• Cadwell CR, Scala F, Fahey PG, Kobak D, Sinz FH, Johnsson P, Li S, Cotton RJ, Sandberg R, Berens P, Jiang X, Tolias AS (2019) Cell type composition and circuit organization of neocortical radial clones bioRxiv 526681; doi:10.1101/526681 Link


  • Walker EY, Sinz FH, Foudarakis E, Fahey PG, Muhammad T, Ecker AS, Cobos E, Reimer J, Pitkow X, Tolias AS (2018) Inception in visual cortex: in vivo-silico loops reveal most exciting images bioRxiv doi:10.1101/506956 Link
  • Scala F, Kobak D, Shan S, Bernaerts Y, Laturnus S, Cadwell CR, Hartamis L, Castro J, Tan ZH, Sandberg R, Berens P, Jiang X, Tolias AS. (2018) Neocortical layer 4 in adult mouse differs in major cell types and circuit organization between primary sensory areas bioRxiv doi:10.1101/507293 Link
  • Edgar Y Walker, R. James Cotton, Wei Ji Ma, Andreas S Tolias (2018) A neural basis of probabilistic computation in visual cortex bioRxiv 365973; doi:10.1101/365973 Link
  • Gido M. van de Ven, Andreas S. Tolias (2018). Generative replay with feedback connections as a general strategy for continual learning. arXiv: Link
  • Sinz FH, Ecker AS, Fahey PG, Walker EY, Cobos E, Froudarakis E, Yatsenko D, Pitkow X, Reimer J, Tolias AS (2018) Stimulus domain transfer in recurrent models for large scale cortical population prediction on video. NIPS (Neural Information Processing Systems) Link
  • Subramaniyan M, Ecker AS, Patel SS, Cotton RJ, Bethge M, Pitkow X, Berens P, Tolias AS (2018) Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion. Journal of Neurophysiology. Aug 22 2018(Epub) . doi: 10.1152/jn.00792.2017 Link |  Data
  • Dimitri Yatsenko, Edgar Y. Walker, Andreas S. Tolias (2018) DataJoint: A Simpler Relational Data Model arXiv: Link
  • Alexander S. Ecker, Fabian H. Sinz, Emmanouil Froudarakis, Paul G. Fahey, Santiago A. Cadena, Edgar Y. Walker, Erick Cobos, Jacob Reimer, Andreas S. Tolias, Matthias Bethge (2018) A rotation-equivariant convolutional neural network model of primary visual cortex arXiv: Link
  • E. Kelly Buchanan, Ian Kinsella, Ding Zhou, Rong Zhu, Pengcheng Zhou, Felipe Gerhard, John Ferrante, Ying Ma, Sharon Kim, Mohammed Shaik, Yajie Liang, Rongwen Lu, Jacob Reimer, Paul Fahey, Taliah Muhammad, Graham Dempsey, Elizabeth Hillman, Na Ji, Andreas Tolias, Liam Paninski (2018) Penalized matrix decomposition for denoising, compression, and improved demixing of functional imaging data. bioRxiv 334706; doi: 10.1101/334706 Link
  • Denfield GH, Ecker AS, Shinn TJ, Bethge M, Tolias AS (2018) Attentional fluctuations induce shared variability in macaque primary visual cortex. Nat Commun. 9(1) : 2654 . doi: 10.1038/s41467-018-05123-6 Link
  • Berens P, Freeman J, Deneux T, Chenkov N, McColgan T, Speiser A, Macke JH, Turaga SC, Mineault P, Rupprecht P, Gerhard S, Friedrich RW, Friedrich J, Paninski L, Pachitariu M, Harris KD, Bolte B, Machado TA, Ringach D, Stone J, Rogerson LE, Sofroniew NJ, Reimer J, Froudarakis E, Euler T, Román Rosón M, Theis L, Tolias AS, Bethge M (2018) Community-based benchmarking improves spike rate inference from two-photon calcium imaging data. PLoS Comput Biol. 14(5) :e1006157 . doi: 10.1371/journal.pcbi.1006157 Link


