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Journal Papers


Dale Chihuly

Preprints.  Not yet peer reviewed.  See GoogleScholar and PubMed.

10. Deo DR, Rezaii P, Hochberg LR,  Okamura AM, Shenoy KV*,  Henderson JM* (2020) Effects of peripheral haptic feedback on Intracortical brain-computer interface control and associated sensory responses in motor cortex. biorXiv. pdf url

9. Willett FR, Avansino DT, Hochberg LR, Henderson JM**, Shenoy KV** (2020) High-performance brain-to-text communication via imagined handwriting. biorXiv. pdf supp-mats.pdf supp-methods.pdf supp-video1.mp4 supp-video2.mp4 supp-video3.mp4 supp-video4.mp4 url 

8. Wilson GH*, Stavisky SD*, Willett FR, Avansino DT, Kelemen JN, Hochberg LR, Henderson JM**, Druckmann S,** Shenoy KV** (2020) Decoding spoken English phonemes from intracortical electrode arrays in dorsal precentral gyrus. biorXiv.  pdf url

7. Rastogi A, Willett FR, Abreu J, Crowder DC, Murphy B, Memberg WD, Vargas-Irwin CE, Miller JP, Sweet J, Walter BL, Rezaii PG, Stavisky SD, Hochberg LR, Shenoy KV, Henderson JM, Kirsch RF, Bolu Ajiboye A (2020) The neural representation of force across grasp types in motor cortex of humans with tetraplegia. bioRxiv. url
6. Sun X, O'Shea DJ, Golub MD, Trautmann EM, Vyas S, Ryu SI, Shenoy KV (2020) Skill-specific changes in cortical preparatory activity during motor learning. bioRxiv. url
5. Simeral JD, Hosman T, Saab J, Flesher SN, Vilela M, Franco B, Kelemen J, Brandman DM, Ciancibello JG, Rezaii PG, Rosler DM, Shenoy KV**, Henderson JM**, Nurmikko AV, Hochberg LR (2019) Home use of a wireless intracortical brain-computer interface by individuals with tetraplegia. MedRxiv. url
4. Trautmann EM*, O'Shea DJ*, Sun X*, Marshel JH, Crow A, Hsueh B, Vesuna S, Cofer L, Bohner G, Allen W, Kauver I, Quirin S, MacDougall M, Chen Y, Whitmire M, Ramakrishnan C, Sahani M, Seidemann E, Ryu SI, Deisseroth K**, Shenoy KV** (2019) Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface. bioRxivpdf url

3. Chandrasekaran C, Soldado-Magraner J, Peixoto D, Newsome WT, Shenoy KV, Sahani M (2018) Brittleness in model selection analysis of single neuron firing rates. bioRxiv url
2. Peixoto D, Kiani R, Chandrasekaran C, Ryu SI, Shenoy KV, Newsome WT (2018) Population dynamics of choice representation in dorsal premotor and primary motor cortex. BioRxiv. pdf url
1. Gao P, Trautmann E, Yu BM, Santhanam G, Ryu SI, Shenoy KV, Ganguli S (2017) A theory of multineuronal dimensionality, dynamics and measurement. bioRxiv. url

Dale Chihuly

Journal Papers.  Peer reviewed.  See also GoogleScholar and PubMed.

127. Tremblay S, Acker L, Afraz A, Albaugh DL, Amita H, Andrei AR, Angelucci A, Aschner A, Balan PF, Basso MA, Benvenuti G, Bohlen MO, Caiola MJ, Calcedo R, Cavanaugh J, Chen Y,  Chen S, Chernov MM, Clark AM, Debes SR, Deisseroth K, Desimone R, Dragoi V, Egger SW, Eldridge M, El-Nahal HG, Fabbrini F, Federer F , Fetsch CR, Fortuna MG, Friedman RM, Fujii N, Gail A, Galvan A, Ghosh S, Gieselmann MA, Gulli RA, Hikosaka O, Hosseini EA, Hu X, Hüer J, Inoue K, Janz R, Jazayeri M, Jiang R, Ju N, Kar K, Klein C, Kohn A, Komatsu M, Maeda K, Martinez-Trujillo JC, Matsumoto M, Maunsell JHR, Mendoza-Halliday D, Monosov IE, Muers RS, Nurminen L, Ortiz-Rios M, O’Shea DJ, Palfi S, Petkov CI, Pojoga S, Rajalingham R, Ramakrishnan C, Remington ED, Revsine C, Roe AW, Sabes PN, Saunders R, Scherberger H, Schmid MC, Schultz W, Seidemann E, Senova Y-S, Shadlen MN, Siu C, Smith Y, Solomon SS, Sommer MA, Spudich JL,  Stauffer WR, Takada M, Tang S, Thiele A, Treue S, Vanduffel W, Vogels R, Whitmire MP, Wichmann T, Wurtz RH, Xu H, Yazdan-Shahmorad A,  Shenoy KV, DiCarlo J, Platt ML (2020) An open resource for non-human primate optogenetics. Neuron. In press.

