For the most up-to-date publications, visit the Google Scholar listing.


  • Turishcheva P, Fahey PG, Hansel L, Froebe R, Ponder K, Vystrčilová M, Willeke KF, Bashiri M, Wang E, Ding Z, Tolias AS, Sinz FH, Ecker AS. The Dynamic Sensorium competition for predicting large-scale mouse visual cortex activity from videos. arXiv preprint arXiv:2305.19654. 2023 May 31. Link
  • Celii B, Papadopoulos S, Ding Zhuokun, Fahey PG, Wang E, Papadopoulos C, Kunin AB .. Tolias AS, Reimer J. NEURD: automated proofreading and feature extraction for connectomics. bioRxiv preprint. 2023 Mar 29; v2. doi: 10.1101/2023.03.14.532674 Link
  • Li Z, Ortega Caro J, Rusak E, Brendel W, Bethge M, Anselmi F, Patel AB, Tolias AS, Pitkow X. Robust deep learning object recognition models rely on low frequency information in natural images. PLOS Computational Biology. 2023 Mar 27; 19(3):e1010932. doi: 10.1371/journal.pcbi.1010932 Link
  • Zador A, Escola S, Richards B, Ölveczky B, Bengio Y, Boahen K, Botvinick M, Chklovskii D, Churchland A, Clopath C, DiCarlo J., Ganguli S, Hawkins J, Körding K, Koulakov A, LeCun Y, Lillicrap T, Marblestone A, Olshausen B, Pouget A, Savin C, Sejnowski T, Simoncelli E, Solla S, Sussillo D, Tolias AS, Tsao D. Catalyzing next-generation Artificial Intelligence through NeuroAI. Nature Communications 2023 Mar 22;14(1):1597. doi: 10.1038/s41467-023-37180-x Link
  • Ding Zhiwei, Tran DT, Ponder K, Cobos E, Ding Zhuokun, Fahey PG, Wang E, Muhammad T, Fu J, Cadena SA, Papadopoulos S, Patel S, Franke K, Reimer J, Sinz FH, Ecker AS, Pitkow X, Tolias AS. Bipartite invariance in mouse primary visual cortex. bioRxiv preprint. 2023 Mar 16. doi: 10.1101/2023.03.15.532836 Link
  • Celii B, Papadopoulos S, Ding Zhuokun, Fahey PG, Wang E, Papadopoulos C, Kunin AB .. Tolias AS, Reimer J. NEURD: A mesh decomposition framework for automated proofreading and morphological analysis of neuronal EM reconstructions. bioRxiv. 2023 Mar 15; v1. doi: 10.1101/2023.03.14.532674 Link
  • Xiao J, Provenza NR, Asfouri J, Myers J, Mathura RK, Metzger B .. Tolias AS, Bijanki KR, Pitkow X, Sheth SA. Decoding depression severity from intracranial neural activity. Biological Psychiatry. 2023 Feb 2; 94(6):445-453. doi: 10.1016/j.biopsych.2023.01.020 Link
  • Schneider-Mizell CM, Bodor A, Brittain D, Buchanan J, Bumbarger DJ .. Tolias AS .. Maçarico da Costa N. Cell-type-specific inhibitory circuitry from a connectomic census of mouse visual cortex. bioRxiv. 2023 Jan 24:2023-01. doi: 10.1101/2023.01.23.525290 Link
  • Franke K, Cai C, Ponder K, Fu J, Sokoloski S, Berens P, Tolias AS. Asymmetric distribution of color-opponent response types across mouse visual cortex supports superior color vision in the sky. bioRxiv. 2023:2023-06. doi: 10.1101/2023.06.01.543054 Link
  • Pierzchlewicz PA, Willeke KF, Nix AF, Elumalai P, Restivo K, Shinn T, Nealley C, Rodriguez G, Patel S, Franke K, Tolias AS, Sinz FH. Energy Guided Diffusion for Generating Neurally Exciting Images. bioRxiv. 2023:2023-05. doi: 10.1101/2023.05.18.541176 Link
  • Willeke KF, Restivo K, Franke K, Nix AF, Cadena SA, Shinn T, Nealley C, Rodriguez G, Patel S, Ecker AS, Sinz FH, Tolias AS. Deep learning-driven characterization of single cell tuning in primate visual area V4 unveils topological organization. bioRxiv. 2023:2023-05. doi: 10.1101/2023.05.12.540591 Link
  • Wang EY, Fahey PG, Ponder K, Ding Z, Change A, Muhammad T, Patel S, Ding Z, Tran DT, Fu J, Papadopoulos S, Franke K, Ecker AS, Reimer J, Pitkow X, Sinz FH, Tolias AS. Towards a foundation model of the mouse visual cortex. bioRxiv 2023:2023-03. doi: 10.1101/2023.03.21.533548 Link
