Publications

The following publications relied on DataJoint open-source software for data analysis. If your work uses DataJoint or DataJoint Elements, please cite the respective manuscripts and RRIDs.

2024

• Mosberger, A.C., Sibener, L.J., Chen, T.X., Rodrigues, H.F., Hormigo, R., Ingram, J.N., Athalye, V.R., Tabachnik, T., Wolpert, D.M., Murray, J.M. and Costa, R.M., 2024. Exploration biases forelimb reaching strategies. Cell Reports, 43(4).

• Guidera, J. A., Gramling, D. P., Comrie, A. E., Joshi, A., Denovellis, E. L., Lee, K. H., ... & Frank, L. M. (2024). Regional specialization manifests in the reliability of neural population codes. bioRxiv, 2024-01.

• Lee, K. H., Denovellis, E. L., Ly, R., Magland, J., Soules, J., Comrie, A. E., Gramling, D. P., Guidera, J. A., Nevers, R., Adenekan, P., Brozdowski, C., Bray, S. R., Monroe, E., Bak, J. H., Coulter, M. E., Sun, X., Broyles, E., Shin, D., Chiang, S., Holobetz, C., … Frank, L. M. (2024).Spyglass: a framework for reproducible and shareable neuroscience research bioRxiv 2024.01.25.577295

• Chen, S., Liu, Y., Wang, Z. A., Colonell, J., Liu, L. D., Hou, H., ... & Svoboda, K. (2024). Brain-wide neural activity underlying memory-guided movement. Cell, 187(3), 676-691.

• Gonzalo Cogno, S., Obenhaus, H. A., Lautrup, A., Jacobsen, R. I., Clopath, C., Andersson, S. O., ... & Moser, E. I. (2024). Minute-scale oscillatory sequences in medial entorhinal cortex. Nature, 625(7994), 338-344.

• Cimorelli, A., Patel, A., Karakostas, T., & Cotton, R. J. (2024). Validation of portable in-clinic video-based gait analysis for prosthesis users. Nature Scientific Reports, 14(1), 3840.

• Papadopouli, M., Koniotakis, E., Smyrnakis, I., Savaglio, M. A., Psilou, E., Brozi, C., ... & Smirnakis, S. M. (2024). Brain orchestra under spontaneous conditions: Identifying communication modules from the functional architecture of area V1. bioRxiv, 2024-02.

2023

• Celii, B., Papadopoulos, S., Ding, Z., Fahey, P. G., Wang, E., Papadopoulos, C., ... & Reimer, J. (2023). NEURD: automated proofreading and feature extraction for connectomics.. bioRxiv. 2023-03.

• Chen, S., Liu, Y., Wang, Z., Colonell, J., Liu, L. D., Hou, H., ... & Svoboda, K. (2023). Brain-wide neural activity underlying memory-guided movement. bioRxiv. 2023-03.

• Cotton, R. J., Cimorelli, A., Shah, K., Anarwala, S., Uhlrich, S., & Karakostas, T. (2023). Improved Trajectory Reconstruction for Markerless Pose Estimation. arXiv. 2303.02413.

• Ding, Z., Fahey, P. G., Papadopoulos, S., Wang, E., Celii, B., Papadopoulos, C., ... & Tolias, A. S. (2023). Functional connectomics reveals general wiring rule in mouse visual cortex. bioRxiv, 2023-03.

• Laboratory, I. B., Bonacchi, N., Chapuis, G. A., Churchland, A. K., DeWitt, E. E., Faulkner, M., ... & Wells, M. J. (2023). A modular architecture for organizing, processing and sharing neurophysiology data. Nature Methods. 1-5.

2022

• Wang, Y., Chiola, S., Yang, G., Russell, C., Armstrong, C. J., Wu, Y., ... & Shcheglovitov, A. (2022). Modeling human telencephalic development and autism-associated SHANK3 deficiency using organoids generated from single neural rosettes. Nature Communications, 13(1), 1-25.

• Franke, K., Willeke, K. F., Ponder, K., Galdamez, M., Zhou, N., Muhammad, T., ... & Tolias, A. S. (2022). State-dependent pupil dilation rapidly shifts visual feature selectivity. Nature, 1-7.

• Pettit, N. H., Yap, E., Greenberg, M. E., Harvey, C. D. (2022). Fos ensembles encode and shape stable spatial maps in the hippocampus. Nature.