126. Peixoto D*, Verhein JR*, Kiani R, Kao JC, Nuyujukian P, Chandrasekaran C, Brown J, Fong S, Ryu SI, Shenoy KV, Newsome WT (2020) Decoding and perturbing decision states in real time. Nature. In press. (bioRxiv 2019 url)

125. Jiang X, Saggar H, Ryu SI, Shenoy KV, Kao JC (2020) Structure in neural activity during observed and executed movements is shared at the neural population level, not in single neurons. Cell Reports. 32:108006. pp. 1-14.  pdf supp_mats url
124. Even-Chen N*,  Muratore DG*, Stavisky SD, Hochberg LR, Henderson JM, Murmann B**, Shenoy KV** (2020) Intracortical neural interface design opportunities for an order of magnitude power saving. Nature Biomedical Engineering. pdf supp_mats url
123. Nason SR, Vaskov AK, Willsey MS, Welle EJ, An H, Vu PP, Bullard AJ, Nu CS, Kao JC, Shenoy KV, Jang T, Kim H-S, Blaauw D, Patil PG, CA Chestek (2020) Low-power “spiking band” feature is dominated by local single units and improves brain-machine interface performance. Nature Biomedical Engineering. pdf supp_mats supp_video_1 supp_video_2
122. Vyas S, Golub MD, Sussillo D, Shenoy KV (2020) Computation through neural population dynamics. Annual Review of Neuroscience43:249–275. pdf url  Review Article

121. Willett FR*, Deo DR*, Avansino DT, Rezaii Paymon, Hochberg LR, Henderson JM**, Shenoy KV** (2020) Hand knob area of motor cortex in people with tetraplegia represents the whole body in a compositional way. Cell. 181:396–409. pdf supp_mats url