  • Fu J, Shrinivasan S, Ponder K, Muhammad T, Ding Z, Wang E, Ding Z, Tran DT, Fahey PG, Papadopoulos S, Patel S, Reimer J, Ecker AS, Pitkow X, Haefner RM, Sinz FH, Franke K, Tolias AS. Pattern completion and disruption characterize contextual modulation in mouse visual cortex. bioRxiv. 2023:2023-03. doi: 10.1101/2023.03.13.532473 Link
  • Ding Zhuokun, Fahey PG, Papadopoulos S, Wang E, Celii B, Papadopoulos C, Kunin A, Chang A, Fu J, Ding Zhiwei, Patel S, .. Tolias AS. Functional connectomics reveals general wiring rule in mouse visual cortex. bioRxiv. 2023:2023-03. doi: 10.1101/2023.03.13.531369 Link
  • Bernaerts Y, Deistler M, Goncalves PJ, Beck J, Stimberg M, Scala F, Tolias AS, Macke JH, Kobak D, Berens P. Combined statistical-mechanistic modeling links ion channel genes to physiology of cortical neuron types. bioRxiv. 2023:2023-03. doi: 10.1101/2023.03.02.530774 Link


  • Weis MA, Papadopoulos S, Hansel L, Lüddecke T, Celii B, Fahey PG .. Tolias AS, Ecker AS. Large-scale unsupervised discovery of excitatory morphological cell types in mouse visual cortex. bioRxiv. 2022 Dec 22. doi: 10.1101/2022.12.22.521541 Link
  • van de Ven GM, Tuytelaars T, Tolias AS. Three types of incremental learning. Nature Machine Intelligence. 2022 Dec 5; 4:1185-1197. doi: 10.1038/s42256-022-00568-3 Link
  • Dorkenwald S, Turner NL, Macrina T, Lee K, Lu R, Wu J .. Tolias AS .. Seung S. Binary and analog variation of synapses between cortical pyramidal neurons. eLife. 2022 Nov 16; 11:e76120. doi: 10.7554/eLife.76120 Link
  • Shen S, Jiang X, Scala F, Fu J, Fahey PG, Kobak D, Tan Z, Zhou N, Reimer J, Sinz FH, Tolias AS. Distinct organization of two cortico-cortical feedback pathways. Nature Communications. 2022 Oct 27; 13:6389. doi: 10.1038/s41467-022-33883-9 Link
  • Zador A, Escola S, Richards B, Ölveczky B, Bengio Y, Boahen K, Botvinick M, Chklovskii D, Churchland A, Clopath C, DiCarlo J., Ganguli S, Hawkins J, Körding K, Koulakov A, LeCun Y, Lillicrap T, Marblestone A, Olshausen B, Pouget A, Savin C, Sejnowski T, Simoncelli E, Solla S, Sussillo D, Tolias AS, Tsao D. Toward Next-Generation Artificial Intelligence: Catalyzing the NeuroAI Revolution. arXiv preprint arXiv:2210.08340. 2022 Oct 15. Link
  • Franke K, Willeke KF, Ponder K, Galdamez M, Zhou N, Muhammad T, Patel S, Froudarakis E, Reimer J, Sinz FH, Tolias AS State-dependent pupil dilation rapidly shifts visual feature selectivity. Nature 2022 Sep 28; 610(7930):128-134. doi: 10.1038/s41586-022-05270-3 Link
  • Tolias AS, Li Z, Pitkow X, Ortega Caro J, Patel A, Reimer J, Bethge M, Sinz F. Learning from biological systems how to regularize machine-learning. US Patent US20220284288A1. 2022 Sep 8; 17641259. Link
  • Liu Z, Lu X, Villette V, Gou Y, Colbert KL, Lai S .. Tolias AS, Reimer J, Dieudonné S, St-Pierre F. Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell. 2022 Sep 1; 185(18):3408-3425. doi: 10.1016/j.cell.2022.07.013 Link
  • Ash RT, Palagina G, Fernandez-Leon JA, Park J, Seilheimer R, Lee S, Sabharwal J, Reyes F, Wang J, Lu D, Sarfraz M, Froudarakis E, Tolias AS, Wu SM, Smirnakis SM. Increased reliability of visually-evoked activity in area V1 of the MECP2-duplication mouse model of autism. Journal of Neuroscience. 2022 Aug 17; 42(33):6469-6482. doi: 10.1523/JNEUROSCI.0654-22.2022 Link
  • Elabbady L, Seshamani S, Mu S, Mahalingam G, Schneider-Mizell C .. Tolias AS, Seung S, Reid C, Maçarico da Costa NM, Collman F. Quantitative census of local somatic features in mouse visual cortex. bioRxiv. 2022 Jul 22. doi: 10.1101/2022.07.20.499976 Link
