, F.; Sigman, M.; Mainen, Z.F.; Meyniel, Florent; Sigman, Mariano; Mainen, Zachary F.. "Confidence as Bayesian Probability: From Neural Origins to Behavior". Neuron 88 1 (2015): 78-92. http://www.scopus.com/inward/record.url?eid=2-s2.0-84943241276&partnerID=MN8TOARS.
    10.1016/j.neuron.2015.09.039
  32. Fonseca, M.S.; Murakami, M.; Mainen, Z.F.. "Activation of dorsal raphe serotonergic neurons promotes waiting but is not reinforcing". Current Biology 25 3 (2015): 306-315. http://hdl.handle.net/10400.26/23195.
    Open access • Published • 10.1016/j.cub.2014.12.002
  33. Murakami, M.; Mainen, Z.F.; Murakami, Masayoshi; Mainen, Zachary F. "Preparing and selecting actions with neural populations: Toward cortical circuit mechanisms". Current Opinion in Neurobiology 33 (2015): 40-46. http://www.scopus.com/inward/record.url?eid=2-s2.0-84922187240&partnerID=MN8TOARS.
    10.1016/j.conb.2015.01.005
  34. Bush, P.C.; Mainen, Z.F.. "Columnar architecture improves noise robustness in a model cortical network". PLoS ONE 10 3 (2015): http://www.scopus.com/inward/record.url?eid=2-s2.0-84925014492&partnerID=MN8TOARS.
    10.1371/journal.pone.0119072
  35. Gomez-Marin, A.; Paton, J.J.; Kampff, A.R.; Costa, R.M.; Mainen, Z.F.. "Big behavioral data: Psychology, ethology and the foundations of neuroscience". Nature Neuroscience 17 11 (2014): 1455-1462. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908500040&partnerID=MN8TOARS.
    10.1038/nn.3812
  36. Murakami, M.; Vicente, M.I.; Costa, G.M.; Mainen, Z.F.; Murakami, Masayoshi; Vicente, M Inês; Costa, Gil M; Mainen, Zachary F. "Neural antecedents of self-initiated actions in secondary motor cortex". Nature Neuroscience 17 11 (2014): 1574-1582. http://www.scopus.com/inward/record.url?eid=2-s2.0-84908572998&partnerID=MN8TOARS.
    10.1038/nn.3826
  37. Lak, A.; Costa, G.M.; Romberg, E.; Koulakov, A.A.; Mainen, Z.F.; Kepecs, A.. "Orbitofrontal cortex is required for optimal waiting based on decision confidence". Neuron 84 1 (2014): 190-201. http://www.scopus.com/inward/record.url?eid=2-s2.0-84907966818&partnerID=MN8TOARS.
    Published • 10.1016/j.neuron.2014.08.039
  38. Dugué, G.P.; Lörincz, M.L.; Lottem, E.; Audero, E.; Matias, S.; Correia, P.A.; Léna, C.; Mainen, Z.F.. "Optogenetic recruitment of dorsal raphe serotonergic neurons acutely decreases mechanosensory responsivity in behaving mice". PLoS ONE 9 8 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84920088541&partnerID=MN8TOARS.
    Published • 10.1371/journal.pone.0105941
  39. Tecuapetla, F.; Matias, S.; Dugue, G.P.; Mainen, Z.F.; Costa, R.M.. "Balanced activity in basal ganglia projection pathways is critical for contraversive movements". Nature Communications 5 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84904013051&partnerID=MN8TOARS.
    10.1038/ncomms5315
  40. Mainen, Z.F.; Pouget, A.. "Put brain project back on course". Nature 511 7511 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84905055618&partnerID=MN8TOARS.
    10.1038/511534b
  41. Mainen, Z.F.; Pouget, A.. "European Commission: Put brain project back on course.". Nature 511 7511 (2014): http://www.scopus.com/inward/record.url?eid=2-s2.0-84907048863&partnerID=MN8TOARS.
  42. Rigato, Joana; Murakami, Masayoshi; Mainen, Zachary. "Spontaneous Decisions and Free Will: Empirical Results and Philosophical Considerations". Cold Spring Harbor Symposia on Quantitative Biology 79 (2014): 177-184. http://dx.doi.org/10.1101/sqb.2014.79.024810.