• Saunders, J. L., Ott, L. A., Wehr, M. (2022). AUTOPILOT: Automating experiments with lots of Raspberry Pis. bioRxiv.

• Born, G. (2022). The effect of feedback on sensory processing in the mouse early visual system. Doctoral dissertation.

• Cobos, E., Muhammad, T., Fahey, P. G., Ding, Z., Ding, Z., Reimer, J., ... & Tolias, A. (2022). It takes neurons to understand neurons: Digital twins of visual cortex synthesize neural metamers. bioRxiv, 2022-12.

• Cadena, S. A., Willeke, K. F., Restivo, K., Denfield, G., Sinz, F. H., Bethge, M., ... & Ecker, A. S. (2022). Diverse task-driven modeling of macaque V4 reveals functional specialization towards semantic tasks. bioRxiv.

• Cotton, R. J. (2022). PosePipe: Open-Source Human Pose Estimation Pipeline for Clinical Research. arXiv. 2203.08792.

• Cotton, R. J., McClerklin, E., Cimorelli, A., & Patel, A. (2022). Spatiotemporal characterization of gait from monocular videos with transformers.

• Cotton, R. J., McClerklin, E., Cimorelli, A., Patel, A., & Karakostas, T. (2022). Transforming Gait: Video-Based Spatiotemporal Gait Analysis. arXiv. 2203.09371.

• Fu, J., Willeke, K. F., Pierzchlewicz, P. A., Muhammad, T., Denfield, G. H., Sinz, F. H., & Tolias, A. S. (2022). Heterogeneous Orientation Tuning Across Sub-Regions of Receptive Fields of V1 Neurons in Mice. Available at SSRN 4029075.

• Zong, W., Obenhaus, H.A., Skytøen, E.R., Eneqvist, H., de Jong, N.L., Vale, R., Jorge, M.R., Moser, M.B. and Moser, E.I., 2022. Large-scale two-photon calcium imaging in freely moving mice(:target="_blank"}. Cell, 185(7), pp.1240-1256.

• Goetz, J., Jessen, Z. F., Jacobi, A., Mani, A., Cooler, S., Greer, D., ... & Schwartz, G. W. (2022). Unified classification of mouse retinal ganglion cells using function, morphology, and gene expression. Cell reports, 40(2), 111040.

• Huang, J. Y., Hess, M., Bajpai, A., Barton, S. J., Li, X., Hobson, L. N., & Lu, H. C. (2022). Sex-and GABAergic-modulated neuronal subnetwork assemblies in the developing somatosensory cortex. bioRxiv, 2022-10.

• Jaffe, A. (2022). Optical investigation of microcircuit computations in mouse primary visual cortex. Doctoral dissertation.

• Obenhaus, H.A., Zong, W., Jacobsen, R.I., Rose, T., Donato, F., Chen, L., Cheng, H., Bonhoeffer, T., Moser, M.B. & Moser, E.I. (2022). Functional network topography of the medial entorhinal cortex. Proceedings of the National Academy of Sciences, 119 (7).

• Roukes, M. L. (2022, May). The Integrated Neurophotonics Paradigm. In CLEO: Applications and Technology (pp. ATh4I-6). Optica Publishing Group.

• Sanchez, M., Moore, D., Johnson, E. C., Wester, B., Lichtman, J. W., & Gray-Roncal, W. (2022). Connectomics Annotation Metadata Standardization for Increased Accessibility and Queryability. Frontiers in Neuroinformatics.

• Spacek, M. A., Crombie, D., Bauer, Y., Born, G., Liu, X., Katzner, S., & Busse, L. (2022). Robust effects of corticothalamic feedback and behavioral state on movie responses in mouse dLGN. Elife, 11, e70469.

• Tseng, S. Y., Chettih, S. N., Arlt, C., Barroso-Luque, R., & Harvey, C. D. (2022). Shared and specialized coding across posterior cortical areas for dynamic navigation decisions. Neuron.

• Turner, N. L., Macrina, T., Bae, J. A., Yang, R., Wilson, A. M., Schneider-Mizell, C., ... & Seung, H. S. (2022). Reconstruction of neocortex: Organelles, compartments, cells, circuits, and activity. Cell, 185(6), 1082-1100.

