---
title: "Suggested further readings"
source: Neuromatch Computational Neuroscience
source_url: https://github.com/NeuromatchAcademy/course-content
licence: CC-BY-4.0
domain: foundations
subdomain: neuromatch-compneuro
date_added: 2026-04-25
---

# Suggested further readings

### Further reading on linear dynamical systems models in neuroscience:

Costa, A. C., Ahamed, T., and Stephens, G. J. (2019). Adaptive, locally linear models of complex dynamics. Proceedings of the National Academy of Sciences 116(5): 1501-1510. doi: [10.1073/pnas.1813476116](https://doi.org/10.1073/pnas.1813476116) {{ open_access }}.

Billeh, Y. N., Cai, B., Gratiy, S. L., Dai, K., Iyer, R., Gouwens, N. W., ... and Arkhipov, A. (2020). Systematic integration of structural and functional data into multi-scale models of mouse primary visual cortex. Neuron 106(3): 388-403. doi: [10.1016/j.neuron.2020.01.040](https://doi.org/10.1016/j.neuron.2020.01.040) {{ open_access }}.

Brunton, B. W., Botvinick, M. M., and Brody, C. D. (2013). Rats and humans can optimally accumulate evidence for decision-making. Science 340(6128): 95-98. doi: [10.1126/science.1233912](https://doi.org/10.1126/science.1233912) {{ closed_access }}.

Brunton, B. W., Johnson, L. A., Ojemann, J. G., and Kutz, J. N. (2016). Extracting spatial–temporal coherent patterns in large-scale neural recordings using dynamic mode decomposition. Journal of neuroscience methods 258: 1-15. doi: [10.1016/j.jneumeth.2015.10.010](https://doi.org/10.1016/j.jneumeth.2015.10.010) {{ open_access }}.

Gilson, M., Burkitt, A. N., Grayden, D. B., Thomas, D. A., and van Hemmen, J. L. (2009). Emergence of network structure due to spike-timing-dependent plasticity in recurrent neuronal networks. I. Input selectivity–strengthening correlated input pathways. Biological cybernetics 101(2): 81-102. doi: [10.1007/s00422-009-0319-4](https://doi.org/10.1007/s00422-009-0319-4) {{ closed_access }}.

Harris, K. D., Aravkin, A., Rao, R., and Brunton, B. W. (2021). Time-Varying Autoregression with Low-Rank Tensors. SIAM Journal on Applied Dynamical Systems 20(4): 2335-2358. doi: [10.1137/20M1338058](https://doi.org/10.1137/20M1338058) {{ closed_access }} (preprint: [arxiv.org/pdf/1905.08389](http://arxiv.org/pdf/1905.08389) {{ open_access }}).

Hodgkin, A. L., and Huxley, A. F. (1952). A quantitative description of membrane current and its application
to conduction and excitation in nerve. The Journal of physiology 117(4): 500–544. doi: [10.1113/jphysiol.1952.sp004764](https://doi.org/10.1113/jphysiol.1952.sp004764) {{ open_access }}.

Hu, Y., Brunton, S. L., Cain, N., Mihalas, S., Kutz, J. N., and Shea-Brown, E. (2018). Feedback through graph motifs relates structure and function in complex networks. Physical Review E 98(6): 062312. doi: [10.1103/physreve.98.062312](https://doi.org/10.1103/physreve.98.062312) {{ open_access }}.

Izhikevich, E.M. (2007). Dynamical Systems in Neuroscience: The Geometry of Excitability and Bursting. MIT Press.

Linderman, S. W., Miller, A. C., Adams, R. P., Blei, D. M., Paninski, L., and Johnson, M. J. (2016). Recurrent switching linear dynamical systems. arXiv preprint. [arXiv:1610.08466](http://arxiv.org/abs/1610.08466).

Mante, V., Sussillo, D., Shenoy, K. V., and Newsome, W. T. (2013). Context-dependent computation by recurrent dynamics in prefrontal cortex. Nature 503(7474): 78-84. doi: [10.1038/nature12742](https://doi.org/10.1038/nature12742) {{ closed_access }} (postprint: [www.ncbi.nlm.nih.gov/pmc/articles/PMC4121670](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4121670) {{ open_access }})

Morrison, K., and Curto, C. (2019). Predicting neural network dynamics via graphical analysis. In: Algebraic and Combinatorial Computational Biology (pp. 241-277). Academic Press. doi: [10.1016/B978-0-12-814066-6.00008-8](https://doi.org/10.1016/B978-0-12-814066-6.00008-8) {{ closed_access }} (preprint: [arxiv.org/pdf/1804.01487](http://arxiv.org/pdf/1804.01487) {{ open_access }}) or [arxiv:1804.01487](http://arxiv.org/abs/1804.01487).

