publications.md

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.

2026

• Cotton, R. J. & Leonard, T. (2026). BiomechAgent: AI-Assisted Biomechanical Analysis Through Code-Generating Agents. arXiv.

• Donahue, S., Djuraskovic, I., Shah, K., Sinz, F., Chafetz, R. & Cotton, R. J. (2026). Calibrated Uncertainty for Trustworthy Clinical Gait Analysis Using Probabilistic Multiview Markerless Motion Capture. arXiv.

• Fu, J., Shrinivasan, S., Baroni, L., Ding, Z., Fahey, P. G., Pierzchlewicz, P. A., Karantzas, N., Ponder, K., Froebe, R., Ntanavara, L., Muhammad, T., Willeke, K. F., Wang, E., Ding, Z., Tran, D., Papadopoulos, S., Patel, S., Reimer, J., Ecker, A. S., Pitkow, X., Antolik, J., Sinz, F. H., Haefner, R. M., Tolias, A. S. & Franke, K. (2026). Statistics of natural scenes shape contextual modulation in the visual cortex. Neuron.

• Sun, X., Comrie, A. E., Kahn, A. E., Monroe, E. J., Joshi, A., Guidera, J. A., Denovellis, E. L., Krausz, T. A., Zhou, J., Thompson, P., Hernandez, J., Yorita, A., Haque, R., Berke, J. D., Daw, N. D. & Frank, L. M. (2026). Meta-learning is expressed through altered prefrontal cortical dynamics. bioRxiv.

2025

• Bae, J. A., Baptiste, M., Bodor, A. L., Brittain, D., Buchanan, J., Bumbarger, D. J., Castro, M. A., Celii, B., Cobos, E., Collman, F., ... (2025). Functional connectomics spanning multiple areas of mouse visual cortex. Nature, 640(8058), 435-447.

• Campagner, D., Bhagat, J., Lopes, G., Calcaterra, L., Pouget, A. G., Almeida, A., ... & SWC GCNU Experimental Neuroethology Group. (2025). Aeon: an open-source platform to study the neural basis of ethological behaviours over naturalistic timescales. bioRxiv.

• Celii, B., Papadopoulos, S., Ding, Z., Fahey, P. G., Wang, E., Papadopoulos, C., ... & Reimer, J. (2025). NEURD offers automated proofreading and feature extraction for connectomics. Nature, 640(8058), 487-496.

• Coulter, M. E., Gillespie, A. K., Chu, J., Denovellis, E. L., Nguyen, T. T. K., Liu, D. F., Wadhwani, K., Sharma, B., Wang, K., Deng, X., Eden, U. T., Kemere, C. & Frank, L. M. (2025). Closed-loop modulation of remote hippocampal representations with neurofeedback. Neuron, 113(6), 949-961.

• Ding, Z., Fahey, P.G., Papadopoulos, S., Wang, E.Y., Celii, B., Papadopoulos, C., Chang, A., Kunin, A.B., Tran, D., Fu, J. ... & Tolias, A. S. (2025). Functional connectomics reveals general wiring rule in mouse visual cortex. Nature, 640(8058), 459-469.

• Dyszkant, N., Oesterle, J., Qiu, Y., Harrer, M., Schubert, T., Gonschorek, D. & Euler, T. (2025). Photoreceptor degeneration has heterogeneous effects on functional retinal ganglion cell types. The Journal of Physiology, 603(21), 6599-6621.

• Finkelstein, A., Daie, K., Rózsa, M., Darshan, R. & Svoboda, K. (2025). Connectivity underlying motor cortex activity during goal-directed behaviour. Nature.

• Gillon, C.J., Baker, C., Ly, R., Balzani, E., Brunton, B.W., Schottdorf, M., Ghosh, S. and Dehghani, N.(2025). Open data in neurophysiology: Advancements, solutions & challenges. eNeuro, 12(11).

• Heiser, H., Kiessler, F., Roggenbach, A., Ibanez, V., Wieckhorst, M., Helmchen, F., Gjorgjieva, J. & Wahl, A.-S. (2025). Brain-wide microstrokes affect the stability of memory circuits in the hippocampus. Nature Communications, 16, 3462.

• Huang, J.Y., Hess, M., Bajpai, A., Li, X., Hobson, L.N., Xu, A.J., Barton, S.J. and Lu, H.C.(2025). From initial formation to developmental refinement: GABAergic inputs shape neuronal subnetworks in the primary somatosensory cortex. iScience, 28(3).

