Publications
Celii, B., Papadopoulos, S., Ding, Z., Fahey, P. G., Wang, E., Papadopoulos, C., Kunin, A. B., Patel, S., Bae, J. A., Bodor, A. L., Brittain, D., Buchanan, J., Bumbarger, D. J., Castro, M. A., Cobos, E., Dorkenwald, S., Elabbady, L., Halageri, A., Jia, Z., … Reimer, J. (2025). NEURD offers automated proofreading and feature extraction for connectomics. Nature, 640, 487–496. https://doi.org/10.1038/s41586-025-08660-5
Ding, Z., Fahey, P. G., Papadopoulos, S., Wang, E. Y., Celii, B., Papadopoulos, C., Chang, A., Kunin, A. B., Tran, D., Fu, J., Ding, Z., Patel, S., Ntanavara, L., Froebe, R., Ponder, K., Muhammad, T., Bae, J. A., Bodor, A. L., Brittain, D., Reimer, J.*, … Tolias, A. S.* (2025). Functional connectomics reveals general wiring rule in mouse visual cortex. Nature, 640, 459–469. https://doi.org/10.1038/s41586-025-08840-3 *co-corresponding authors
Neyhart, E., Zhou, N., Munn, B. R., Law, R. G., Smith, C., Mridha, Z. H., Blanco, F. A., Li, G., Li, Y., Hu, M., McGinley, M. J., Shine, J. M., & Reimer, J. (2024). Cortical acetylcholine dynamics are predicted by cholinergic axon activity and behavior state. Cell Reports, 43(10). https://doi.org/10.1016/j.celrep.2024.114808
Pirhayati*, D., Smith*, C. L., Kroeger, R., Navlakha, S., Pfaffinger, P., Reimer, J., Arenkiel, B. R., Patel, A., & Moss, E. H. (2024). Dense and persistent odor representations in the olfactory bulb of awake mice. Journal of Neuroscience, 44(39). https://doi.org/10.1523/JNEUROSCI.0116-24.2024 *co-first authors
Franke, K., Willeke, K. F., Ponder, K., Galdamez, M., Zhou, N., Muhammad, T., Patel, S., Froudarakis, E., Reimer, J., Sinz, F. H., & Tolias, A. S. (2022). State-dependent pupil dilation rapidly shifts visual feature selectivity. Nature, 610(7930), Article 7930. https://doi.org/10.1038/s41586-022-05270-3
Liu, Z., Lu, X., Villette, V., Gou, Y., Colbert, K. L., Lai, S., Guan, S., Land, M. A., Lee, J., Assefa, T., Zollinger, D. R., Korympidou, M. M., Vlasits, A. L., Pang, M. M., Su, S., Cai, C., Froudarakis, E., Zhou, N., Patel, S. S., … St-Pierre, F. (2022). Sustained deep-tissue voltage recording using a fast indicator evolved for two-photon microscopy. Cell, 185(18), 3408-3425.e29. https://doi.org/10.1016/j.cell.2022.07.013
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(1), 13289. https://doi.org/10.1038/ncomms13289
Selected Preprints
Fahey, P. G., Muhammad, T., Smith, C., Froudarakis, E., Cobos, E., Fu, J., Walker, E. Y., Yatsenko, D., Sinz, F. H., Reimer, J.*, & Tolias, A. S.* (2019). A global map of orientation tuning in mouse visual cortex. bioRxiv. https://doi.org/10.1101/745323 *co-corresponding authors
Ling, D., Moss, E. H., Smith, C. L., Kroeger, R., Reimer, J., Raman, B., & Arenkiel, B. R. (2023). Conserved neural dynamics and computations across species in olfaction (p. 2023.04.24.538157). bioRxiv. https://doi.org/10.1101/2023.04.24.538157