PUBLICATIONS

Sabatini DA, Kaufman MT (2021, preprint). A curved manifold orients rotational dynamics in motor cortex. bioRxiv. [link]

Zhu F, Grier HA, Tandon R, Cai C, Giovannucci A, Kaufman MT*, Pandarinath C* (2021, preprint). A deep learning framework for inference of single-trial neural population activity from calcium imaging with sub-frame temporal resolution. bioRxiv. [link]

Malonis PJ, Hatsopoulos NG, MacLean JN*, Kaufman MT* (2021, preprint). M1 dynamics share similar inputs for initiating and correcting movement. bioRxiv. [link]

Zhu F, Sedler AR, Grier HA, Ahad N, Davenport MA, Kaufman MT, Giovannucci A, Pandarinath C (2021, preprint). Deep inference of latent dynamics with spatio-temporal super-resolution using selective backpropagation through time. arXiv. [link]

Pei F, Ye J, Zoltowski D, Wu A, Chowdhury RH, Sohn H, O'Doherty JE, Shenoy KV, Kaufman MT, Churchland M, Jazayeri M, Miller LE, Pillow J, Park IM, Dyer EL, Pandarinath C (2021, preprint). Neural Latents Benchmark '21: Evaluating latent variable models of neural population activity. arXiv. [link]

Huang L, Kebschull JM, Furth D, Musall S, Kaufman MT, Churchland AK, Zador AM (2020). BRICseq bridges brain-wide interregional connectivity to neural activity and gene expression in single animals. Cell. 182(1):177-88. [link]

Suresh AK, Goodman JM, Okorokova EV, Kaufman MT, Hatsopoulos NG, Bensmaia SJ (2020). Neural population dynamics are different for reach and grasp. eLife. 2020 Nov 17;e58848. [link]

Musall S*, Kaufman MT*, Juavinett AL, Gluf S, Churchland AK (2019). Single-trial neural dynamics are dominated by richly varied movements. Nature Neuroscience. 22, 1677-86. [link]

Trautmann EM, Stavisky SD, Lahiri S, Ames KC, Kaufman MT, O’Shea DJ, Vyas S, Sun X, Ryu SI, Ganguli S, Shenoy KV (2019). Accurate estimation of neural population dynamics without spike sorting. Neuron. 103(2):292-308. [link]

Kaufman MT (2018). Adapting fine with a little help from the null space [Spotlight]. Neuron. 100(4):771-3. [link]

Pandarinath C, O’Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann EM, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo D (2018). Inferring single-trial neural population dynamics using sequential auto-encoders. Nature Methods. 15(10):805-15. [link]

O’Shea DJ*, Kalanithi P*, Ferenczi E, Hsueh B, Chandrasekaran C, Goo W, Diester I, Ramakrishnan C, Kaufman MT, Ryu SI, Yeom KW, Deisseroth K**, Shenoy KV** (2018). Development of an optogenetic toolkit for neural circuit dissection in squirrel monkeys. Scientific Reports. 8(1):6775. [link]

Giovannucci A, Friedrich J, Kaufman M, Churchland AK, Chklovskii D, Paninski L, Pnevmatikakis EA (2017). OnACID: Online Analysis of Calcium Imaging Data in Real Time. Advances in Neural Information Processing Systems 30 (NIPS 2017). [link]

Omrani M, Kaufman MT, Hatsopoulos NG, Cheney PD (2017). Perspectives on classical controversies about the motor cortex. Journal of Neurophysiology. [link]

Licata AM, Kaufman MT, Raposo D, Ryan MB, Sheppard JP, Churchland AK (2017). Posterior parietal cortex guides visual decisions in rats. Journal of Neuroscience, 37(19):4954-66. [link]

Kaufman MT, Seely JS, Sussillo D, Ryu SI, Shenoy KV, Churchland MM (2016). The largest response component in motor cortex reflects movement timing but not movement type. eNeuro, 3(4): ENEURO.0085-16.2016. [link]