  • Karantzas N, Besier E, Ortega Caro J, Pitkow X, Tolias AS, Patel AB, Anselmi F. Understanding robustness and generalization of artificial neural networks through Fourier masks. Frontiers in Artificial Intelligence. 2022 Jul 12; 5:890016. doi: 10.3389/frai.2022.890016 Link
  • Willeke KF, Fahey PG, Bashiri M, Pede L, Burg MF, Blessing C, Cadena SA, Ding Zhiwei, Lurz K, Ponder K, Muhammad T, Patel SS, Ecker AS, Tolias AS, Sinz FH. The Sensorium competition on predicting large-scale mouse primary visual cortex activity. arXiv preprint. 2022 Jun 17; arXiv:2206.08666. doi: 10.48550/arXiv.2206.08666 Link
  • Cadena SA, Willeke KF, Restivo K, Denfield G, Sinz FH, Bethge M, Tolias AS, Ecker AS. Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks. bioRxiv. 2022 May 19. doi: 10.1101/2022.05.18.492503 Link
  • Turner NL .. Tolias AS .. Seung HS (2022). Reconstruction of neocortex: Organelles, compartments, cells, circuits and activity. Cell Feb 23: doi: 10.1016/j.cell.2022.01.023 Link
  • Kudithipudi D. Tolias AS .. Siegelmann H. Biological underpinnings for lifelong learning machines. Nature Machine Intelligence: 2022 Mar. 4, pages 196–210 Link
  • Li Z, Tolias AS, Pitkow X. Learning dynamics and structure of complex systems using graph neural networks. arXiv preprint. 2022 Feb 22; arXiv:2202.10996. doi: 10.48550/arXiv.2202.10996 Link
  • Ustyuzhaninov I, Burg MF, Cadena SA, Fu J, Muhammad T, Ponder K, Froudarakis E, Ding Zhiwei, Bethge M, Tolias AS, Ecker AS. Digital twin reveals combinatorial code of non-linear computations in the mouse primary visual cortex. bioRxiv. 2022 Feb 10. doi: 10.1101/2022.02.10.479884 Link
  • Lusk SJ, McKinney A, Hunt PJ, Fahey PG, Patel J, Chang A, Sun JJ, Martinez VK, Zhu PJ, Egbert JR, Allen G, Jiang X, Arenkiel BR, Tolias AS, Costa-Mattioli M, Ray RS.(2022). A CRISPR toolbox for generating intersectional genetic mouse models for functional, molecular and anatomical circuit mapping. BMC Biol. 20(1). PDF
  • Cobos E, Muhammad T, Fahey PG, Ding Zhiwei, Ding Zhuokun, Reimer J, Sinz FH, Tolias AS. It takes neurons to understand neurons: Digital twins of visual cortex synthesize neural metamers. bioRxiv. 2022. doi: 10.1101/2022.12.09.519708 Link
  • Fu J, Willeke KF, Pierzchlewicz PA, Muhammad T, Denfield GH, Sinz FH, Tolias AS. Heterogeneous orientation tuning across Sub-Regions of receptive fields of V1 neurons in mice. Cell Reports. 2022 Feb 7. SSRN: 4029075 Link


  • Scala, F., Kobak, D., Bernabucci, M., Bernaerts, Y., Cadwell, C.R., Castro, J.R., Hartmanis, L., Jiang, X., Laturnus, S., Miranda, E. and Mulherkar, S., Tan, Z., Yao, Z., Zeng, R., Sandberg, R., Berens, P., and Tolias A.S., (2021). Phenotypic variation of transcriptomic cell types in mouse motor cortex. Nature, 598(7879): 144-150. Link
  • BRAIN Initiative Cell Census Network (BICCN) et al., including Tolias A.S. as co- corresponding author (2021). A multimodal cell census and atlas of the mammalian primary motor cortex. Nature doi: 10.1038/s41586-021-03950-0 Link
  • Hu SX, Arefin MdR, Nguyen V, Dipani A, Pitkow X, Tolias AS (2021) AvaTr: One- Shot Speaker Extraction with Transformers arXiv:2105.00609; accepted in InterSpeech PDF
  • Yang, Q., Walker, E.Y., Cotton, R.J., Tolias, A.S. and Pitkow, X., (2021). Revealing nonlinear neural decoding by analyzing choices. BioRxiv, p.332353. accepted in Nature Communications Link
  • Bashiri M., Walker E.Y., Lurz K., Jagadish A., Muhammad T., Ding Z., Ding Z., Tolias A.S ., Sinz F (2021) A flow-based latent state generative model of neural population responses to natural images NeurIPS (Advances in Neural Information Processing Systems 34). PDF