    10.1101/sqb.2014.79.024810
  43. Mainen, Zachary. "BRAIN Initiative and Human Brain Project: Hopes and Reservations". Cell 155 2 (2013): 265-266. http://dx.doi.org/10.1016/j.cell.2013.09.037.
    10.1016/j.cell.2013.09.037
  44. Zariwala, H.A.; Kepecs, A.; Uchida, N.; Hirokawa, J.; Mainen, Z.F.. "The limits of deliberation in a perceptual decision task". Neuron 78 2 (2013): 339-351. http://www.scopus.com/inward/record.url?eid=2-s2.0-84876796316&partnerID=MN8TOARS.
    10.1016/j.neuron.2013.02.010
  45. Rennie, S.M.; Moita, M.M.; Mainen, Z.F.. "Social cognition in the rodent: Nothing to be sniffed at". Trends in Cognitive Sciences 17 7 (2013): 306-307. http://www.scopus.com/inward/record.url?eid=2-s2.0-84879785732&partnerID=MN8TOARS.
    10.1016/j.tics.2013.04.011
  46. Miura, K.; Mainen, Z.F.; Uchida, N.. "Odor Representations in Olfactory Cortex: Distributed Rate Coding and Decorrelated Population Activity". Neuron 74 6 (2012): 1087-1098. http://www.scopus.com/inward/record.url?eid=2-s2.0-84862703885&partnerID=MN8TOARS.
    10.1016/j.neuron.2012.04.021
  47. Felsen, G.; Mainen, Z.F.. "Midbrain contributions to sensorimotor decision making". Journal of Neurophysiology 108 1 (2012): 135-147. http://www.scopus.com/inward/record.url?eid=2-s2.0-84863313235&partnerID=MN8TOARS.
    10.1152/jn.01181.2011
  48. Kepecs, A.; Mainen, Z.F.. "A computational framework for the study of confidence in humans and animals". Philosophical Transactions of the Royal Society B: Biological Sciences 367 1594 (2012): 1322-1337. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859551502&partnerID=MN8TOARS.
    10.1098/rstb.2012.0037
  49. Vicente, M.I.; Mainen, Z.. "Convergence in the Piriform Cortex". Neuron 70 1 (2011): 1-2. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953787346&partnerID=MN8TOARS.
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  50. Feierstein, C.E.; Mainen, Z.F.. "Listening to the crowd: Neuronal ensembles rule". Neuron 66 3 (2010): 334-336. http://www.scopus.com/inward/record.url?eid=2-s2.0-77952729435&partnerID=MN8TOARS.
    10.1016/j.neuron.2010.04.042
  51. Ranade, S.P.; Mainen, Z.F.. "Transient firing of dorsal raphe neurons encodes diverse and specific sensory, motor, and reward events". Journal of Neurophysiology 102 5 (2009): 3026-3037. http://www.scopus.com/inward/record.url?eid=2-s2.0-70449377692&partnerID=MN8TOARS.
    10.1152/jn.00507.2009
  52. Mainen, Z.F.; Kepecs, A.. "Neural representation of behavioral outcomes in the orbitofrontal cortex". Current Opinion in Neurobiology 19 1 (2009): 84-91. http://www.scopus.com/inward/record.url?eid=2-s2.0-67649344125&partnerID=MN8TOARS.
    10.1016/j.conb.2009.03.010
  53. Dugué, G.P.; Mainen, Z.F.. "How serotonin gates olfactory information flow". Nature Neuroscience 12 6 (2009): 673-675. http://www.scopus.com/inward/record.url?eid=2-s2.0-66749158491&partnerID=MN8TOARS.
    10.1038/nn0609-673
  54. Quirk, M.C.; Sosulski, D.L.; Feierstein, C.E.; Uchida, N.; Mainen, Z.F.. "A defined network of fast-spiking interneurons in orbitofrontal cortex: Responses to behavioral contingencies and ketamine administration". Frontiers in Systems Neuroscience 3 NOV (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-77955950673&partnerID=MN8TOARS.