Ocker, G. K., Litwin-Kumar, A., and Doiron, B. (2015). Self-organization of microcircuits in networks of spiking neurons with plastic synapses. PLoS computational biology 11(8): e1004458. doi: [10.1371/journal.pcbi.1004458](https://doi.org/10.1371/journal.pcbi.1004458) {{ open_access }}.

Ocker, G. K., Josić, K., Shea-Brown, E., and Buice, M. A. (2017). Linking structure and activity in nonlinear spiking networks. PLoS computational biology 13(6): e1005583. doi: [10.1371/journal.pcbi.1005583](https://doi.org/10.1371/journal.pcbi.1005583) {{ open_access }}.

Pillow, J. W., Shlens, J., Paninski, L., Sher, A., Litke, A. M., Chichilnisky, E. J., and Simoncelli, E. P. (2008). Spatio-temporal correlations and visual signalling in a complete neuronal population. Nature 454(7207): 995-999. doi: [10.1038/nature07140](https://doi.org/10.1038/nature07140) {{ closed_access }} (postprint: [europepmc.org/articles/pmc2684455?pdf=render](https://europepmc.org/articles/pmc2684455?pdf=render) {{ open_access }}).

Seung, H. S. (1996). How the brain keeps the eyes still. Proceedings of the National Academy of Sciences 93(23): 13339-13344. doi: [10.1073/pnas.93.23.13339](https://doi.org/10.1073/pnas.93.23.13339) {{ open_access }}.

Usher, M., and McClelland, J. L. (2001). The time course of perceptual choice: the leaky, competing accumulator model. Psychological review 108(3): 550. doi: [10.1037/0033-295X.108.3.550](https://doi.org/10.1037/0033-295X.108.3.550) {{ closed_access }}.

### Further reading from Outro lecture:

Ames, K. C., Ryu, S. I., and Shenoy, K. V. (2019). Simultaneous motor preparation and execution in a last-moment reach correction task. Nature communications 10(1): 1-13. doi: [10.1038/s41467-019-10772-2](https://doi.org/10.1038/s41467-019-10772-2) {{ open_access }}.

Churchland, M. M., Cunningham, J. P., Kaufman, M. T., Foster, J. D., Nuyujukian, P., Ryu, S. I., and Shenoy, K. V. (2012). Neural population dynamics during reaching. Nature 487(7405): 51-56. doi: [10.1038/nature11129](https://doi.org/10.1038/nature11129) {{ closed_access }} (postprint: [europepmc.org/articles/pmc3393826?pdf=render](https://europepmc.org/articles/pmc3393826?pdf=render) {{ open_access }}).

Gilja, V., Pandarinath, C., Blabe, C. H., Nuyujukian, P., Simeral, J. D., Sarma, A. A., ... and Henderson, J. M. (2015). Clinical translation of a high-performance neural prosthesis. Nature medicine 21(10): 1142-1145. doi: [10.1038/nm.3953](https://doi.org/10.1038/nm.3953) {{ closed_access }} (postprint: [europepmc.org/articles/pmc4805425?pdf=render](https://europepmc.org/articles/pmc4805425?pdf=render) {{ open_access }}).

Kao, J. C., Nuyujukian, P., Ryu, S. I., Churchland, M. M., Cunningham, J. P., and Shenoy, K. V. (2015). Single-trial dynamics of motor cortex and their applications to brain-machine interfaces. Nature communications 6(1): 1-12. doi: [10.1038/ncomms8759](https://doi.org/10.1038/ncomms8759) {{ open_access }}.

Kao, J. C., Nuyujukian, P., Ryu, S. I., and Shenoy, K. V. (2016). A high-performance neural prosthesis incorporating discrete state selection with hidden Markov models. IEEE Transactions on Biomedical Engineering: 64(4) 935-945. doi: [10.1109/TBME.2016.2582691](https://doi.org/10.1109/TBME.2016.2582691) {{ closed_access }}.

Nuyujukian, P., Kao, J. C., Ryu, S. I., and Shenoy, K. V. (2016). A nonhuman primate brain–computer typing interface. Proceedings of the IEEE 105(1): 66-72. doi: [10.1109/JPROC.2016.2586967](https://doi.org/10.1109/JPROC.2016.2586967) {{ closed_access }} (postprint: [www.ncbi.nlm.nih.gov/pmc/articles/PMC7970827](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7970827) {{ open_access }}).

Nuyujukian, P., Albites Sanabria, J., Saab, J., Pandarinath, C., Jarosiewicz, B., Blabe, C. H., ... and Henderson, J. M. (2018). Cortical control of a tablet computer by people with paralysis. PloS one 13(11): e0204566. doi: [10.1371/journal.pone.0204566](https://doi.org/10.1371/journal.pone.0204566) {{ open_access }}.

Pandarinath, C., O’Shea, D. J., Collins, J., Jozefowicz, R., Stavisky, S. D., Kao, J. C., ... and Sussillo, D. (2018). Inferring single-trial neural population dynamics using sequential auto-encoders. Nature methods: 15(10) 805-815. doi: [10.1038/s41592-018-0109-9](https://doi.org/10.1038/s41592-018-0109-9) {{ closed_access }} (postprint: [europepmc.org/articles/pmc6380887?pdf=render](https://europepmc.org/articles/pmc6380887?pdf=render) {{ open_access }}).