  • Cadwell CR, Scala F, Li S,  Livrizzi G.,  Shen S., Sandberg R, Jiang X & Tolias AS(2017) Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq Nature Protocols 12, 2531–2553 (2017) Link
  • Cadwell CR, Sandberg R, Jiang X, Tolias AS (2017). Q&A: using Patch-seq to profile single cells. BMC Biol. Jul 6;15(1):58. doi: 10.1186/s12915-017-0396-0. Link
  • S. A. Cadena, G. H. Denfield, E. Y. Walker, L. A. Gatys, A. S. Tolias, M. Bethge, and A. S. Ecker  (2017) Deep convolutional models improve predictions of macaque V1 responses to natural images bioRxiv, 2017 Link
  • G. H. Denfield, A. S. Ecker, T. J. Shinn, M. Bethge, and A. S. Tolias (2017) Attentional fluctuations induce shared variability in macaque primary visual cortex bioRxiv, 2017 Link
  • Ouzounov DG, Wang T, Wang M, Feng DD, Horton NG, Cruz-Hernández JC, Cheng YT, Reimer J, Tolias AS, Nishimura N, Xu C. (2017) In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain. Nature MethodsApr;14(4):388-390. doi: 10.1038/nmeth.4183. Epub 2017 Feb 20. Link
  • Quast KB, Ung K, Froudarakis E, Huang L, Garca I, Addison AP, Ortiz-Guzman J, Cordiner K, Saggau P, Tolias AS, Arenkiel BR (2017). Developmental Broadening of Inhibitory Network Sensory Maps. Nature Neuroscience Dec 26. doi: 10.1038/nn.4467. Link
  • Segev E, Reimer J, Moreaux LC, Fowler TM, Chi D, Sacher WD, Lo M, Deisseroth K, Tolias AS, Faraon A, Roukes ML (2017). Patterned photostimulation via visible-wavelength photonic probes for deep brain optogenetics. Neurophotonics. Jan;4(1):011002 Link


  • Reimer J, McGinley M, Liu Y, Rodenkirch C, Wang Q, McCormick D., Tolias AS (2016). Pupil Fluctuations Track Rapid Changes in the Adrenergic and Cholinergic Activity in Cortex. Nature Communications Nov 8;7:13289. dos: 10.1038/ncomms13289. Link
  • Quast KB, Ung K, Froudarakis E, Huang L, Garca I, Addison AP, Ortiz-Guzman J, Cordiner K, Saggau P, Tolias AS, Arenkiel BR (2016). Developmental Broadening of Inhibitory Network Sensory Maps. Nature Neuroscience Dec 26. doi: 10.1038/nn.4467. Link
  • Jiang X, Shen S, Sinz F, Reimer J, Cadwell CR, Berens P, Ecker AS, Patel S, Denfield GH, Froudarakis E, Li S, Walker E, Tolias AS (2016). Response to Comment on “Principles of connectivity among morphologically defined cell types in adult neocortex”. Science 353(6304):1108. doi: 10.1126/science.aaf6102. Link
  • Denfield GH, Fahey PG, Reimer J, Tolias AS (2016). Investigating the Limits of Neurovascular Coupling. Neuron 7;91(5):954-6. doi: 10.1016/j.neuron.2016.08.026. Link
  • L. Theis, P. Berens, E. Froudarakis, J. Reimer, M. Roman-Roson, T. Baden, T. Euler, A. S. Tolias, M. Bethge (2016): Benchmarking spike rate inference in population calcium imaging, Neuron 4:90(3):471-82 doi: 10.1016/j.neuron.2016.04.014. Link
  • Rossant C, Shabnam KN, Goodman DFM, Schulman J, Hunter MLD, Saleem AB, Grosmark A, Belluscio M, Denfield GH, Ecker AS, Tolias AS, Solomon S, Buzsaki G, Carandini M, Harri  KD. Spike sorting for large, dense electrode arrays. Nature Neuroscience doi: 10.1038/nn.4268.
  • Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Bethge M, Tolias KF, Sandberg R & Tolias AS (2016). Morphological, electrophysiological and transcriptomic profiling of single neurons using Patch-seq. Nature Biotechnology 34(2):199-203. doi: 10.1038/nbt.3445. Epub 2015 Dec 21. Link
  • Ecker AS, Denfield GH, Bethge M, Tolias AS (2016). On the Structure of Neuronal Population Activity under Fluctuations in Attentional State. J Neurosci. 3:36(5):1775-89. doi: 10. 1523/JNEUROSCI.2044-15.2016. PMID: 26843656 Link