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  55. Vicente, Ines. "Towards an image of a memory trace". Frontiers in Neuroscience 2 2 (2008): 131-132. http://dx.doi.org/10.3389/neuro.01.041.2008.
    10.3389/neuro.01.041.2008
  56. Huber, D.; Petreanu, L.; Ghitani, N.; Ranade, S.; Hromádka, T.; Mainen, Z.; Svoboda, K.. "Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice". Nature 451 7174 (2008): 61-64. http://www.scopus.com/inward/record.url?eid=2-s2.0-38049061220&partnerID=MN8TOARS.
    10.1038/nature06445
  57. Uchida, N.; Mainen, Z.F.. "Odor concentration invariance by chemical ratio coding". Frontiers in Systems Neuroscience 1 AUG (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-84890862534&partnerID=MN8TOARS.
    10.3389/neuro.06.003.2007
  58. Felsen, G.; Mainen, Z.F.. "Neural Substrates of Sensory-Guided Locomotor Decisions in the Rat Superior Colliculus". Neuron 60 1 (2008): 137-148. http://www.scopus.com/inward/record.url?eid=2-s2.0-53049106257&partnerID=MN8TOARS.
    10.1016/j.neuron.2008.09.019
  59. Kepecs, A.; Uchida, N.; Zariwala, H.A.; Mainen, Z.F.. "Neural correlates, computation and behavioural impact of decision confidence". Nature 455 7210 (2008): 227-231. http://www.scopus.com/inward/record.url?eid=2-s2.0-51649116802&partnerID=MN8TOARS.
    10.1038/nature07200
  60. Sato, T.R.; Gray, N.W.; Mainen, Z.F.; Svoboda, K.. "The functional microarchitecture of the mouse barrel cortex". PLoS Biology 5 7 (2007): 1440-1452. http://www.scopus.com/inward/record.url?eid=2-s2.0-34547100567&partnerID=MN8TOARS.
    10.1371/journal.pbio.0050189
  61. Kepecs, A.; Uchida, N.; Mainen, Z.F.. "Rapid and precise control of sniffing during olfactory discrimination in rats". Journal of Neurophysiology 98 1 (2007): 205-213. http://www.scopus.com/inward/record.url?eid=2-s2.0-34447542050&partnerID=MN8TOARS.
    10.1152/jn.00071.2007
  62. Yun, X.; Kim, D.; Stanacevic, M.; Mainen, Z.. "Low-power high-resolution 32-channel neural recording system.". Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference (2007): 2373-2376. http://www.scopus.com/inward/record.url?eid=2-s2.0-84903802472&partnerID=MN8TOARS.
  63. Gurden, H.; L'Heureux, B.; Pain, F.; Guillermier, M.; Pinot, L.; Lefebvre, F.; Dubois, A.; et al. "Central role of astrocytic glutamate uptake activity in odor-evoked functional signals in olfactory glomeruli". Journal of Cerebral Blood Flow and Metabolism 27 SUPPL. 1 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-36348951386&partnerID=MN8TOARS.
  64. Mainen, Z.F.. "The main olfactory bulb and innate behavior: Different perspectives on an olfactory scene". Nature Neuroscience 10 12 (2007): 1511-1512. http://www.scopus.com/inward/record.url?eid=2-s2.0-36448973137&partnerID=MN8TOARS.
    10.1038/nn1207-1511
  65. Wilson, R.I.; Mainen, Z.F.. "Early events in olfactory processing". Annual Review of Neuroscience 29 (2006): 163-201. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746571725&partnerID=MN8TOARS.
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  66. Kepecs, A.; Uchida, N.; Mainen, Z.F.. "The sniff as a unit of olfactory processing". Chemical Senses 31 2 (2006): 167-179. http://www.scopus.com/inward/record.url?eid=2-s2.0-32544440216&partnerID=MN8TOARS.
    10.1093/chemse/bjj016
  67. Gurden, H.; Uchida, N.; Mainen, Z.F.. "Sensory-Evoked Intrinsic Optical Signals in the Olfactory Bulb Are Coupled to Glutamate Release and Uptake". Neuron 52 2 (2006): 335-345. http://www.scopus.com/inward/record.url?eid=2-s2.0-33749643843&partnerID=MN8TOARS.
