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

• Kyu Hyun Lee, Eric L. Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison E. Comrie, Daniel P. Gramling, Jennifer A. Guidera, Rhino Nevers, Philip Adenekan, Chris Brozdowski, Samuel R. Bray, Emily Monroe, Ji Hyun Bak, Michael E. Coulter, Xulu Sun, Emrey Broyles, Donghoon Shin, Sharon Chiang, Cristofer Holobetz, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Loren M. Frank Spyglass: a framework for reproducible and shareable neuroscience research bioRxiv 2024.01.25.577295

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.

• 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.

• 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.