  • Jiang X, Shen S, Cadwell CR, Berens P, Sinz F, Ecker AS, Patel S & Tolias AS (2015). Principles of Connectivity among Morphologically Defined Cell Types in Adult Neocortex. Science. Vol. 350 no. 6264 DOI: 10.1126 Link
  • McGinley MJ, Vinck M, Reimer J, Batista-Brito R, Zagha E, Cadwell CR, Tolias AS, Cardin JA & McCormick DA. (2015). Waking State: Rapid Variations Modulate Neural and Behavioral Responses. Neuron. 2015 Sep 23;87(6). Link
  • Yatsenko D, Josić K, Ecker AS, Froudarakis E, Cotton RJ, & Tolias, AS (2015). Improved Estimation and Interpretation of Correlations in Neural Circuits. PLoS Computational Biology, 11(3), e1004083-e1004083.  Link | Code & data
  • Ecker AS, Denfield GH, Bethge M & Tolias AS (2015). On the structure of neuronal population activity under fluctuations in attentional state. bioRxiv, 018226. Link
  • Subramaniyan M, Ecker AS, Patel S, Cotton RJ, Bethge M, Berens P & Tolias AS (2015). Faster processing of moving compared to flashed bars in awake macaque V1 provides a neural correlate of the flash lag illusion. bioRxiv Link
  • Yatsenko D, Reimer J, Ecker AS, Walker EY, Sinz F, Berens P, Hoenselaar A, Cotton RJ, Siapas AG &Tolias AS (2015). DataJoint: managing big scientific data using MATLAB or Python. bioRxiv Link
  • Reddy GD, Cotton RJ, Tolias AS & Saggau P. (2015). Random-Access Multiphoton Microscopy for Fast Three-Dimensional Imaging.Adv Exp Med Biol. 2015;859:455-72. Link
  • Theis L, Berens P, Froudarakis E, Reimer J, Roman-Roson M, Baden, T, Euler T, Tolias AS, & Bethge, M. (2015). Supervised learning sets benchmark for robust spike detection from calcium imaging signals. bioRxiv, 010777.  Link


  • Reimer, J., Froudarakis E., Cadwell, C.R., Yatsenko, D., Denfield, G.H., Tolias, A.S. (2014). Pupil Fluctuations Track Fast Switching of Cortical States during Quiet Wakefulness. Neuron.
  • Ecker A.S., Tolias A.S. (2014). Is there signal in the noise?. Nature Neuroscience. 17(6), 750-1
  • Froudarakis E., Berens P., Ecker A.S., Cotton R.J., Sinz F.H., Yatsenko D., Saggau P., Bethge M., Tolias A.S. (2014). Population code in mouse V1 facilitates read-out of natural scenes through increased sparseness. Nature Neuroscience. 17(6), 851-7
  • Ecker A.S., Berens P., Cotton R.J., Subramaniyan M., Denfield G.H., Cadwell C.R., Smirnakis S.M., Bethge M., Tolias A.S. (2014). State dependence of noise correlations in macaque primary visual cortex. Neuron. 82(1), 235–248.  Link | Data & Code | PDF