    10.1016/j.neuron.2006.07.022
  68. Uchida, N.; Kepecs, A.; Mainen, Z.F.. "Seeing at a glance, smelling in a whiff: Rapid forms of perceptual decision making". Nature Reviews Neuroscience 7 6 (2006): 485-491. http://www.scopus.com/inward/record.url?eid=2-s2.0-33745752234&partnerID=MN8TOARS.
    10.1038/nrn1933
  69. Feierstein, C.E.; Quirk, M.C.; Uchida, N.; Sosulski, D.L.; Mainen, Z.F.. "Representation of Spatial Goals in Rat Orbitofrontal Cortex". Neuron 51 4 (2006): 495-507. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746895444&partnerID=MN8TOARS.
    10.1016/j.neuron.2006.06.032
  70. Mainen, Z.F.. "Behavioral analysis of olfactory coding and computation in rodents". Current Opinion in Neurobiology 16 4 (2006): 429-434. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746552792&partnerID=MN8TOARS.
    10.1016/j.conb.2006.06.003
  71. Egger, V.; Svoboda, K.; Mainen, Z.F.. "Dendrodendritic synaptic signals in olfactory bulb granule cells: Local spine boost and global low-threshold spike". Journal of Neuroscience 25 14 (2005): 3521-3530. http://www.scopus.com/inward/record.url?eid=2-s2.0-17044404514&partnerID=MN8TOARS.
    10.1523/JNEUROSCI.4746-04.2005
  72. Egger V; Svoboda K; Mainen ZF. "Mechanisms of lateral inhibition in the olfactory bulb: efficiency and modulation of spike-evoked calcium influx into granule cells.". The Journal of neuroscience : the official journal of the Society for Neuroscience (2003): http://europepmc.org/abstract/med/12930793.
    10.1523/jneurosci.23-20-07551.2003
  73. Uchida, N.; Mainen, Z.F.. "Speed and accuracy of olfactory discrimination in the rat". Nature Neuroscience 6 11 (2003): 1224-1229. http://www.scopus.com/inward/record.url?eid=2-s2.0-0242321787&partnerID=MN8TOARS.
    10.1038/nn1142
  74. Egger, V.; Svoboda, K.; Mainen, Z.F.. "Mechanisms of lateral inhibition in the olfactory bulb: Efficiency and modulation of spike-evoked calcium influx into granule cells". Journal of Neuroscience 23 20 (2003): 7551-7558. http://www.scopus.com/inward/record.url?eid=2-s2.0-0042922885&partnerID=MN8TOARS.
  75. Mainen, Zachary F.. "Thinking about feeling". Nature Neuroscience 3 9 (2000): 857-857. http://dx.doi.org/10.1038/78751.
    10.1038/78751
  76. Maravall, M.; Mainen, Z.F.; Sabatini, B.L.; Svoboda, K.. "Estimating Intracellular Calcium Concentrations and Buffering without Wavelength Ratioing". Biophysical Journal 78 5 (2000): 2655-2667. http://dx.doi.org/10.1016/s0006-3495(00)76809-3.
    10.1016/s0006-3495(00)76809-3
  77. Malinow, R.; Mainen, Z.F.; Hayashi, Y.. "LTP mechanisms: From silence to four-lane traffic". Current Opinion in Neurobiology 10 3 (2000): 352-357. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034122617&partnerID=MN8TOARS.
    10.1016/S0959-4388(00)00099-4
  78. Svoboda K; Mainen ZF. "Synaptic [Ca2+]: intracellular stores spill their guts.". Neuron (1999): http://europepmc.org/abstract/med/10197523.
    10.1016/s0896-6273(00)80698-4
  79. Mainen, Z.F.; Maletic-Savatic, M.; Shi, S.H.; Hayashi, Y.; Malinow, R.; Svoboda, K.. "Two-photon imaging in living brain slices". Methods: A Companion to Methods in Enzymology 18 2 (1999): 231-239. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032845224&partnerID=MN8TOARS.
