Gutierrez-Castellanos N, Sarra D, Godinho BS, Mainen ZF (2022) Maturation of prefrontal input to dorsal raphe increases behavioral persistence in mice. bioRxiv. doi:

Fonseca MS, Bergomi M, Mainen ZF, Shemesh N (2020) Functional MRI of large scale activity in behaving mice. bioRxiv doi:


Cazettes F, Mazzucato L, Murakami M, Morais JP, Augusto E, Renart A, Mainen ZF (2023) A reservoir of foraging decision variables in the mouse brain. Nat Neurosci.


Ligneul R, Mainen ZF, Ly V, Cools R (2022) Stress-sensitive inference of task controllability. Nat Hum Behav 6, 812.

Recanatesi S, Pereira U, Murakami M, Mainen ZF, Mazucatto L (2022) Metastable attractors explain the variable timing of stable behavioral action sequences. Neuron 110 (1), 139.

Snitz K, Honigstein D, Weissgross R, Ravia A, Mishor E, Perl O, Karagach S, Medhanie A, Harel N, Shushan S, Roth Y, Iravani B, Arshamian A, Ernst G, Okamoto M, Poo C, Bonacchi N, Mainen ZF, Monteleone E, Dinnella C, Spinelli S, Mariño-Sánchez F, Ferdenzi C, Smeets M, Touhara K, Bensafi M, Hummel T, Lundström JN, Sobel N (2022). A Novel Olfactory Self-Test Effectively Screens for COVID-19. Commun Med 2, 34.


Poo C, Agarwal G, Bonacchi N, Mainen ZF (2021) Spatial maps in olfactory cortex during olfactory navigation. Nature 601, 595-599.

The IBL, Aguillon-Rodriguez V, Angelaki DE, Bayer HM, Bonacchi N, Carandini M, Cazettes F, Chapuis GA, Churchland AK, Dan Y, Dewitt EE, Faulkner M, Forrest H, Haetzel LM, Hausser M, Hofer SB, Hu F, Khanal A, Krasniak CS, Laranjeira I, Mainen ZF, Meijer GT, Miska NJ, Mrsic-Flogel TD, Murakami M, Noel JP, Pan-Vazquez A, Sanders JI, Socha KZ, Terry R, Urai AE, Vergara HM, Wells MJ, Wilson CJ, Witten IB, Wool LE, Zador A (2021). A standardized and reproducible method to measure decision-making in mice. eLife 2021; 10:e63711.

Urai A, Aguillon-Rodriguez V, Laranjeira IC, Cazettes F, The IBL, Mainen ZF, Churchland AK (2021). Citric Acid as an alternative to water restrictions for high-yield mouse behavior. eNeuro 8 (1) ENEURO.0230-20.2020.

Cazettes F, Reato D, Morais JP, Renart A, Mainen ZF (2021). Phasic activation of dorsal raphe serotonergic neurons increases pupil size. Current Biology 31 (1), 192.


Mendonça AG, Drugowitsch J, Vicente MI, Dewitt EEJ, Pouget A, Mainen ZF (2020). The impact of learning of perceptual decision and its implication for speed-accuracy tradeoffs. Nature Communications 11 (1), 2757.

Iravani B, Arshamian A, Ravia A, Mishor E, Snitz K, Shushan S, Roth Y, Perl O, Honigstein D, Weissgross R, Karagach S, Ernst G, Okamoto M, Mainen ZF, Monteleone E, Dinnella C, Spinelli S, Marino-Sanchez F, Ferdenzi C, Smeets M, Touhara K, Bensafi M, Hummel T, Sobel N, Lundström J (2020). Relationship Between Odor Intensity Estimates and COVID-19 Prevalence Prediction in a Swedish Population. Chemical Senses 45 (6), 449.

Vertechi P, Lottem E, Sarra D, Godinho B, Treves I, Quendera T, Oude Lohuis MN, Mainen ZF (2020). Inference-based decisions in a hidde state foraging task: differential contributions of prefrontal areas. Neuron 106 (1), 166.


