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John Patrick Cunningham, Phd - Publications

Affiliations: 
Electrical Engineering Stanford University, Palo Alto, CA 
 Columbia University, New York, NY 
Area:
Computation and Theory, Theoretical Neuroscience, Cognitive/Systems Neuroscience, statistical Machine Learning, Motor Systems
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50 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Biderman D, Whiteway MR, Hurwitz C, Greenspan N, Lee RS, Vishnubhotla A, Warren R, Pedraja F, Noone D, Schartner M, Huntenburg JM, Khanal A, Meijer GT, Noel JP, Pan-Vazquez A, ... ... Cunningham JP, et al. Lightning Pose: improved animal pose estimation via semi-supervised learning, Bayesian ensembling, and cloud-native open-source tools. Biorxiv : the Preprint Server For Biology. PMID 37162966 DOI: 10.1101/2023.04.28.538703  0.557
2022 Marshall NJ, Glaser JI, Trautmann EM, Amematsro EA, Perkins SM, Shadlen MN, Abbott LF, Cunningham JP, Churchland MM. Flexible neural control of motor units. Nature Neuroscience. PMID 36216998 DOI: 10.1038/s41593-022-01165-8  0.807
2022 Abe T, Kinsella I, Saxena S, Buchanan EK, Couto J, Briggs J, Kitt SL, Glassman R, Zhou J, Paninski L, Cunningham JP. Neuroscience Cloud Analysis As a Service: An open-source platform for scalable, reproducible data analysis. Neuron. PMID 35870448 DOI: 10.1016/j.neuron.2022.06.018  0.482
2022 Saxena S, Russo AA, Cunningham J, Churchland MM. Motor cortex activity across movement speeds is predicted by network-level strategies for generating muscle activity. Elife. 11. PMID 35621264 DOI: 10.7554/eLife.67620  0.68
2021 Whiteway MR, Biderman D, Friedman Y, Dipoppa M, Buchanan EK, Wu A, Zhou J, Bonacchi N, Miska NJ, Noel JP, Rodriguez E, Schartner M, Socha K, Urai AE, Salzman CD, ... ... Cunningham JP, et al. Partitioning variability in animal behavioral videos using semi-supervised variational autoencoders. Plos Computational Biology. 17: e1009439. PMID 34550974 DOI: 10.1371/journal.pcbi.1009439  0.545
2021 Couto J, Musall S, Sun XR, Khanal A, Gluf S, Saxena S, Kinsella I, Abe T, Cunningham JP, Paninski L, Churchland AK. Chronic, cortex-wide imaging of specific cell populations during behavior. Nature Protocols. PMID 34075229 DOI: 10.1038/s41596-021-00527-z  0.568
2020 Kimmel DL, Elsayed GF, Cunningham JP, Newsome WT. Value and choice as separable and stable representations in orbitofrontal cortex. Nature Communications. 11: 3466. PMID 32651373 DOI: 10.1038/S41467-020-17058-Y  0.351
2020 Russo AA, Khajeh R, Bittner SR, Perkins SM, Cunningham JP, Abbott LF, Churchland MM. Neural Trajectories in the Supplementary Motor Area and Motor Cortex Exhibit Distinct Geometries, Compatible with Different Classes of Computation. Neuron. PMID 32516573 DOI: 10.1016/J.Neuron.2020.05.020  0.72
2020 Saxena S, Kinsella I, Musall S, Kim SH, Meszaros J, Thibodeaux DN, Kim C, Cunningham J, Hillman EMC, Churchland A, Paninski L. Localized semi-nonnegative matrix factorization (LocaNMF) of widefield calcium imaging data. Plos Computational Biology. 16: e1007791. PMID 32282806 DOI: 10.1371/Journal.Pcbi.1007791  0.577
2019 Najafi F, Elsayed GF, Cao R, Pnevmatikakis E, Latham PE, Cunningham JP, Churchland AK. Excitatory and Inhibitory Subnetworks Are Equally Selective during Decision-Making and Emerge Simultaneously during Learning. Neuron. PMID 31753580 DOI: 10.1016/J.Neuron.2019.09.045  0.583
2019 Saxena S, Cunningham JP. Towards the neural population doctrine. Current Opinion in Neurobiology. 55: 103-111. PMID 30877963 DOI: 10.1016/J.Conb.2019.02.002  0.405
2018 Lara AH, Elsayed GF, Zimnik AJ, Cunningham JP, Churchland MM. Conservation of preparatory neural events in monkey motor cortex regardless of how movement is initiated. Elife. 7. PMID 30132759 DOI: 10.7554/Elife.31826  0.711
2018 Lara AH, Cunningham JP, Churchland MM. Different population dynamics in the supplementary motor area and motor cortex during reaching. Nature Communications. 9: 2754. PMID 30013188 DOI: 10.1038/s41467-018-05146-z  0.697
2018 Paninski L, Cunningham JP. Neural data science: accelerating the experiment-analysis-theory cycle in large-scale neuroscience. Current Opinion in Neurobiology. 50: 232-241. PMID 29738986 DOI: 10.1016/J.Conb.2018.04.007  0.64