  • Supplemental video 1. Real-time, discrete neural decoding of attempted movements from among 16 possible directional movements spanning the wrists and ankles (related to Fig. 6).
  • Supplemental video 2. Real-time, discrete neural decoding of attempted movements from among 32 possible movements spanning the hands, arms, feet, and legs from both sides of the body (related to Fig. 6).
120. Vyas S, O’Shea DJ, Ryu SI, Shenoy KV (2020) Causal role of motor preparation during error-driven learning. Neuron. 106:329-339. pdf pdf_supp_mats url
119. Stavisky SD, Willett FR, Avansino DT, Hochberg LR, Shenoy KV**, Henderson JM** (2020) Speech-related dorsal motor cortex activity does not interfere with iBCI cursor control. Journal of Neural Engineering. 17:016049 (13pp). pdf url
118. Rastogi A, Vargas-Irwin C, Willett F, Abreu J, Crowder DC, Murphy B, Memberg W, Miller J, Sweet J, Walter B, Cash S, Rezaii P, Franco B, Saab J, Stavisky SD, Shenoy KV**, Henderson J**, Hochberg LR, Kirsch R, Ajiboye AB (2020) Neural representation of observed, imagined, and attempted grasping force in motor cortex of individuals with chronic tetraplegia. Scientific Reports. 10:1429. pdf url
117. Williams A, Poole B, Maheswaranathan N, Dhawale AK, Fisher T, Wilson CD, Brann DH, Trautmann E, Ryu SI, Shusterman R, Rinberg D, lveczky BPO, Shenoy KV, Ganguli S (2020) Discovering precise temporal patterns in large-scale neural recordings through robust and interpretable time warping, Neuron. 105: 1–14. pdf supp mats url
116. Stavisky SD,  Willett FR, Wilson GH, Murphy BA, Rezaii P, Avansino D, Memberg WD, Miller JP, Kirsch RF, Hochberg LR, Ajiboye AB, Druckmann S, Shenoy KV**, Henderson JM** (2019) Neural ensemble dynamics in dorsal motor cortex during speech in people with paralysis. eLife. 8:e46015. pdf figure-supplements url
115. 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. 103:1-17. pdf supp mats url
Rossi-Pool R, Romo R (2019) Low dimensionality, high robustness in neural population dynamics. Neuron. Preview. 103:177-179. pdf url
114. Ames KC, Ryu SI, Shenoy KV (2019) Simultaneous movement preparation and execution in a last-moment reach correction task. Nature Communications. 10(1):2718. pdf supp mats url
113. Willett FR, Young DR, Murphy BA, Memberg WD, Blabe CH, Pandarinath C, Stavisky SD, Rezaii P, Saab J, Walter BL, Sweet JA, Miller JP, Henderson JM, Shenoy KV, Simeral J, Jarosiewicz B, Hochberg LR, Kirsch RF, Ajiboye AB (2019) Principled BCI decoder design and parameter selection using a feedback control model. Scientific Reports. 9(1):8881. pdf supp mats url
112. Milekovic T, Bacher D, Sarma A, Simeral J, Saab J, Pandarinath C, Yvert B, Sorice B, Blabe C, Oakley E, Tringale K, Eskandar E, Cash S, Shenoy KV, Henderson JM, Hochberg LR, Donoghue JP (2019) Volitional control of single-electrode high gamma local field potentials (LFPs) by people with paralysis. Journal of Neurophysiology. 121:1428-1450. pdf url
111. Even-Chen N*, Sheffer B*, Vyas S, Ryu SI, Shenoy KV (2019) Structure and variability of delay activity in premotor cortex. PLoS Computational Biology. 15(2): e1006808. pdf url
110. Wang M*, Montanede C*, Chandrasekaran C, Peixoto D, Shenoy KV** & Kalaska JF** (2019) Macaque dorsal premotor cortex exhibits decision-related activity only when specific stimulus-response associations are known. Nature Communications10:1793 pdf supp mats url
109. Chandrasekaran C*, Bray IE*, Shenoy KV (2019) Frequency shifts and depth dependence of premotor beta band activity during perceptual decision-making. Journal of Neuroscience39:1420-1435. pdf url
108. Young D, Willett F, Memberg W, Murphy B, Rezaii P, Walter B, Sweet J, Miller J, Shenoy KV, Hochberg LR, Kirsch R, Ajiboye AB (2019) Closed-loop cortical control of virtual reach and posture using cartesian and joint velocity commands. Journal of Neural Engineering. 16:026011 (14pp). pdf url
107. Nuyujukian P*, Sanabria JA*, Saab J*, Pandarinath C, Jarosiewicz B, Blabe C, Franco B, Mernoff ST, Eskandar EN, Simeral JD, Hochberg LR**, Shenoy KV**, Henderson JM** (2018) Cortical control of a tablet computer by people with paralysis. PLoS One. 13:e0204566 pdf url-with-all-movies
106. Stavisky SD, Kao JC, Nuyujukian P, Pandarinath C, Blabe C, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV (2018) Brain-machine interface cursor position only weakly affects monkey and human motor cortical activity in the absence of arm movements. Scientific Reports.8:1635.7pdf url
105. 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.15:805-815. pdf url
Batista AP, DiCarlo JJ (2018) Deep learning reaches the motor system. Nature Methods. News & Views. 15:772-773. pdf
Seminar talk on LFADS by David Sussillo, Simons Institute for the Theory of Computing meeting, UC Berkeley, 3/22/18. video
104. Williams AH, Kim TH, Wang F, Vyas S, Ryu SI, Shenoy KV, Schnitzer M, Kolda TG, Ganguli S (2018) Unsupervised discovery of demixed, low-dimensional neural dynamics across multiple timescales through tensor components analysis. Neuron.98:1-17 pdf url