• Joshi, A., Comrie, A. E., Bray, S., Mankili, A., Guidera, J. A., Nevers, R., Sun, X., Monroe, E., Kharazia, V., Ly, R., Astudillo Maya, D., Morales-Rodriguez, D., Yu, J., Kiseleva, A., Perez, V. & Frank, L. M. (2025). Disruption of theta-timescale spiking impairs learning but spares hippocampal replay. bioRxiv.

• 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. (2025). Spyglass: a data analysis framework for reproducible and shareable neuroscience research. eLife.

• Lees, R.M., Bianco, I.H., Campbell, R.A.A., Orlova, N., Peterka, D.S., Pichler, B., Smith, S.L., Yatsenko, D., Yu, C.H. & Packer, A.M. (2025). Standardized measurements for monitoring and comparing multiphoton microscope systems. Nature Protocols, 20, 2171–2208.

• Oesterle, J., Ran, Y., Stahr, P., Kerr, J. N. D., Schubert, T., Berens, P. & Euler, T. (2025). Task-specific regional circuit adaptations in distinct mouse retinal ganglion cells. Science Advances, 11(17).

• Panzeri, M., Thiem, N., Hoffmann, C., Schillinger, U., Barapatre, N., Musall, S., Helmchen, F. & Wahl, A.-S. (2025). Contralesional activity reflects compensation, while brainstem detour pathways support skilled motor recovery after stroke. bioRxiv.

• Peiffer, J. D., Shah, K., Djuraskovic, I., Anarwala, S., Abdou, K., Patel, R., Jayabalan, P., Pennicooke, B. & Cotton, R. J. (2025). Portable Biomechanics Laboratory: Clinically accessible movement analysis from a handheld smartphone. arXiv.

• Schmors, L., Kotkat, A.H., Bauer, Y., Huang, Z., Crombie, D., Meyerolbersleben, L.S., Sokoloski, S., Berens, P. & Busse, L. (2025). Effects of corticothalamic feedback depend on visual responsiveness and stimulus type. iScience, 28, 112481.

• Sutlief, E., Zhang, S., Foresberg, K., Kaneko, R. & Hussain Shuler, M. G. (2025). Reward-reset interval timing drives patch foraging decisions through neural state transitions in dorsomedial striatum. bioRxiv.

• Sibener, L.J., Mosberger, A.C., Chen, T.X., Athalye, V.R., Murray, J.M. & Costa, R.M. (2025). Dissociable roles of distinct thalamic circuits in learning reaches to spatial targets. Nature Communications, 16, 2962.

2024

• 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.

• Korympidou, M.M., Strauss, S., Schubert, T., Franke, K., Berens, P., Euler, T. & Vlasits, A.L. (2024). GABAergic amacrine cells balance biased chromatic information in the mouse retina. Cell Reports, 43(11), 114953.

• 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).

• Reimer, M. L., Kauer, S. D., Benson, C. A., King, J. F., Patwa, S., Feng, S., Estacion, M. A., Bangalore, L., Waxman, S. G., & Tan, A. M. (2024). A FAIR, open-source virtual reality platform for dendritic spine analysis. Patterns, 5(9).

2023

• Willeke, K.F., Restivo, K., Franke, K., Nix, A.F., Cadena, S.A., Shinn, T., Nealley, C., Rodriguez, G., Patel, S., Ecker, A.S., Sinz, F.H. & Tolias, A.S. (2023). Deep learning-driven characterization of single cell tuning in primate visual area V4 supports topological organization. bioRxiv.

• 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

• Claudi, F., Campagner, D. & Branco, T. (2022). Innate heuristics and fast learning support escape route selection in mice. Current Biology, 32(13), 2980-2987.

• 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, 610(7930), 128-134.

• 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, 5688.

• 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.

• 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).

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

• 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.

• Zong, W., Obenhaus, H.A., Skytoen, 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. Cell, 185(7), 1240-1256.

2021

• 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.

• 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.

• 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.

• 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.

• Reimer, M. L., Bangalore, L., Waxman, S. G. & Tan, A. M. (2021). Core principles for the implementation of the neurodata without borders data standard. Journal of Neuroscience Methods, 348, 108972.

• 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.

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.

• 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.

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

2019

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

• 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.

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.

• 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., Rosen, M. R., Bethge, M., & Euler, T. (2016). The functional diversity of retinal ganglion cells in the mouse. Nature, 529(7586), 345-350.

• 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.

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 Computational Biology, 11(3), e1004083.

2014

• 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. Nature Neuroscience, 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.