Selected Publications

The following publications are a representative sample of recent work central to the Grossman Center mission. For full publication lists, see the pages of individual Center members.

Russo AA, Bittner SR, Perkins SM, Seely JS, London BM, Lara AH, Miri A, Marshall NJ, Kohn A, Jessell TM, Abbott LF, Cunningham JP, Churchland MM (2018). Motor cortex embeds muscle-like commands in an untangled population response. Neuron.
Link

Zhou P et al (2018). Efficient and accurate extraction of in vivo calcium signals from microendoscopic video data. eLife.
Link

Elsayed GF and Cunningham JP (2017). Structure in neural population recordings: an expected byproduct of simpler phenomena? Nature Neuroscience.
Link

Miri A, Warriner CL, Seely JS, Elsayed GF, Cunningham JP, Churchland MM, Jessell TM (2017). Behaviorally selective engagement of short-latency effector pathways by motor cortex. Neuron.
Link

International Brain Lab (2017). An international laboratory for systems and computational neuroscience. Neuron.
Link

Gao Y, Archer E, Paninski L, Cunningham JP (2016) Linear dynamical neural population models through nonlinear embeddings. NIPS.
Link

Elsayed GF, Lara AH, Churchland MM, Cunningham JP (2016). Complete reorganization of population response across linked computations in motor cortex. Nature Communications.
Link

Merel J, Carlson D, Paninski L, Cunningham JP (2016) Neuroprosthetic decoder training as imitation learning. PLOS Computational Biology.
Link

Friedrich, J. et al (2016). Multi-scale approaches for high-speed imaging and analysis of large neural populations. bioRxiv.
Link

Gabitto M., Pakman A., Bikoff J., Abbott L., Jessell T. & Paninski, L. (2016). Bayesian sparse regression analysis reveals the extent of spinal V1 interneuron diversity. Cell.
Link

Pnevmatikakis, E. et al (2016). Simultaneous denoising, deconvolution, and demixing of calcium imaging data. Neuron.
Link

Seely JS, Kaufman MT, Ryu SI, Shenoy KV, Cunningham JP, Churchland MM (2016). Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1. PLoS Comput. Bio.
Link

Cunningham, J.P. and Ghahramani, Z. (2015). Linear dimensionality reduction: survey, insights, and generalizations. Journal of Machine Learning Research.
Link

Machado, T.A., Pnevmatikakis, E., Paninski, L., Jessell, T.M., Miri, A. (2015). Primacy of flexor locomotor pattern revealed by ancestral reversion of motor neuron identity Cell.
Link

Merel J, Pianto DM, Cunningham JP, and Paninski L (2015) Encoder-decoder optimization for brain-computer interfaces. PLOS Computational Biology.
Link

Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV (2015) Incorporating neural population dynamics increases brain-machine interface performance. Nature Communications.
Link

Kaufman MT, Churchland MM, Ryu SI, and Shenoy KV (2015) Vacillation, indecision and hesitation in moment-by-moment decoding of monkey motor cortex. eLife.
Link

Sussillo D, Churchland MM, Kaufman MT, and Shenoy KV (2015) A neural network that finds naturalistic solutions for the production of muscle activity. Nature Neuroscience.
Link

Soudry, D., Keshri, S., Stinson, P., Oh, M.-W., Iyengar, G. & Paninski, L. (2015). Efficient 'shotgun' inference of neural connectivity from highly sub-sampled activity data. PLoS Comp. Bio.
Link

L. Buesing, T. Machado, J.P. Cunningham, and L. Paninski. (2014) Clustered factor analysis of multineuronal spike data. NIPS 27.
Link

Kaufman MT, Churchland MM, Ryu SI, Shenoy KV (2014). Cortical activity in the null space: permitting preparation without movement. Nature Neuroscience.
Link

J.P. Cunningham and B.M. Yu. (2014) Dimensionality reduction for large-scale neural recordings. Nature Neuroscience.
Link

Gilboa E, Saatci Y, Cunningham JP (2014) Scaling multidimensional inference for structured Gaussian Processes, IEEE Transactions on Pattern Analysis and Machine Intelligence, In Press.
Link

Shenoy KV, Sahani M, Churchland MM (2013) Cortical control of arm movements: a dynamical systems perspective. Annual Review of Neuroscience 36:337-359.
Link

Caron, S.J.C, Ruta, V., Abbott, L.F. and Axel, R. (2013) Random Convergence of Afferent Olfactory Inputs in the Drosophila Mushroom Body. Nature 497:113-117.
Link

Shababo, B., Paige, B., Pakman, A. & Paninski, L. (2013). Bayesian inference and online experimental design for mapping neural microcircuits. NIPS.
Link

Pnevmatikakis, E. and Paninski, L. (2013). Sparse nonnegative deconvolution for compressive calcium imaging: algorithms and phase transitions. NIPS.
Link

Ramirez, A. & Paninski, L. (2013). Fast generalized linear model estimation via expected log-likelihoods. J. Comput. Neurosci.
Link

Churchland MM*, Cunningham JP* (contributing equally), Kaufman MT, Nuyujukian P, Foster JD, Ryu SI, and Shenoy KV (2012) Structure of neural population dynamics during reaching. Nature 487: 51-56.
Link

Pillow, J., Ahmadian, Y. & Paninski, L. (2011). Model-based decoding, information estimation, and change-point detection in multi-neuron spike trains. Neural Computation 23: 1-45.
Link

Field, G., Gauthier, J., Sher, A. et al. (2010). Functional connectivity in the retina at the resolution of photoreceptors. Nature 467, 673-677.
Link

« Back to the Grossman Center for the Statistics of Mind main page