Drugowitsch J, Mendonça AG, Mainen ZF, Pouget A (2019). Learning optimal decisions with confidence. PNAS 116 (46), 24872.

Pardo-Vazquez JL, Castiñeiras-de Saa JR, Valente M, Damião I, Costa T, Vicente MI, Mendonça AG, Mainen ZF, Renart A (2019). The mechanistic foundation of Weber’s law. Nature Neuroscience 22 (9), 1493.

Rigato J, Rennie SM, Mainen ZF (2019). The overlooked ubiquity of first-person experience in the cognitive sciences. Synthese 198, 8005.


Iigaya K, Fonseca MS, Murakami M, Mainen ZF, Dayan P (2018). An effect of serotonergic stimulation on learning rates for rewards apparent after long inter-trial intervals. Nature Communications 9 (1), 2477.

Lottem E, Banerjee D, Vertechi P, Sarra D, oude Lohuis M, Mainen ZF (2018). Activation of serotonin neurons promotes active persistence in a probabilistic foraging taskNature Communications 9, 1000.


Correia, PA, Matias, S, Mainen ZF (2017). Stereotaxic Adeno-associated Virus Injection and Cannula Implantation in the Dorsal Raphe Nucleus of Mice. Bio-protocol 7 (18), e2549.

Murakami M, Shteingart H, Loewenstein Y, Mainen ZF (2017). Distinct Sources of Deterministic and Stochastic Components of Action Timing Decisions in Rodent Frontal Cortex. Neuron 94 (4), 908.

Matias S, Lottem E, Dugué GP, Mainen ZF (2017). Activity patterns of serotonin neurons underlying cognitive flexibility. eLife pii: e20552.

Correia PA, Lottem E, Banerjee D, Machado AS, Carey MR, Mainen ZF (2017) Transient inhibition and long-term facilitation of locomotion by phasic optogenetic activation of serotonin neuronseLife pii: e20975.


Kobak D, Brendel W, Constantinidis C, Feierstein CE, Kepecs A, Mainen ZF, Romo R, Qi XL, Uchida N, Machens CK (2016). Demixed principal component analysis of neural population data. eLife 2016 (5), e10989 (doi:10.7554/eLife.10989).

Gomez-Marin A, Mainen ZF (2016). Expanding perspectives on cognition in humans, animals, and machines. Current Opinion Neurobiology, 37 , 85–91.

Lottem E*, Lörincz ML*, Mainen ZF (2016). Optogenetic Activation of Dorsal Raphe Serotonin Neurons Rapidly Inhibits Spontaneous But Not Odor-Evoked Activity in Olfactory Cortex. Journal of Neuroscience, 36 (1), 7-18.


Meyniel F, Sigman M, Mainen ZF (2015). Confidence as Bayesian Probability: From Neural Origins to Behavior. Neuron 88 (1), 78–92.

Bush PC, Mainen ZF (2015). Columnar architecture improves noise robustness in a model cortical network. PLoS ONE 10 (3), e0119072.

Murakami M, Mainen ZF (2015). Preparing and selecting actions with neural populations: toward cortical circuit mechanisms. Current Opinion Neurobiology 33 (C), 40–46.

Fonseca MS, Murakami M, Mainen ZF (2015). Activation of Dorsal Raphe Serotonergic Neurons Promotes Waiting but Is Not ReinforcingCurrent Biology 25 (3), 306-315.


Gomez-Marin A, Paton JJ, Kampff AR, Costa RM, Mainen ZF (2014). Big behavioral data: psychology, ethology and the foundations of neuroscienceNature Neuroscience (17), 1455–1462.

Murakami M, Vicente MI, Costa GM, Mainen ZF (2014). Neural antecedents of self-initiated actions in secondary motor cortex Nature Neuroscience 17 (11), 1455-62.

Lak A, Costa GM, Romberg E, Koulakov AA, Mainen ZF, Kepecs A (2014). Orbitofrontal Cortex Is Required for Optimal Waiting Based on Decision ConfidenceNeuron 84 (1), p190–201.