Kaufman MT, Churchland AK (2016). Many paths from state to state (News and Views). Nature Neuroscience, 19(12):1541-2. [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 Computational Biology, 12(11):e1005164. [link]

Elsayed GF, Lara AH, Kaufman MT, Churchland MM, Cunningham JP (2016). Complete reorganization of the population response across linked computations in motor cortex. Nature Communications, 7:13239. [link]

Kaufman MT, Churchland MM, Ryu SI, Shenoy KV (2015). Vacillation, indecision and hesitation in moment-by-moment decoding of monkey motor cortex. eLife, 2015;4:e04677. [link] [Stanford press release] [F1000 recommendation summary] [IFLScience article]

Sussillo D, Churchland MM, Kaufman MT, Shenoy KV (2015). A neural network that finds a naturalistic solution for the production of muscle activity. Nature Neuroscience, 18(7):1025-33. [link]

Raposo D*, Kaufman MT*, Churchland AK (2014). A category-free neural population supports evolving demands during decision making. Nature Neuroscience, 17(12):1784-92. [link] [CSHL press release]

Kaufman MT, Churchland MM, Ryu SI, Shenoy KV (2014). Cortical activity in the null space: permitting preparation without movement. Nature Neuroscience, 17(3):440-8. [link] [News and Views] [Stanford press release]

Kaufman MT, Churchland MM, Shenoy KV (2013). The roles of monkey M1 neuron classes in movement preparation and execution. Journal of Neurophysiology, 110:817-25. [link]

Kaufman MT, Churchland AK (2013). Cognitive neuroscience: sensory noise drives bad decisions (News and Views). Nature, 496(7444):172-3. [link]

Cowley BR, Kaufman MT, Butler ZS, Churchland MM, Ryu SI, Shenoy KV, Yu BM (2013). DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural activity. Journal of Neural Engineering, 10:066012. [link]

Gilja V, Nuyujukian P, Chestek CA, Cunningham JP, Yu BM, Fan J, Churchland MM, Kaufman MT, Ryu SI, Shenoy KV (2012). A high-performance neural prosthesis enabled by control algorithm design. Nature Neuroscience, 15:1752-1757. [link] [Stanford press release]

Churchland MM*, Cunningham JP*, Kaufman MT, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV (2012). Neural population dynamics during reaching. Nature, 487:51-56. [link] [Stanford press release] [F1000 recommendation summary]

Diester I, Kaufman MT, Mogri M, Pashaie R, Goo W, Yizhar O, Ramakrishnan C, Deisseroth K, Shenoy KV (2011). An optogenetic toolbox designed for primates. Nature Neuroscience, 14(3):387-97. [link]

Chestek CA, Gilja V, Nuyujukian P, Foster JD, Fan JM, Kaufman MT, Churchland MM, Rivera-Alvidrez Z, Cunningham JP, Ryu SI, Shenoy KV (2011). Long-term stability of neural prosthetic control signals from silicon cortical arrays in rhesus macaque motor cortex. Journal of Neural Engineering. [link]

Shenoy KV, Kaufman MT, Sahani M, Churchland MM (2011). A dynamical systems view of motor preparation: Implications for neural prosthetic system design. Chapter in Progress in Brain Research: Enhancing Performance for Action and Perception, edited by Green A, Chapman E, Kalaska JF, Lepore F. Vol. 190. Elsevier. [link]

Kaufman MT, Churchland MM, Santhanam G, Yu BM, Afshar A, Ryu SI, Shenoy KV (2010). The roles of monkey premotor neuron classes in movement preparation and execution. Journal of Neurophysiology, 104:799-810. [link]

Churchland MM, Cunningham JP, Kaufman MT, Ryu SI, Shenoy KV (2010). Cortical preparatory activity: Representation of movement or first cog in a dynamical machine? Neuron, 68:387-400. [link]

Knutson B, Taylor J, Kaufman M, Peterson R, Glover G (2005). What do you expect?: fMRI of Expected Utility. Journal of Neuroscience, 25(19): 4806-12. [link]