  • Burg, M.F., Cadena, S.A., Denfield, G.H., Walker, E.Y., Tolias, A.S., Bethge, M. and Ecker*, A.S., (2021). Learning divisive normalization in primary visual cortex. PLOS Computational Biology, 17(6), p.e1009028. Link
  • Shah Safarani, Arne Nix, Konstantin Willeke, Santiago A. Cadena, Kelli Restivo, George Denfield, Andreas S. Tolias and Fabian H. Sinz. (2021) Towards robust vision by multi-task learning on monkey visual cortex. arXiv NeurIPS 2021 (Neural Information Processing Systems) Link
  • Schneider-Mizell CM, Bodor AL,  Collman F,  Brittain D,  Bleckert AA,  Dorkenwald S, Turner NL,  Macrina T,  Lee K,  Lu R,  Wu J , Zhuang J,  Nandi A, Hu B,  Buchanan J, Takeno MM,  Torres R,  Mahalingam,  Bumbarger DJ,  Li Y,  Chartrand T, Kemnitz N, Silversmith WM,  Ih D, Zung J,  Zlateski A , Tartavull I, Popovych S,  Wong W,  Castro M,  Jordan CS,  Froudarakis E,  Becker L, Suckow S,  Reimer J,  Tolias AS, Anastassiou C, H. Seung HS, R. Reid RC and Maçarico da Costa N (2021). Structure and function of axo-axonic inhibition Elife 10 (e73783) Link
  • Mohammad Bashiri, Edgar Y. Walker, Konstantin-Klemens Lurz, Akshay Kumar Jagadish, Taliah Muhammad, Zhiwei Ding, Zhuokun Ding, Andreas S. Tolias and Fabian H. Sinz. (2021) A flow-based latent stage generative model of neural population responses to nautral images. NeurIPS 2021 (Neural Information Processing Systems) PDF
  • Kobak, D., Bernaerts, Y., Weis, M.A., Scala, F., Tolias, A.S. and Berens, P., (2021). Sparse reduced‐rank regression for exploratory visualisation of paired multivariate data. Journal of the Royal Statistical Society: Series C (Applied Statistics). Link
  • Tehovnik EJ, Froudarakis E, Scala F, Smirnakis SM, Patel SS, Tolias AS. Visuomotor control in mice and primates. Neurosci Biobehav Rev. 2021 Aug 17;130:185-200. doi: 10.1016/j.neubiorev.2021.08.009. Epub ahead of print. PMID: 34416241. Link


  • Edgar Y Walker, R. James Cotton, Wei Ji Ma, Andreas S Tolias (2020) A neural basis of probabilistic computation in visual cortex. Nature Neuroscience. Jan.23(1), 122-129. doi: 10.1038/s41593-019-0554-5 [Epub] 2019 Dec 23. PMID: 31873286 Link
  • Cadwell CR, Scala F, Fahey PG, Kobak D, Mulherkar S, Sinz FH, Papadopoulos S, Tan ZH, Johnsson P, Hartmanis L, Li S, Cotton RJ, Tolias KF, Sandberg R, Berens P, Jiang X, Tolias AS. (2020) Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex. Elife. 2020 Mar5;9. pii: e52951. doi: 10.7554/eLife.52951 [Epub ahead of print] Link
  • van de Ven, G.M., Siegelmann, H.T. and Tolias, A.S. (2020) Brain-inspired replay for continual learning with artificial neural networks. Nature Communications, 11(1), pp.1-14. doi: 10.1038/s41467-020-17866-2 Link
  • Cotton, R.J., Sinz, F. and Tolias, A. (2020) Factorized Neural Processes for Neural Processes: K-Shot Prediction of Neural Responses. Advances in Neural Information Processing Systems, 33. arXiv:2010.11810 Link
  • Froudarakis, E., Cohen, U., Diamantaki, M., Walker, E.Y., Reimer, J., Berens, P., Sompolinsky, H. and Tolias, A.S. (2020) Object manifold geometry across the mouse cortical visual hierarchy. bioRxiv. doi: 10.1101/2020.08.20.258798 Link
  • Shan Shen, Xiaolong Jiang, Federico Scala, Jiakun Fu, Paul Fahey, Dmitry Kobak, Zhenghuan Tan, Jacob Reimer, Fabian H. Sinz, Andreas Tolias (2020) Distinct organization of two cortico-cortical feedback pathways. bioRxiv. doi: 10.1101/2020.02.27.968792 Link
    Nature Communications, under revision.