  • Cotton R.J., Froudarakis E., Storer P., Saggau P., Tolias A.S. (2013). Three-dimensional mapping of microcircuit correlation structure. Front Neural Circuits. 10(7), 151. Link
  • Subramaniyan M., Ecker A.S., Berens P., Tolias A.S. (2013). Macaque monkeys perceive the flash lag illusion. PLOS One 8(3).  Link | Data
  • Qamar A.T., Cotton R.J., George R.G., Beck J.M., Prezhdo E., Laudano A., Tolias A.S., Ma W.J. (2013). Trial-to-trial, uncertainty-based adjustment of decision boundaries in visual categorization. Proceedings of the National Academy of Sciences. 110(50), 20332-7.  Link


  • Berens P., Ecker A.S., Cotton R.J., Ma W.J., Bethge M., Tolias A.S. (2012). A fast and simple population code for orientation in primate V1. Journal of Neuroscience 31(31): 10618-10636. Link | Code & data
  • Beauchamp M.S., Sun P., Baum S.H., Tolias A.S., Yoshor D (2012). Electrocorticography Links Human Temporoparietal Junction to Visual Perception. Nature Neuroscience. 3;15(7):957-9


  • Ecker A.S., P. Berens, A. S. Tolias, M. Bethge: The effect of noise correlations in populations of diversely tuned neurons. Journal of Neuroscience. 31(40):14272-83. Link
  • Sultan F., M. Augath, Y. Murayama, A.S. Tolias, N. K. Logothetis: esfMRI of the upper STS: further evidence for the lack of electrically induced polysynaptic propagation of activity in the neocortex. Magn Reson Imaging. 29(10):1374-81. Link
  • Ku S. P., A. S. Tolias, N. K. Logothetis, J. Goense: FMRI of the face-processing network in the ventral temporal lobe of awake and anesthetized macaques. Neuron. 70(2):352-62. Link
  • Berens, P., A. S. Ecker, S. Gerwinn, A. S. Tolias and M. Bethge: Reassessing optimal neural population codes with neurometric functions. Proceedings of the National Academy of Sciences 108(11), 4423-4428 Link


  • Keliris G. A., N. K. Logothetis, A. S. Tolias: The role of the primary visual cortex in perceptual suppression of salient visual stimuli. Journal of Neuroscience 30(37):12353-65. Link
  • Ecker, A. S., P. Berens, G. A. Keliris, M. Bethge, N. K. Logothetis and A. S. Tolias: Decorrelated Firing in Cortical Microcircuits. Science, 327(5965), 584-587. Link | Data


  • Tehovnik E. J., W. M. Slocum, S. M. Smirnakis S. M.,  A. S. Tolias: Microstimulation of visual cortex to restore vision. Progress in Brain Research 175:347-75. Link
  • Macke, J. H., P. Berens, A. S. Ecker, A. S. Tolias and M. Bethge: Generating Spike Trains with Specified Correlation Coefficients. Neural Computation 21(2), 397-423 Link


  • Berens, P., G. A. Keliris, A. S. Ecker, N. K. Logothetis and A. S. Tolias : Feature selectivity of the gamma-band of the local field potential in primate primary visual cortex. Frontiers in Neuroscience 2(2)199-207; Focused Review Link
  • Berens, P., G. A. Keliris, A. S. Ecker, N. K. Logothetis and A. S. Tolias: Comparing the feature selectivity of the gamma-band of the local field potential and the underlying spiking activity in primate visual cortex. Frontiers in Systems Neuroscience 2(2) Link
  • Goense J. B., S. P. Ku, H. Merkle, A. S. Tolias, N. K. Logothetis: fMRI of the temporal lobe of the awake monkey at 7 T. Neuroimage 39(3):1081-93. Link


  • A. S. Tolias, A. S. Ecker, A. G. Siapas, A. Hoenselaar, G. A. Keliris, N. K. Logothetis: Recording chronically from the same neurons in awake, behaving primates. Journal of Neurophysiology 98(6):3780-90. Link

For older publications, go to Pubmed.