Semedo, J. D., Zandvakili, A., Machens, C. K., Yu, B. M. & Kohn, A. Cortical areas interact through a communication subspace. Neuron 102, 249–259 (2019).
Buzsáki, G. Two-stage model of memory trace formation: a role for ‘noisy’ brain states. Neuroscience 31, 551–570 (1989).
Squire, L. R. Memory and the hippocampus: a synthesis from findings with rats, monkeys, and humans. Psychol. Rev. 99, 195–231 (1992).
O’Keefe, J. & Nadel, L. The Hippocampus as a Cognitive Map (Oxford Univ. Press, 1978).
Chaudhuri, R., Gerçek, B., Pandey, B., Peyrache, A. & Fiete, I. The intrinsic attractor manifold and population dynamics of a canonical cognitive circuit across waking and sleep. Nat. Neurosci. 22, 1512–1520 (2019).
Sussillo, D., Churchland, M. M., Kaufman, M. T. & Shenoy, K. V. A neural network that finds a naturalistic solution for the production of muscle activity. Nat. Neurosci. 18, 1025–1033 (2015).
Wang, J., Narain, D., Hosseini, E. A. & Jazayeri, M. Flexible timing by temporal scaling of cortical responses. Nat. Neurosci. 21, 102–110 (2018).
Oby, E. R. et al. Dynamical constraints on neural population activity. Nat. Neurosci. 28, 383–393 (2025).
Ebrahimi, S. et al. Emergent reliability in sensory cortical coding and inter-area communication. Nature 605, 713–721 (2022).
Jun, J. J. et al. Fully integrated silicon probes for high-density recording of neural activity. Nature 551, 232–236 (2017).
Buzsáki, G. Hippocampal sharp wave-ripple: a cognitive biomarker for episodic memory and planning. Hippocampus 25, 1073–1188 (2015).
Mizuseki, K., Diba, K., Pastalkova, E. & Buzsáki, G. Hippocampal CA1 pyramidal cells form functionally distinct sublayers. Nat. Neurosci. 14, 1174–1181 (2011).
Masurkar, A. V. et al. Medial and lateral entorhinal cortex differentially excite deep versus superficial CA1 pyramidal neurons. Cell Rep. 18, 148–160 (2017).
Leland, M., John, H. & James, M. UMAP: uniform manifold approximation and projection for dimension reduction. Preprint at https://doi.org/10.48550/arXiv.1802.03426 (2020).
Harris, K. D., Csicsvari, J., Hirase, H., Dragoi, G. & Buzsáki, G. Organization of cell assemblies in the hippocampus. Nature 424, 552–556 (2003).
Grosmark, A. D. & Buzsáki, G. Diversity in neural firing dynamics supports both rigid and learned hippocampal sequences. Science 351, 1440–1443 (2016).
Skaggs, W. E. & McNaughton, B. L. Replay of neuronal firing sequences in rat hippocampus during sleep following spatial experience. Science 271, 1870–1873 (1996).
Wilson, M. A. & McNaughton, B. L. Reactivation of hippocampal ensemble memories during sleep. Science 265, 676–679 (1994).
Yang, W. et al. Selection of experience for memory by hippocampal sharp wave ripples. Science 383, 1478–1483 (2024).
Gillespie, A. K. et al. Hippocampal replay reflects specific past experiences rather than a plan for subsequent choice. Neuron 109, 3149–3163 (2021).
Denovellis, E. L. et al. Hippocampal replay of experience at real-world speeds. eLife 10, e64505 (2021).
Mallory, C. S., Widloski, J. & Foster, D. J. The time course and organization of hippocampal replay. Science 387, 541–548 (2025).
Berners-Lee, A. et al. Hippocampal replays appear after a single experience and incorporate greater detail with more experience. Neuron 110, 1829–1842 (2022).
McClelland, J. L., McNaughton, B. L. & O’Reilly, R. C. Why there are complementary learning systems in the hippocampus and neocortex: insights from the successes and failures of connectionist models of learning and memory. Psychol. Rev. 102, 419–457 (1995).
Kim, J., Joshi, A., Frank, L. & Ganguly, K. Cortical-hippocampal coupling during manifold exploration in motor cortex. Nature 613, 103–110 (2023).
Auger, S. D., Zeidman, P. & Maguire, E. A. A central role for the retrosplenial cortex in de novo environmental learning. eLife 4, e09031 (2015).