  • Zhou P, Reimer J, Zhou D, Pasarkar, Pasarkar A, Kinsella I, Froudarakis E, Yatsenko D, Fakey P, Bodor A, Buchanan J, Bumbarger D, Mahalingam G, Torres R, Dorkenwald S, Ih D, Lee K, Lu R, Macrona T, Wu J, da Costa N, Reid C, Tolias AS, Paninski L. (2020) EASE-EM-Assisted Source Extraction from calcium imaging data bioRxiv. doi: 10.1101/2020.03.25.007468. Link
    Nature Neuroscience, under revision.
  • Shemesh, O.A., Linghu, C., Piatkevich, K.D., Goodwin, D., Celiker, O.T., Gritton, H.J., Romano, M.F., Gao, R., Yu, C.C.J., Tseng, H.A. and Bensussen, S., et al. (2020) Precision calcium imaging of dense neural populations via a cell body-targeted calcium indicator. Neuron, 107(3), pp.470-486. doi: 10.1016/j.neuron.2020.05.029 Link
  • Moreaux, L.C., Yatsenko, D., Sacher, W.D., Choi, J., Lee, C., Kubat, N.J., Cotton, R.J., Boyden, E.S., Lin, M.Z., Tian, L. and Tolias, A.S., et al. (2020) Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity—at Depth and in Real Time. Neuron. 108(1), pp.66-92. doi: 10.1016/j.neuron.2020.09.043. Link
  • Mengye Ren, Eleni Triantafillou, Kuan-Chieh Wang, James Lucas, Jake Snell, Xaq Pitkow, Andreas S. Tolias, Richard Zemel (2020) Flexible Few-Shot Learning with Contextual Similarity. arXiv:2012.05895  Link
  • Baker C, Froudarakis E, Yatsenko D, Tolias AS, Rosenbaum R. (2020) Inference of synaptic connectivity and external variability in neural microcircuits. Journal of Computational Neuroscience. doi: 10.1007/s10827-020-00739-4. [Epub ahread of print] PMID: 32080777 Link
  • Yuste, R., Hawrylycz, M., Aalling, N., Aguilar-Valles, A., Arendt, D., Arnedillo, R.A., Ascoli, G.A., Bielza, C., Bokharaie, V., Bergmann, T.B. and Bystron, I., et al. (2020) A community-based transcriptomics classification and nomenclature of neocortical cell types. Nature Neuroscience. Aug.24(23)pp. 1456-1468. Link
  • Turner, N.L., Macrina, T., Bae, J.A., Yang, R., Wilson, A.M., Schneider-Mizell, C., Lee, K., Lu, R., Wu, J., Bodor, A.L. and Bleckert, A.A., et al. (2020) Multiscale and multimodal reconstruction of cortical structure and function. bioRxiv. doi: 10.1101/2020.10.14.338681 Link
  • Qianli Yang, Edgar Walker, R. James Cotton, Andreas S. Tolias, Xaq Pitkow (2020) Revealing nonlinear neural decoding by analyzing choices. bioRxiv. doi: 10.1101/332353 Link
  • Schnieder-Mizell C …. Tolias AS ..da Costa NM (2020) Chandelier cell anatomy and function reveal a variability distributed but common signal. bioRxiv. doi: 10.1101/2020.03.31.018952 Link
  • Dorkenwald S, ...Tolias AS, ..Seung S (2020) Binary and analog variation of synapses between pyramidal neurons. bioRxiv. doi: 10.1101/2019.12.29.890319 Link


  • Zhe Li, Wieland Brendel, Edgar Y. Walker, Erick Cobos, Taliah Muhammad, Jacob Reimer, Matthias Bethge, Fabian H. Sinz, Xaq Pitkow, Andreas S. Tolias (2019) Learning From Brains How to Regularize Machines. arXiv Link
    NeurIPS 2019 (Neural Information Processing Systems) Link
  • van de Ven GM, Tolias AS (2019) Three scenarios for continual learning. arXiv arxiv:1904.07734 Link