    10.1006/meth.1999.0776
  80. Mainen, Z.F.; Malinow, R.; Svoboda, K.. "Synaptic calcium transients in single spines indicate that NMDA receptors are not saturated". Nature 399 6732 (1999): 151-155. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033551327&partnerID=MN8TOARS.
    10.1038/20187
  81. Svoboda, K.; Mainen, Z.F.. "Synaptic [Ca2+]: Intracellular stores spill their guts". Neuron 22 3 (1999): 427-430. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033084192&partnerID=MN8TOARS.
  82. Mainen ZF; Jia Z; Roder J; Malinow R. "Use-dependent AMPA receptor block in mice lacking GluR2 suggests postsynaptic site for LTP expression.". Nature neuroscience (1998): http://europepmc.org/abstract/med/10196565.
    10.1038/2812
  83. Mainen, Z.F.; Jia, Z.; Roder, J.; Malinow, R.. "Use-dependent AMPA receptor block in mice lacking GluR2 suggests postsynaptic site for LTP expression". Nature Neuroscience 1 7 (1998): 579-586. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032200428&partnerID=MN8TOARS.
  84. Mainen ZF; Carnevale NT; Zador AM; Claiborne BJ; Brown TH. "Electrotonic architecture of hippocampal CA1 pyramidal neurons based on three-dimensional reconstructions.". Journal of neurophysiology (1996): http://europepmc.org/abstract/med/8890303.
    10.1152/jn.1996.76.3.1904
  85. Malinow, R.; Mainen, Z.F.. "Long-term potentiation in the CA1 hippocampus". Science 271 5255 (1996): 1604-1606. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029869914&partnerID=MN8TOARS.
    10.1126/science.271.5255.1604
  86. Mainen, Z.F.; Sejnowski, T.J.. "Influence of dendritic structure on firing pattern in model neocortical neurons". Nature 382 6589 (1996): 363-366. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029741078&partnerID=MN8TOARS.
    10.1038/382363a0
  87. Mainen, Z.F.; Carnevale, N.T.; Zador, A.M.; Claiborne, B.J.; Brown, T.H.. "Electrotonic architecture of hippocampal CA1 pyramidal neurons based on three-dimensional reconstructions". Journal of Neurophysiology 76 3 (1996): 1904-1923. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029786071&partnerID=MN8TOARS.
  88. Mainen ZF; Sejnowski TJ. "Reliability of spike timing in neocortical neurons.". Science (New York, N.Y.) (1995): http://europepmc.org/abstract/med/7770778.
    10.1126/science.7770778
  89. Mainen, Z.F.; Sejnowski, T.J.. "Reliability of spike timing in neocortical neurons". Science 268 5216 (1995): 1503-1506. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029030249&partnerID=MN8TOARS.
  90. Mainen, Z.F.; Joerges, J.; Huguenard, J.R.; Sejnowski, T.J.. "A model of spike initiation in neocortical pyramidal neurons". Neuron 15 6 (1995): 1427-1439. http://www.scopus.com/inward/record.url?eid=2-s2.0-0029584238&partnerID=MN8TOARS.
    10.1016/0896-6273(95)90020-9
  91. Destexhe, A.; Mainen, Z. F.; Sejnowski, T. J.. "An Efficient Method for Computing Synaptic Conductances Based on a Kinetic Model of Receptor Binding". Neural Computation 6 1 (1994): 14-18. http://dx.doi.org/10.1162/neco.1994.6.1.14.
    10.1162/neco.1994.6.1.14
  92. Destexhe, A.; Mainen, Z.F.; Sejnowski, T.J.. "Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism.". Journal of computational neuroscience 1 3 (1994): 195-230. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028490340&partnerID=MN8TOARS.
    10.1007/bf00961734
Preprint
  1. Findling, Charles; Hubert, Felix; Acerbi, Luigi; Benson, Brandon; Benson, Julius; Birman, Daniel; Bonacchi, Niccolò; et al. "Brain-wide representations of prior information in mouse decision-making". 2023. http://dx.doi.org/10.1101/2023.07.04.547684.
    10.1101/2023.07.04.547684
  2. Benson, Brandon; Benson, Julius; Birman, Daniel; Bonacchi, Niccolò; Carandini, Matteo; Catarino, Joana A; Chapuis, Gaelle A; et al. "A Brain-Wide Map of Neural Activity during Complex Behaviour". 2023. http://dx.doi.org/10.1101/2023.07.04.547681.