Dugué GP, Lörincz ML, Lottem E, Audero E, Matias S, Correia PA, Léna C, Mainen ZF (2014). Optogenetic recruitment of dorsal raphe serotonergic neurons acutely decreases mechanosensory responsivity in behaving mice. PLoS ONE 9 (8), e105941.

Mainen ZF & Pouget A (2014). European Commission: Put brain project back on course. Nature 511, 534.

Tecuapetla F, Matias S, Dugue GP, Mainen ZF, Costa RM (2014). Balanced activity in basal ganglia projection pathways is critical for contraversive movements. Nature Communications (5), 4315.

Rigato J, Murakami M, Mainen ZF (2014). Spontaneous Decisions and Free Will: Empirical Results and Philosophical Considerations. Cold Spring Harb Symp Quant Biol. (79), 177-184.


Rennie SM, Moita MM, Mainen ZF (2013). Social cognition in the rodent: nothing to be sniffed at. Trends Cogn Sci. 17 (7), 306-7.

Zariwala HA, Kepecs A, Uchida N, Hirokawa J, Mainen ZF (2013). The Limits of Deliberation in a Perceptual Decision Task. Neuron S0896-6273 (13), 00168-2.


Miura K, Mainen ZF, Uchida N (2012). Odor Representations in Olfactory Cortex: Distributed Rate Coding and Decorrelated Population ActivityNeuron 74 (6), 1087-1098.

Kepecs A, Mainen ZF (2012). A computational framework for the study of confidence in humans and animals. Philos. Trans. R. Soc. Lond., B, Biol. Sci. 367 (1594), 1322-1337.

Felsen G, Mainen ZF (2012). Midbrain contributions to sensorimotor decision making. Journal of Neurophysiology 108 (1), 135-47.


Vicente MI, Mainen ZF (2011). Convergence in the piriform cortex. Neuron 70 (1), 1-2.


Feierstein CE, Mainen ZF (2010). Listening to the crowd: neuronal ensembles rule. Neuron 66 (3), 334-6.


Ranade SP, Mainen ZF (2009). Transient firing of dorsal raphe neurons encodes diverse and specific sensory, motor, and reward events. Journal of Neurophysiology. 102 , 3026-3037.

Quirk MC, Sosulski DL, Feierstein CE, Uchida N and Mainen ZF (2009). A defined network of fast-spiking interneurons in orbitofrontal cortex: responses to behavioral contingencies and ketamine administration. Frontiers Systems Neuroscience 3 (13).

Dugué GP, Mainen ZF (2009). How serotonin gates olfactory information flow. Nature Neuroscience 12, 673-675.

Mainen ZF, Kepecs A (2009). Neural representation of behavioral outcomes in the orbitofrontal cortex. Current Opinion Neurobiology 19 , 84-91.


Vicente MI, Mainen ZF (2008). Towards an image of a memory trace. Frontiers Neuroscience 2 (2), 131-132.

Felsen G, Mainen ZF (2008). Neural substrates of sensory-guided locomotor decisions in the rat superior colliculus. Neuron 60 (1), 137-148.

Kepecs A, Uchida N, Zariwala HA, Mainen ZF (2008). Neural correlates, computation and behavioural impact of decision confidence. Nature 455 , 227-231.

Huber D, Petreanu L, Ghitani N, Ranade S, Hromádka T, Mainen ZF, Svoboda K (2008). Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature 451 , 61-64.


Uchida N, Mainen ZF (2007). Odor concentration invariance by chemical ratio coding. Frontiers Systems Neuroscience 1 (3).

Mainen ZF (2007). The main olfactory bulb and innate behavior: different perspectives on an olfactory scene. Nature Neuroscience 10 (12), 1511-1512.

Yup X, Kim D, Stanacevic M, Mainen ZF (2007). Low-power high-resolution 32-channel neural recording system. Conf Proc IEEE Eng Med Biol Soc , 2373-2376.

Sato TR, Gray NW, Mainen ZF, Svoboda K (2007). The functional microarchitecture of the mouse barrel cortex. PLoS Biology 5 (7), e189.