  • Cody Baker, Emmanouil Froudarakis, Dimitri Yatsenko, Andreas S. Tolias, Robert Rosenbaum (2019) Inference of Synaptic Connectivity and External Variability in Neural Microcircuits. bioRxiv doi: 10.1101/650069 Link
  • Max F. Günthner, Santiago A. Cadena, George H. Denfield, Edgar Y. Walker, Andreas S. Tolias, Matthias Bethge, Alexander S. Ecker (2019) Learning Divisive Normalization in Primary Visual Cortex. bioRxiv. doi:10.1101/767285 Link
  • Dmitry Kobak, Yves Bernaerts, Marissa A. Weis, Federico Scala, Andreas Tolias, Philipp Berens. (2019) Sparse reduced-rank regression for exploratory visualization of multimodal data sets. bioRxiv doi: 10.1101/302208 Link
  • Paul G. Fahey, Taliah Muhammad, Cameron Smith, Emmanouil Froudarakis, Erick Cobos, Jiakun Fu, Edgar Y. Walker, Dimitri Yatsenko, Fabian H. Sinz, Jacob Reimer, Andreas S. Tolias. (2019) A global map of orientation tuning in mouse visual cortex. bioRxiv doi: 10.1101/745323 Link
  • 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
  • Egbert JR, Fahey PG, Reimer J, Owen CM, Evsikov AV, Nikolaev VO, Griesbeck O, Ray RS, Tolias AS, Jaffe LA. (2019) Follicle-stimulating hormone and luteinizing hormone increase Ca2+ in the granulosa cells of mouse ovarian follicles. Biol Reprod. doi:10.1093/biolre/ioz085 Link
  • Or A. Shemesh, Andreas Tolias, et al. (2019) Precision calcium imaging of dense neural populations via a cell body-targeted calcium indicator. bioRxiv doi: 10.1101/773069 Link
  • Walker EY, Sinz FH, Cobos E, Muhammad T, Froudarakis E, Fahey PG, Ecker AS, Reimer J, Pitkow X, Tolias AS (2019) Inception loops discover what excites neurons most using deep predictive models. Nature Neuroscience. doi: 10.1038/s41593-019-0517-x Link
  • Sinz FH, Pitkow X, Reimer J, Bethge M, Tolias AS. (2019) Engineering a Less Artificial Intelligence. Neuron doi: 10.1016/j.neuron.2019.08.034 Link
  • Froudarakis, E., Fahey, P.G., Reimer, J., Smirnakis, S.M., Tehovnik, E.J., Tolias, A.S., 2019. The Visual Cortex in Context. Annual Review of Vision Science 5, 317–339. doi:10.1146/annurev-vision-091517-034407 Link
  • Scala F, Kobak D, Shan S, Bernaerts Y, Laturnus S, Cadwell CR, Hartmanis L, Froudarakis E, Castro JR, Tan ZH, Papadopoulos S, Patel SS, Sandberg R, Berens P, Jiang X, Tolias AS. Layer 4 of mouse neocortex differs in cell types and circuit organization between sensory areas. Nat Commun. 2019 Sep 13;10(1):4174. doi:10.1038/s41467-019-12058-z Link
  • Cadena SA, Denfield GH, Walker EY, Gatys LA, Tolias AS, Bethge M, and Ecker AS (2019) Deep convolutional models improve predictions of macaque V1 responses to natural images PLoS Comput Biol. doi: 10.1371/journal.pcbi.1006897 Link
  • Liu G, Froudarakis E, Patel JM, Kochukov MY, Pekarek B, Hunt PJ, Patel M, Ung K, Fu CH, Jo J, Lee HK, Tolias AS, Arenkiel BR. (2019) Target specific functions of EPL interneurons in olfactory circuits Nat Commun. doi: 10.1038/s41467-019-11354-y 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.