Pandarinath, C., Nuyujukian, P., Blabe, C. H., Sorice, B. L., Saab, J., Willett, F. R., ... and Henderson, J. M. (2017). High performance communication by people with paralysis using an intracortical brain-computer interface. Elife 6: e18554. doi: [10.7554/eLife.18554](https://doi.org/10.7554/eLife.18554) {{ open_access }}.

Santhanam, G., Yu, B. M., Gilja, V., Ryu, S. I., Afshar, A., Sahani, M., and Shenoy, K. V. (2009). Factor-analysis methods for higher-performance neural prostheses. Journal of neurophysiology 102(2): 1315-1330. doi: [10.1152/jn.00097.2009](https://doi.org/10.1152/jn.00097.2009) {{ open_access }}.

Shenoy, K. V., Sahani, M., and Churchland, M. M. (2013). Cortical control of arm movements: a dynamical systems perspective. Annual review of neuroscience 36: 337-359. doi: [10.1146/annurev-neuro-062111-150509](https://doi.org/10.1146/annurev-neuro-062111-150509) {{ closed_access }}.

Stavisky, S. D., Kao, J. C., Ryu, S. I., and Shenoy, K. V. (2017). Motor cortical visuomotor feedback activity is initially isolated from downstream targets in output-null neural state space dimensions. Neuron 95(1): 195-208. doi: [10.1016/j.neuron.2017.05.023](https://doi.org/10.1016/j.neuron.2017.05.023) {{ open_access }}.

Stavisky, S. D., Willett, F. R., Wilson, G. H., Murphy, B. A., Rezaii, P., Avansino, D. T., ... and Henderson, J. M. (2019). Neural ensemble dynamics in dorsal motor cortex during speech in people with paralysis. Elife 8: e46015. doi: [10.7554/eLife.46015](https://doi.org/10.7554/eLife.46015) {{ open_access }}.

Trautmann, E. M., Stavisky, S. D., Lahiri, S., Ames, K. C., Kaufman, M. T., O’Shea, D. J., ... and Shenoy, K. V. (2019). Accurate estimation of neural population dynamics without spike sorting. Neuron 103(2): 292-308. doi: [10.1016/j.neuron.2019.05.003](https://doi.org/10.1016/j.neuron.2019.05.003) {{ open_access }}.

Vyas, S., Even-Chen, N., Stavisky, S. D., Ryu, S. I., Nuyujukian, P., and Shenoy, K. V. (2018). Neural population dynamics underlying motor learning transfer. Neuron 97(5): 1177-1186. doi: [10.1016/j.neuron.2018.01.040](https://doi.org/10.1016/j.neuron.2018.01.040) {{ open_access }}.

Vyas, S., Golub, M. D., Sussillo, D., and Shenoy, K. V. (2020). Computation through neural population dynamics. Annual Review of Neuroscience 43: 249-275. doi: [10.1146/annurev-neuro-092619-094115](https://doi.org/10.1146/annurev-neuro-092619-094115) {{ closed_access }} (postprint: [www.ncbi.nlm.nih.gov/pmc/articles/PMC7402639](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402639) {{ open_access }}).

Vyas, S., O’Shea, D. J., Ryu, S. I., and Shenoy, K. V. (2020). Causal role of motor preparation during error-driven learning. Neuron 106(2): 329-339. doi: [10.1016/j.neuron.2020.01.019](https://doi.org/10.1016/j.neuron.2020.01.019) {{ open_access }}.

Willett, F. R., Deo, D. R., Avansino, D. T., Rezaii, P., Hochberg, L. R., Henderson, J. M., and Shenoy, K. V. (2020). Hand knob area of premotor cortex represents the whole body in a compositional way. Cell 181(2): 396-409. doi: [10.1016/j.cell.2020.02.043](https://doi.org/10.1016/j.cell.2020.02.043) {{ open_access }}.

Williams, A. H., Kim, T. H., Wang, F., Vyas, S., Ryu, S. I., Shenoy, K. V., ... and Ganguli, S. (2018). Unsupervised discovery of demixed, low-dimensional neural dynamics across multiple timescales through tensor component analysis. Neuron 98(6): 1099-1115. doi: [10.1016/j.neuron.2018.05.015](https://doi.org/10.1016/j.neuron.2018.05.015) {{ open_access }}.

Yu, B. M., Cunningham, J. P., Santhanam, G., Ryu, S., Shenoy, K. V., and Sahani, M. (2008). Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity. Advances in neural information processing systems, 21. url: [NIPS2008](https://proceedings.neurips.cc/paper/2008/hash/ad972f10e0800b49d76fed33a21f6698-Abstract.html).