2018 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. Motor Cortex Embeds Muscle-like Commands in an Untangled Population Response. Neuron. PMID 29398358 DOI: 10.1016/J.Neuron.2018.01.004  0.698
2017 Mena GE, Grosberg LE, Madugula S, Hottowy P, Litke A, Cunningham J, Chichilnisky EJ, Paninski L. Electrical stimulus artifact cancellation and neural spike detection on large multi-electrode arrays. Plos Computational Biology. 13: e1005842. PMID 29131818 DOI: 10.1371/Journal.Pcbi.1005842  0.629
2017 Elsayed GF, Cunningham JP. Structure in neural population recordings: an expected byproduct of simpler phenomena? Nature Neuroscience. PMID 28783140 DOI: 10.1038/Nn.4617  0.381
2017 Miri A, Warriner CL, Seely JS, Elsayed GF, Cunningham JP, Churchland MM, Jessell TM. Behaviorally Selective Engagement of Short-Latency Effector Pathways by Motor Cortex. Neuron. PMID 28735748 DOI: 10.1016/J.Neuron.2017.06.042  0.702
2017 Mandt S, Wenzel F, Nakajima S, Cunningham J, Lippert C, Kloft M. Sparse probit linear mixed model Machine Learning. 106: 1621-1642. DOI: 10.1007/S10994-017-5652-6  0.312
2016 Seely JS, Kaufman MT, Ryu SI, Shenoy KV, Cunningham JP, Churchland MM. Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1. Plos Computational Biology. 12: e1005164. PMID 27814353 DOI: 10.1371/Journal.Pcbi.1005164  0.782
2016 Elsayed GF, Lara AH, Kaufman MT, Churchland MM, Cunningham JP. Reorganization between preparatory and movement population responses in motor cortex. Nature Communications. 7: 13239. PMID 27807345 DOI: 10.1038/Ncomms13239  0.799
2016 Merel J, Carlson D, Paninski L, Cunningham JP. Neuroprosthetic Decoder Training as Imitation Learning. Plos Computational Biology. 12: e1004948. PMID 27191387 DOI: 10.1371/Journal.Pcbi.1004948  0.607
2015 Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV. Single-trial dynamics of motor cortex and their applications to brain-machine interfaces. Nature Communications. 6: 7759. PMID 26220660 DOI: 10.1038/Ncomms8759  0.812
2015 Merel J, Pianto DM, Cunningham JP, Paninski L. Encoder-decoder optimization for brain-computer interfaces. Plos Computational Biology. 11: e1004288. PMID 26029919 DOI: 10.1371/Journal.Pcbi.1004288  0.591
2015 Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV. Single-trial dynamics of motor cortex and their applications to brain-machine interfaces Nature Communications. 6. DOI: 10.1038/ncomms8759  0.783
2014 Churchland MM, Cunningham JP. A Dynamical Basis Set for Generating Reaches. Cold Spring Harbor Symposia On Quantitative Biology. 79: 67-80. PMID 25851506 DOI: 10.1101/Sqb.2014.79.024703  0.721
2014 Cunningham JP, Yu BM. Dimensionality reduction for large-scale neural recordings. Nature Neuroscience. 17: 1500-9. PMID 25151264 DOI: 10.1038/Nn.3776  0.643
2014 Buesing L, Machado TA, Cunningham JP, Paninski L. Clustered factor analysis of multineuronal spike data Advances in Neural Information Processing Systems. 4: 3500-3508.  0.477
2012 Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Yu BM, Fan JM, Ryu SI, Shenoy KV. A brain machine interface control algorithm designed from a feedback control perspective. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2012: 1318-22. PMID 23366141 DOI: 10.1109/EMBC.2012.6346180  0.775
2012 Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Yu BM, Fan JM, Churchland MM, Kaufman MT, Kao JC, Ryu SI, Shenoy KV. A high-performance neural prosthesis enabled by control algorithm design. Nature Neuroscience. 15: 1752-7. PMID 23160043 DOI: 10.1038/Nn.3265  0.783
2012 Churchland MM, Cunningham JP, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV. Neural population dynamics during reaching. Nature. 487: 51-6. PMID 22722855 DOI: 10.1038/Nature11129  0.807
2012 Zhao M, Batista A, Cunningham JP, Chestek C, Rivera-Alvidrez Z, Kalmar R, Ryu S, Shenoy K, Iyengar S. An L₁-regularized logistic model for detecting short-term neuronal interactions. Journal of Computational Neuroscience. 32: 479-97. PMID 22038503 DOI: 10.1007/S10827-011-0365-5  0.745
2011 Chestek CA, Gilja V, Nuyujukian P, Foster JD, Fan JM, Kaufman MT, Churchland MM, Rivera-Alvidrez Z, Cunningham JP, Ryu SI, Shenoy KV. Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex. Journal of Neural Engineering. 8: 045005. PMID 21775782 DOI: 10.1088/1741-2560/8/4/045005  0.756
2011 Cunningham JP, Nuyujukian P, Gilja V, Chestek CA, Ryu SI, Shenoy KV. A closed-loop human simulator for investigating the role of feedback control in brain-machine interfaces. Journal of Neurophysiology. 105: 1932-49. PMID 20943945 DOI: 10.1152/Jn.00503.2010  0.813