Alexander, A. S. & Nitz, D. A. Retrosplenial cortex maps the conjunction of internal and external spaces. Nat. Neurosci. 18, 1143–1151 (2015).
Mankin, E. A. et al. Neuronal code for extended time in the hippocampus. Proc. Natl Acad. Sci. USA 109, 19462–19467 (2012).
Swanson, R. A. et al. Topography of putative bi-directional interaction between hippocampal sharp-wave ripples and neocortical slow oscillations. Neuron 113, 754–768 (2025).
Lee, J. S., Briguglio, J. J., Cohen, J. D., Romani, S. & Lee, A. K. The statistical structure of the hippocampal code for space as a function of time, context, and value. Cell 183, 620–635 (2020).
Olshausen, B. A. & Field, D. J. Emergence of simple-cell receptive field properties by learning a sparse code for natural images. Nature 381, 607–609 (1996).
El-Gaby, M. et al. An emergent neural coactivity code for dynamic memory. Nat. Neurosci. 24, 694–704 (2021).
Churchland, M. M. & Shenoy, K. V. Preparatory activity and the expansive null-space. Nat. Rev. Neurosci. 25, 213–236 (2024).
Huszár, R., Zhang, Y., Blockus, H. & Buzsáki, G. Preconfigured dynamics in the hippocampus are guided by embryonic birthdate and rate of neurogenesis. Nat. Neurosci. 25, 1201–1212 (2022).
Soltesz, I. & Losonczy, A. CA1 pyramidal cell diversity enabling parallel information processing in the hippocampus. Nat. Neurosci. 21, 484–493 (2018).
Geiller, T., Fattahi, M., Choi, J.-S. & Royer, S. Place cells are more strongly tied to landmarks in deep than in superficial CA1. Nat. Commun. 8, 14531 (2017).
Valero, M. et al. Determinants of different deep and superficial CA1 pyramidal cell dynamics during sharp-wave ripples. Nat. Neurosci. 18, 1281–1290 (2015).
Lee, S.-H. et al. Parvalbumin-positive basket cells differentiate among hippocampal pyramidal cells. Neuron 82, 1129–1144 (2014).
Danielson, N. B. et al. Sublayer-specific coding dynamics during spatial navigation and learning in hippocampal area CA1. Neuron 91, 652–665 (2016).
Sharif, F., Tayebi, B., Buzsáki, G., Royer, S. & Fernandez-Ruiz, A. Subcircuits of deep and superficial CA1 place cells support efficient spatial coding across heterogeneous environments. Neuron 109, 363–376 (2021).
Hunt, D. L., Linaro, D., Si, B., Romani, S. & Spruston, N. A novel pyramidal cell type promotes sharp-wave synchronization in the hippocampus. Nat. Neurosci. 21, 985–995 (2018).
Zheng, Z. et al. Connectomic reconstruction from hippocampal CA3 reveals spatially graded mossy fiber inputs and selective feedforward inhibition to pyramidal cells. Preprint at bioRxiv https://doi.org/10.1101/2025.07.09.663979 (2025).
Watson, J. F. et al. Human hippocampal CA3 uses specific functional connectivity rules for efficient associative memory. Cell 188, 501–514 (2025).
Peng, Y., Barreda Tomás, F. J., Klisch, C., Vida, I. & Geiger, J. R. P. Layer-specific organization of local excitatory and inhibitory synaptic connectivity in the rat presubiculum. Cereb. Cortex 27, 2435–2452 (2017).
Peng, Y. et al. Directed and acyclic synaptic connectivity in the human layer 2-3 cortical microcircuit. Science 384, 338–343 (2024).
Mishkin, M., Ungerleider, L. G. & Macko, K. A. Object vision and spatial vision: two cortical pathways. Trends Neurosci. 6, 414–417 (1983).
Eichenbaum, H. Time cells in the hippocampus: a new dimension for mapping memories. Nat. Rev. Neurosci. 15, 732–744 (2014).
Leutgeb, J. K., Leutgeb, S., Moser, M.-B. & Moser, E. I. Pattern separation in the dentate gyrus and CA3 of the hippocampus. Science 315, 961–966 (2007).
Fernández-Ruiz, A. et al. Gamma rhythm communication between entorhinal cortex and dentate gyrus neuronal assemblies. Science 372, eabf3119 (2021).
Harvey, R. E., Robinson, H. L., Liu, C., Oliva, A. & Fernandez-Ruiz, A. Hippocampo-cortical circuits for selective memory encoding, routing, and replay. Neuron 111, 2076–2090 (2023).