• Ustyuzhaninov, I., Burg, M.F., Cadena, S.A., Fu, J., Muhammad, T., Ponder, K., Froudarakis, E., Ding, Z., Bethge, M., Tolias, A. & Ecker, A.S. (2022). Digital twin reveals combinatorial code of non-linear computations in the mouse primary visual cortex. bioRxiv.

• Willeke, K. F., Fahey, P. G., Bashiri, M., Pede, L., Burg, M. F., Blessing, C., ... & Sinz, F. H. (2022). The Sensorium competition on predicting large-scale mouse primary visual cortex activity. arXiv preprint arXiv:2206.08666.

2021

• Bae, J. A., Baptiste, M., Bodor, A. L., Brittain, D., Buchanan, J., Bumbarger, D. J., Castro, M. A., Celii, B., Cobos, E., Collman, F., ... (2021). Functional connectomics spanning multiple areas of mouse visual cortex. bioRxiv.

• Born, G., Schneider-Soupiadis, F. A., Erisken, S., Vaiceliunaite, A., Lao, C. L., Mobarhan, M. H., Spacek, M. A., Einevoll, G. T., & Busse, L. (2021). Corticothalamic feedback sculpts visual spatial integration in mouse thalamus. Nature Neuroscience, 24(12), 1711–1720.

• Burg, M. F., Cadena, S. A., Denfield, G. H., Walker, E. Y., Tolias, A. S., Bethge, M., & Ecker, A. S. (2021). Learning divisive normalization in primary visual cortex. PLOS Computational Biology, 17(6), e1009028.

• Claudi, F., Campagner, D., & Branco, T. (2021). Innate heuristics and fast learning support escape route selection in mice. bioRxiv.

• Cohrs, K.H. (2021). Investigation of feedback mechanisms in visual cortex using deep learning models. Master’s thesis. University of Göttingen.

• Dennis, E. J., El Hady, A., Michaiel, A., Clemens, A., Tervo, D. R. G., Voigts, J., & Datta, S. R. (2021). Systems neuroscience of natural behaviors in rodents. Journal of Neuroscience, 41(5), 911-919.

• Finkelstein, A., Fontolan, L., Economo, M. N., Li, N., Romani, S., & Svoboda, K. (2021). Attractor dynamics gate cortical information flow during decision-making. Nature Neuroscience. 24(6), 843-850.

• Franke, K., Willeke, K. F., Ponder, K., Galdamez, M., Muhammad, T., Patel, S., Froudarakis, E., Reimer, J., Sinz, F., & Tolias, A. (2021). Behavioral state tunes mouse vision to ethological features through pupil dilation. bioRxiv.

• Jacobsen, R. I., Nair, R. R., Obenhaus, H. A., Donato, F., Slettmoen, T., Moser, M.-B., & Moser, E. I. (2021). All-viral tracing of monosynaptic inputs to single birthdate-defined neurons in the intact brain. bioRxiv.

• Laboratory, T. I. B., Aguillon-Rodriguez, V., Angelaki, D., Bayer, H., Bonacchi, N., Carandini, M., Cazettes, F., Chapuis, G., Churchland, A. K., Dan, Y., ... (2021). Standardized and reproducible measurement of decision-making in mice. eLife, 10.

• Strauss, S., Korympidou, M. M., Ran, Y., Franke, K., Schubert, T., Baden, T., Berens, P., Euler, T., & Vlasits, A. L. (2021). Center-surround interactions underlie bipolar cell motion sensing in the mouse retina. bioRxiv.

• Subramaniyan, M., Manivannan, S., Chelur, V., Tsetsenis, T., Jiang, E., & Dani, J. A. (2021). Fear conditioning potentiates the hippocampal CA1 commissural pathway in vivo and increases awake phase sleep. Hippocampus, 31(10), 1154–1175.

• Urai, A. E., Aguillon-Rodriguez, V., Laranjeira, I. C., Cazettes, F., Laboratory, T. I. B., Mainen, Z. F., & Churchland, A. K. (2021). Citric acid water as an alternative to water restriction for high-yield mouse behavior. Eneuro, 8(1).

• Wal, A., Klein, F. J., Born, G., Busse, L., & Katzner, S. (2021). Evaluating visual cues modulates their representation in mouse visual and cingulate cortex. Journal of Neuroscience, 41(15), 3531–3544.

• Wang, Y., Chiola, S., Yang, G., Russell, C., Armstrong, C. J., Wu, Y., Spampanato, J., Tarboton, P., Chang, A. N., Harmin, D. A., ... (2021). Modeling autism-associated SHANK3 deficiency using human cortico-striatal organoids generated from single neural rosettes. bioRxiv.