2011 Petreska B, Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M. Dynamical segmentation of single trials from population neural data Advances in Neural Information Processing Systems 24: 25th Annual Conference On Neural Information Processing Systems 2011, Nips 2011.  0.786
2011 MacKe JH, Büsing L, Cunningham JP, Yu BM, Shenoy KV, Sahani M. Empirical models of spiking in neural populations Advances in Neural Information Processing Systems 24: 25th Annual Conference On Neural Information Processing Systems 2011, Nips 2011.  0.75
2010 Churchland MM, Cunningham JP, Kaufman MT, Ryu SI, Shenoy KV. Cortical preparatory activity: representation of movement or first cog in a dynamical machine? Neuron. 68: 387-400. PMID 21040842 DOI: 10.1016/J.Neuron.2010.09.015  0.796
2010 Churchland MM, Yu BM, Cunningham JP, Sugrue LP, Cohen MR, Corrado GS, Newsome WT, Clark AM, Hosseini P, Scott BB, Bradley DC, Smith MA, Kohn A, Movshon JA, Armstrong KM, et al. Stimulus onset quenches neural variability: a widespread cortical phenomenon. Nature Neuroscience. 13: 369-78. PMID 20173745 DOI: 10.1038/Nn.2501  0.794
2009 Chestek CA, Cunningham JP, Gilja V, Nuyujukian P, Ryu SI, Shenoy KV. Neural prosthetic systems: current problems and future directions. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 2009: 3369-75. PMID 19963796 DOI: 10.1109/IEMBS.2009.5332822  0.817
2009 Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M. Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity. Journal of Neurophysiology. 102: 614-35. PMID 19357332 DOI: 10.1152/jn.90941.2008  0.823
2009 Cunningham JP, Gilja V, Ryu SI, Shenoy KV. Methods for estimating neural firing rates, and their application to brain-machine interfaces. Neural Networks : the Official Journal of the International Neural Network Society. 22: 1235-46. PMID 19349143 DOI: 10.1016/J.Neunet.2009.02.004  0.798
2009 Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M. Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity (Journal of Neurophysiology (2009) 102, (614-635) DOI: 10.1152/jn.90941.2008) Journal of Neurophysiology. 102. DOI: 10.1152/jn.z9k-9684-corr.2009  0.792
2009 Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV, Sahani M. Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity Advances in Neural Information Processing Systems 21 - Proceedings of the 2008 Conference.  0.792
2009 Cunningham JP, Yu BM, Shenoy KV, Sahani M. Inferring neural firing rates from spike trains using Gaussian Processes Advances in Neural Information Processing Systems 20 - Proceedings of the 2007 Conference.  0.735
2008 Cunningham JP, Yu BM, Gilja V, Ryu SI, Shenoy KV. Toward optimal target placement for neural prosthetic devices. Journal of Neurophysiology. 100: 3445-57. PMID 18829845 DOI: 10.1152/Jn.90833.2008  0.798
2008 Yu BM, Cunningham JP, Shenoy KV, Sahani M. Neural decoding of movements: From linear to nonlinear trajectory models Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 4984. DOI: 10.1007/978-3-540-69158-7_61  0.741
2008 Cunningham JP, Shenoy KV, Sahani M. Fast Gaussian process methods for point process intensity estimation Proceedings of the 25th International Conference On Machine Learning.  0.579
2007 Chestek CA, Batista AP, Santhanam G, Yu BM, Afshar A, Cunningham JP, Gilja V, Ryu SI, Churchland MM, Shenoy KV. Single-neuron stability during repeated reaching in macaque premotor cortex. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 27: 10742-50. PMID 17913908 DOI: 10.1523/Jneurosci.0959-07.2007  0.803
2006 Shenoy KV, Santhanam G, Ryu SI, Afshar A, Yu BM, Gilja V, Linderman MD, Kalmar RS, Cunningham JP, Kemere CT, Batista AP, Churchland MM, Meng TH. Increasing the performance of cortically-controlled prostheses. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 6652-6. PMID 17959477 DOI: 10.1109/IEMBS.2006.260912  0.775
2006 Cunningham JP, Yu BM, Shenoy KV. Optimal target placement for neural communication prostheses. Conference Proceedings : ... Annual International Conference of the Ieee Engineering in Medicine and Biology Society. Ieee Engineering in Medicine and Biology Society. Annual Conference. 1: 2912-5. PMID 17945745 DOI: 10.1109/IEMBS.2006.259676  0.742
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