Vöröslakos, M., Petersen, P. C., Vöröslakos, B. & Buzsáki, G. Metal microdrive and head cap system for silicon probe recovery in freely moving rodent. eLife 10, e65859 (2021).
Angotzi, G. N. et al. Multi-shank 1024 channels active SiNAPS probe for large multi-regional topographical electrophysiological mapping of neural dynamics. Adv. Sci. 12, e2416239 (2025).
Osborne, J. E. & Dudman, J. T. RIVETS: a mechanical system for in vivo and in vitro electrophysiology and imaging. PLoS ONE 9, e89007 (2014).
Steinmetz, N. A. et al. Neuropixels 2.0: a miniaturized high-density probe for stable, long-term brain recordings. Science 372, eabf4588 (2021).
Vöröslakos, M. et al. 3D-printed recoverable microdrive and base plate system for rodent electrophysiology. Bio Protoc. 11, e4137 (2021).
Siegle, J. H. et al. Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology. J. Neural Eng. 14, 045003 (2017).
Mathis, A. et al. DeepLabCut: markerless pose estimation of user-defined body parts with deep learning. Nat. Neurosci. 21, 1281–1289 (2018).
Karadas, M., Gill, J. V., Ceballo, S., Shoham, S. & Rinberg, D. Rapid temporal processing in the olfactory bulb underlies concentration-invariant odor identification and signal decorrelation. Nat. Neurosci. https://doi.org/10.1038/s41593-026-02250-y (2026).
Siegle, J. H. et al. Survey of spiking in the mouse visual system reveals functional hierarchy. Nature 592, 86–92 (2021).
Pachitariu, M., Sridhar, S., Pennington, J. & Stringer, C. Spike sorting with Kilosort4. Nat. Methods 21, 914–921 (2024).
Petersen, P. C., Siegle, J. H., Steinmetz, N. A., Mahallati, S. & Buzsáki, G. CellExplorer: a framework for visualizing and characterizing single neurons. Neuron 109, 3594–3608 (2021).
Watson, B. O., Levenstein, D., Greene, J. P., Gelinas, J. N. & Buzsáki, G. Network homeostasis and state dynamics of neocortical sleep. Neuron 90, 839–852 (2016).
Gonzalez, J., Torterolo, P. & Tort, A. B. L. Mechanisms and functions of respiration-driven gamma oscillations in the primary olfactory cortex. eLife 12, e83044 (2023).
Csicsvari, J., Jamieson, B., Wise, K. D. & Buzsáki, G. Mechanisms of gamma oscillations in the hippocampus of the behaving rat. Neuron 37, 311–322 (2003).
Gonzalez, J., Torterolo, P., Bolding, K. A. & Tort, A. B. L. Communication subspace dynamics of the canonical olfactory pathway. iScience 27, 111275 (2024).
Hill, D. N., Mehta, S. B. & Kleinfeld, D. Quality metrics to accompany spike sorting of extracellular signals. J. Neurosci. 31, 8699–8705 (2011).
Semedo, J. D. et al. Feedforward and feedback interactions between visual cortical areas use different population activity patterns. Nat. Commun. 13, 1099 (2022).
Veuthey, T. L., Derosier, K., Kondapavulur, S. & Ganguly, K. Single-trial cross-area neural population dynamics during long-term skill learning. Nat. Commun. 11, 4057 (2020).
Wainwright, M. J. High-Dimensional Statistics: A Non-asymptotic Viewpoint (Cambridge Univ. Press, 2019).
González, J. et al. Low frequency oscillations drive EEG’s complexity changes during wakefulness and sleep. Neuroscience 494, 1–11 (2022).
Zutshi, I. et al. Hippocampal neuronal activity is aligned with action plans. Nature 639, 153–161 (2025).
Sebastian, E. R., Esparza, J. & M de la Prida, L. Quantifying the distribution of feature values over data represented in arbitrary dimensional spaces. PLoS Comput. Biol. 20, e1011768 (2024).
Davidson, T. J., Kloosterman, F. & Wilson, M. A. Hippocampal replay of extended experience. Neuron 63, 497–507 (2009).
Pfeiffer, B. E. & Foster, D. J. Hippocampal place-cell sequences depict future paths to remembered goals. Nature 497, 74–79 (2013).
English, D. F. et al. Pyramidal cell-interneuron circuit architecture and dynamics in hippocampal networks. Neuron 96, 505–520 (2017).