2020

• Angelaki, D. E., Ng, J., Abrego, A. M., Cham, H. X., Asprodini, E. K., Dickman, J. D., & Laurens, J. (2020). A gravity-based three-dimensional compass in the mouse brain. Nature Communications, 11(1), 1–13.

• Cotton, R. J., Sinz, F. H., & Tolias, A. S. (2020). Factorized neural processes for neural processes: K-shot prediction of neural responses. arXiv Preprint arXiv:2010.11810.

• Heath, S. L., Christenson, M. P., Oriol, E., Saavedra-Weisenhaus, M., Kohn, J. R., & Behnia, R. (2020). Circuit mechanisms underlying chromatic encoding in drosophila photoreceptors. Current Biology.

• Laturnus, S., Kobak, D., & Berens, P. (2020). A systematic evaluation of interneuron morphology representations for cell type discrimination. Neuroinformatics, 18(4), 591–609.

• Sinz, F. H., Sachgau, C., Henninger, J., Benda, J., & Grewe, J. (2020). Simultaneous spike-time locking to multiple frequencies. Journal of Neurophysiology, 123(6), 2355–2372.

• Yatsenko, D., Moreaux, L. C., Choi, J., Tolias, A., Shepard, K. L., & Roukes, M. L. (2020). Signal separability in integrated neurophotonics. bioRxiv.

• Zhao, Z., Klindt, D. A., Chagas, A. M., Szatko, K. P., Rogerson, L., Protti, D. A., Behrens, C., Dalkara, D., Schubert, T., Bethge, M., others. (2020). The temporal structure of the inner retina at a single glance. Scientific Reports, 10(1), 1–17.

2019

• Cadena, S. A., Denfield, G. H., Walker, E. Y., Gatys, L. A., Tolias, A. S., Bethge, M., & Ecker, A. S. (2019). Deep convolutional models improve predictions of macaque V1 responses to natural images. PLoS Computational Biology, 15(4), e1006897.

• Chettih, S. N., & Harvey, C. D. (2019). Single-neuron perturbations reveal feature-specific competition in V1. Nature, 567(7748), 334–340.

• Fahey, P. G., Muhammad, T., Smith, C., Froudarakis, E., Cobos, E., Fu, J., Walker, E. Y., Yatsenko, D., Sinz, F. H., Reimer, J., ... (2019). A global map of orientation tuning in mouse visual cortex. bioRxiv, 745323.

• Laurens, J., Abrego, A., Cham, H., Popeney, B., Yu, Y., Rotem, N., Aarse, J., Asprodini, E. K., Dickman, J. D., & Angelaki, D. E. (2019). Multiplexed code of navigation variables in anterior limbic areas. bioRxiv, 684464.

• Liu, G., Froudarakis, E., Patel, J. M., Kochukov, M. Y., Pekarek, B., Hunt, P. J., Patel, M., Ung, K., Fu, C.-H., Jo, J., ... (2019). Target specific functions of EPL interneurons in olfactory circuits. Nature Communications, 10(1), 1–14.

• Rosón, M. R., Bauer, Y., Kotkat, A. H., Berens, P., Euler, T., & Busse, L. (2019). Mouse dLGN receives functional input from a diverse population of retinal ganglion cells with limited convergence. Neuron, 102(2), 462–476.

• Walker, E. Y., Sinz, F. H., Cobos, E., Muhammad, T., Froudarakis, E., Fahey, P. G., Ecker, A. S., Reimer, J., Pitkow, X., & Tolias, A. S. (2019). Inception loops discover what excites neurons most using deep predictive models. Nature Neuroscience, 22(12), 2060–2065.

2018

• Denfield, G. H., Ecker, A. S., Shinn, T. J., Bethge, M., & Tolias, A. S. (2018). Attentional fluctuations induce shared variability in macaque primary visual cortex. Nature Communications, 9(1), 2654.

• Ecker, A. S., Sinz, F. H., Froudarakis, E., Fahey, P. G., Cadena, S. A., Walker, E. Y., Cobos, E., Reimer, J., Tolias, A. S., & Bethge, M. (2018). A rotation-equivariant convolutional neural network model of primary visual cortex. arXiv Preprint arXiv:1809.10504.