    10.1101/2023.07.04.547681
  3. Bimbard, C.; Takács, F.; Catarino, J. A.; Fabre, J. M. J.; Gupta, S.; Lenzi, S. C.; Melin, M. D.; et al. "An adaptable, reusable, and light implant for chronic Neuropixels probes". 2023. http://dx.doi.org/10.1101/2023.08.03.551752.
    10.1101/2023.08.03.551752
  4. Gutierrez-Castellanos, Nicolas; Sarra, Dario; Godinho, Beatriz S.; Mainen, ZF. "Maturation of prefrontal input to dorsal raphe nucleus increases behavioral persistence in mice". 2022. http://dx.doi.org/10.1101/2022.01.01.474690.
    10.1101/2022.01.01.474690
  5. Cazettes F; Murakami M; Renart A; Mainen ZF. "Reservoir of decision strategies in the mouse brain". 2021. http://europepmc.org/abstract/PPR/PPR306618.
    10.1101/2021.04.01.438090
  6. Fonseca MS; Bergomi MG; Mainen ZF; Shemesh N. "Functional MRI of large scale activity in behaving mice". 2020. http://europepmc.org/abstract/PPR/PPR152245.
    10.1101/2020.04.16.044941
Thesis / Dissertation
  1. "Latent variable decoding in biological and artificial agents: Towards a unified approach". PhD, Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, 2020. https://run.unl.pt/handle/10362/107818.
  2. Meyler, Samuel Viana. "Insights into perceptual ambiguity and inference in art- : a practice-based approach derived from the corporeal form". PhD, 2018. http://hdl.handle.net/10451/34789.
  3. Bonacchi, N.. "Spatial goals and actions in the orbitofrontal cortex". PhD, 2017. http://hdl.handle.net/10362/76957.
  4. Fonseca, Ana Rita Secca da. "Pombal’s maze: a novel decision making paradigm". PhD, 2016. http://hdl.handle.net/10362/51885.
  5. Vicente, Maria Inês. "Uncertainty in olfactory decision-making". PhD, 2015. http://hdl.handle.net/10362/17526.
  6. Mendonça, André Gil. "The role of reinforcement learning in perceptual decision-making". PhD, 2015. http://hdl.handle.net/10362/20500.
  7. Matias, Sara Pinto dos Santos. "Dynamics of serotonergic neurons revealed by fiber photometry". PhD, 2015. http://hdl.handle.net/10362/16807.
  8. Costa, Gil Miguel Pereira da. "Neural and behavioral correlates of decision confidence". PhD, 2015. http://hdl.handle.net/10316/26999.
  9. Correia, Patrícia. "The role of serotonin in behavior". PhD, 2015. http://hdl.handle.net/10362/20495.
  10. Turco, Katherine. "Mapping the Serotonergic System : Topographical Organization of Serotonergic Projections from the Dorsal Raphe Nucleus". Master, 2013. http://hdl.handle.net/10316/24639.
  11. Fernandes, Hugo L.. "Uncertainty, generalization, and neural representation of relevant variables for decision making". PhD, 2013. http://hdl.handle.net/10362/12033.

Intellectual property

Patent
  1. 2006. "State adaptation devices and methods for wireless communications". United States.
  2. 2003. "System and method for context-based document retrieval". United States.
Distinctions

Award

2001 Searle Scholar Award
Searle Scholars Program, United States
1997 Burroughs-Wellcome Career Development Award
Burroughs-Wellcome Fund, United States

Other distinction

2015 ERC Advanced Investigator Grant
European Research Council, Belgium
2010 ERC Advanced Investigator Grant
European Research Council, Belgium
2010 EMBO Elected Member
European Molecular Biology Organization (EMBO), Germany
2005 NARSAD Lattner Foundation Investigator
Brain and Behavior Research Foundation, United States
1995 NRSA Postdoctoral Fellowship
National Research Service Award, United States
1991 Howard Hughes Medical Institute Predoctoral Fellowship
Howard Hughes Medical Institute, United States