Kepecs AC, Uchida N, Mainen ZF (2007). Rapid and precise control of sniffing during olfactory discrimination in rats. Journal of Neurophysiology 98 (1), 205-13.


Gurden H, Uchida N, Mainen ZF (2006). Sensory-evoked intrinsic optical signals in the olfactory bulb are coupled to glutamate release and uptake. Neuron 52 (2), 335-345.

Feierstein CE, Quirk MC, Uchida N, Sosulski DL, Mainen ZF (2006). Representation of spatial goals in rat orbitofrontal cortex. Neuron 51 (4), 495-507.

Mainen ZF (2006). Behavioral analysis of olfactory coding and computation in rodents. Current Opinion Neurobiology. 16 , 429-423.

Wilson R, Mainen ZF (2006). Early events in olfactory processing. Annual Review Neuroscience 29 , 163-201.

Uchida N, Kepecs A, Mainen ZF (2006). Seeing at a glance, smelling in a whiff: rapid forms of perceptual decision making. Nature Reviews Neuroscience 7 , 485-491.

Kepecs A, Uchida N, Mainen ZF (2006). The sniff as a unit of olfactory processing. Chemical Senses 31 , 167-79.


Egger V, Svoboda K, Mainen ZF (2005). Dendrodendritic synaptic signals in olfactory bulb granule cells: local spine boost and global low-threshold spike. Journal of Neuroscience 25 , 3521-30.


Uchida N, Mainen ZF (2003). Speed and accuracy of olfactory discrimination in the rat. Nature Neuroscience 6, 1224-1229.

Egger V, Svoboda K, Mainen ZF (2003). Mechanisms of lateral inhibition in the olfactory bulb: efficiency and modulation of spike-evoked calcium influx into granule cells. Journal of Neuroscience 23 (20), 7551-8.


Malinow R, Mainen ZF, Hayashi Y (2000). LTP mechanisms: from silence to four-lane traffic. Current Opinion Neurobiology 10 (3), 352-357.

Maravall M, Mainen ZF, Sabatini BL, Svoboda K (2000). Estimating intracellular calcium concentrations and buffering without wavelength ratioing. Biophys. J. 78 (5), 2655-2667.


Mainen ZF, Maletic-Savatic M, Shi SH, Hayashi Y, Malinow R, Svoboda K (1999). Two-photon imaging in living brain slices. Methods 18 (2), 231-239.

Mainen ZF, Malinow R, Svoboda K (1999). Synaptic calcium transients in single spines indicate that NMDA receptors are not saturated. Nature 399 (6732), 151-155.

Svoboda K, Mainen ZF (1999). Synaptic [Ca2+]: intracellular stores spill their guts. Neuron 22 (3), 427-430.


Mainen ZF, Jia Z, Roder J, Malinow R (1998). Use-dependent AMPA receptor block in mice lacking GluR2 suggests postsynaptic site for LTP expression. Nature Neuroscience 1 (7), 579-586.


Mainen ZF, Carnevale NT, Zador AM, Claiborne BJ, Brown TH (1996). Electrotonic architecture of hippocampal CA1 pyramidal neurons based on three-dimensional reconstructions. Journal of Neurophysiology 76 (3), 1904-1923.

Malinow R, Mainen ZF (1996). Long-term potentiation in the CA1 hippocampus. Science 271 (5255), 1604-1606.

Mainen ZF, Sejnowski TJ (1996). Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382 (6589), 363-366.


Mainen ZF, Joerges J, Huguenard JR, Sejnowski TJ (1995). A model of spike initiation in neocortical pyramidal neurons. Neuron 15 (6), 1427-1439.

Mainen ZF, Sejnowski TJ (1995). Reliability of spike timing in neocortical neurons. Science 268 (5216), 1503-1506.


Destexhe A, Mainen ZF, Sejnowski TJ (1994). Synthesis of models for excitable membranes, synaptic transmission and neuromodulation using a common kinetic formalism. Journal of Computational Neuroscience 1 (3), 195-230.