• Sinz, F., Ecker, A. S., Fahey, P., Walker, E., Cobos, E., Froudarakis, E., Yatsenko, D., Pitkow, Z., Reimer, J., & Tolias, A. (2018). Stimulus domain transfer in recurrent models for large scale cortical population prediction on video. Advances in Neural Information Processing Systems, 7199–7210.

• Walker, E. Y., Sinz, F. H., Froudarakis, E., Fahey, P. G., Muhammad, T., Ecker, A. S., Cobos, E., Reimer, J., Pitkow, X., & Tolias, A. S. (2018). Inception in visual cortex: In vivo-silico loops reveal most exciting images. bioRxiv, 506956.

2017

• Franke, K., Berens, P., Schubert, T., Bethge, M., Euler, T., & Baden, T. (2017). Inhibition decorrelates visual feature representations in the inner retina. Nature, 542(7642), 439.

• Jurjut, O., Georgieva, P., Busse, L., & Katzner, S. (2017). Learning enhances sensory processing in mouse V1 before improving behavior. Journal of Neuroscience, 37(27), 6460–6474.

• Shan, K. Q., Lubenov, E. V., & Siapas, A. G. (2017). Model-based spike sorting with a mixture of drifting t-distributions. Journal of Neuroscience Methods, 288, 82–98.

2016

• Baden, T., Berens, P., Franke, K., Rosón, M. R., Bethge, M., & Euler, T. (2016). The functional diversity of retinal ganglion cells in the mouse. Nature, 529(7586), 345–350.

• Cadwell, C. R., Palasantza, A., Jiang, X., Berens, P., Deng, Q., Yilmaz, M., Reimer, J., Shen, S., Bethge, M., Tolias, K. F., others. (2016). Electrophysiological, transcriptomic and morphologic profiling of single neurons using patch-seq. Nature Biotechnology, 34(2), 199–203.

• Hartmann, L., Drewe-Boß, P., Wießner, T., Wagner, G., Geue, S., Lee, H.-C., Obermüller, D. M., Kahles, A., Behr, J., Sinz, F. H., ... (2016). Alternative splicing substantially diversifies the transcriptome during early photomorphogenesis and correlates with the energy availability in arabidopsis. The Plant Cell, 28(11), 2715–2734.

• Khastkhodaei, Z., Jurjut, O., Katzner, S., & Busse, L. (2016). Mice can use second-order, contrast-modulated stimuli to guide visual perception. Journal of Neuroscience, 36(16), 4457–4469.

• Reimer, J., McGinley, M. J., Liu, Y., Rodenkirch, C., Wang, Q., McCormick, D. A., & Tolias, A. S. (2016). Pupil fluctuations track rapid changes in adrenergic and cholinergic activity in cortex. Nature Communications, 7, 13289.

• Shan, K. Q., Lubenov, E. V., Papadopoulou, M., & Siapas, A. G. (2016). Spatial tuning and brain state account for dorsal hippocampal CA1 activity in a non-spatial learning task. eLife, 5, e14321.

2015

• Jiang, X., Shen, S., Cadwell, C. R., Berens, P., Sinz, F., Ecker, A. S., Patel, S., & Tolias, A. S. (2015). Principles of connectivity among morphologically defined cell types in adult neocortex. Science, 350(6264), aac9462.

• Yatsenko, D., Josić, K., Ecker, A. S., Froudarakis, E., Cotton, R. J., & Tolias, A. S. (2015). Improved estimation and interpretation of correlations in neural circuits. PLoS Comput Biol, 11(3), e1004083.

2014

• 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.

• Erisken, S., Vaiceliunaite, A., Jurjut, O., Fiorini, M., Katzner, S., & Busse, L. (2014). Effects of locomotion extend throughout the mouse early visual system. Current Biology, 24(24), 2899–2907.

• 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 readout of natural scenes through increased sparseness. Nat Neurosci, 17(6), 851–857.

• 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, 84(2), 355–362.

2013

• Cotton, R. J., Froudarakis, E., Storer, P., Saggau, P., & Tolias, A. S. (2013). Three-dimensional mapping of microcircuit correlation structure. Frontiers in Neural Circuits, 7, 151.

• Vaiceliunaite, A., Erisken, S., Franzen, F., Katzner, S., & Busse, L. (2013). Spatial integration in mouse primary visual cortex. Journal of Neurophysiology, 110(4), 964–972.