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
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