103. Milekovic T, Sarma A, Bacher D, Simeral J, Saab J, Pandarinath C, Sorice B, Blabe C, Oakley E, Tringale K, Eskandar E, Cash S, Henderson JM, Shenoy KV, Donoghue JP, Hochberg LR (2018) Stable long-term BCI-enabled communication in ALS and locked-in syndrome using LFP signals. Journal of Neurophysiology. 120:343-360. pdf url
102. 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. 8:1-20. pdf url
101. Vyas S, Even-Chen N, Stavisky SD, Ryu SI,  Nuyujukian P, Shenoy KV (2018) Neural population dynamics underlying motor learning transfer. Neuron. 97: 1-10. pdf supp mats url
​​Preview piece by Natraj N & Ganguly K (2018) Shaping reality through mental rehearsal. Neuron. 97:998-1000pdf url
100. O’Shea DJ, Shenoy KV (2018) ERAASR: An algorithm for removing electrical stimulation artifacts from multielectrode array recordings. Journal of Neural Engineering. 15:026020 (17pp) pdf url github
99. Willett FR, Murphy BA, Young D, Memberg WD, Blabe CH, Pandarinath C, Franco B, Saab J, Walter BL, Sweet JA, Miller JP, Henderson JM, Shenoy KV, Simeral JD, Jarosiewicz B, Hochberg LR, Kirsch RF, Ajiboye AB (2018) A comparison of intention estimation methods for decoder calibration in intracortical brain-computer interfaces. IEEE Transactions in Biomedical Engineering. 65:2066-2078. pdf url
98. Even-Chen N, Stavisky SD, Pandarinath C, Nuyujukian P, Blabe CH, Hochberg LR, Henderson* JM, Shenoy* KV (2018) Feasibility of automatic error detect-and-undo system in human intracortical brain-computer interfaces. IEEE Transactions in Biomedical Engineering. 65:1771-1784. pdf url
97. Brandman D, Hosman T, Saab J, Burkhart M, Shanahan B, Ciancibello J, Sarma A, Milstein D, Vargas-Irwin C, Franco B, Kelemen J, Blabe C, Murphy B, Young D, Willett F, Pandarinath C, Stavisky S, Kirsch R, Walter B, Ajiboye A, Cash S, Eskandar E, Miller J, Sweet J, Shenoy KV, Henderson JM, Jarosiewicz B, Harrison M, Simeral J, Hochberg, LR (2018) Rapid calibration of an intracortical brain computer interface for people with tetraplegia. Journal of Neural Engineering. 15:026007. pdf url
96. Even-Chen N, Stavisky S, Kao J, Ryu SI, Shenoy KV (2017) Augmenting intracortical brain-machine interface with neurally driven error detectors. Journal of Neural Engineering. 14:066007 (16pp). pdf url
95. Chandrasekaran C, Peixoto D, Newsome WT, Shenoy KV (2017) Laminar differences in decision-related neural activity in dorsal premotor cortex. Nature Communications. 8:614. pdf supp mats url
94. Kao JC, Ryu SI, Shenoy KV (2017) Leveraging neural dynamics to extend functional lifetime of brain-machine interfaces. Scientific Reports. 7: 7395:1-16. pdf supp mats movie 1 movie 2 url 
93. Stavisky SD, Kao JC, Ryu SI, Shenoy KV (2017) Motor cortical visuomotor feedback activity is initially isolated from downstream targets in output-null neural state space dimensions. Neuron. 95:195-208. pdf supp mats url
Preview piece by Scott S (2017) Stalling for time: It’s not the magnitude, but the way neurons fire that matters. Neuron. 95:6-8. pdf url
92. Pandarinath C*, Nuyujukian P*, Blabe CH, Sorice B, Saab J, Willett F, Hochberg LR, Shenoy KV**, Henderson JM** (2017) High performance communication by people with paralysis using an intracortical brain-computer interface. eLife. 6:e18554 pdf url-with-all-movies NPTL
91. Willett FR, Murphy B, Memberg W, Blabe C, Pandarinath C, Walter B, Sweet J, Miller J, Henderson JM, Shenoy KV, Hochberg LR, Kirsch R, Ajiboye AB (2017) Signal-independent noise in intracortical brain-computer interfaces causes movement time properties inconsistent with Fitts' law. Journal of Neural Engineering. 14:026010.  pdf
90. Stavisky SD, Kao, JC, Ryu SI, Shenoy KV (2017) Trial-by-trial motor cortical correlates of a rapidly adapting visuomotor internal model. Journal of Neuroscience. 37:1721-1732. pdf
89. Kao JC*, Nuyujukian P*, Ryu SI, Shenoy KV (2017) A high-performance neural prosthesis incorporating discrete state selection with hidden Markov models. IEEE Transactions on Biomedical Engineering. 64:935-945. pdf supp mats
88. Nuyujukian P, Kao JC, Ryu SI, Shenoy KV (2017) A non-human primate brain computer typing interface. Proceedings of the IEEE.105:66-72. video abstract pdf video 1 video 2 video 3
87. Willett F, Pandarinath C, Jarosiewicz B, Murphy B, Memberg W, Blabe C, Saab J, Walter B, Sweet J, Miller J, Henderson J, Shenoy KV, Simeral J, Hochberg LR, Kirsch R, Ajiboye AB. (2017) Feedback control policies employed by people using intracortical brain-computer interfaces. Journal of Neural Engineering. 14:016001 (16pp). pdf
86. O'Shea DJ, Trautmann EM, Chandrasekaran C, Stavisky SD, Kao JC, Sahani M, Ryu SI, Deisseroth K, Shenoy KV (2017) The need for calcium imaging in nonhuman primates: New motor neuroscience and brain-machine interfaces. Experimental Neurology. 287:437-451pdf
85. Sussillo D*, Stavisky SD*, Kao JC*, Ryu SI, Shenoy KV (2016) Making brain-machine interfaces robust to future neural variability. Nature Communications. 7:13749. doi: 10.1038/ncomms13749 pdf supp mats video1 video2 video captions
84. O'Shea DJ, Shenoy KV (2016) The importance of planning in motor learning. Neuron. 92:669-671. pdf  Preview Article
​​Preview piece on Sheahan HR, Franklin DF, Wolpert DM (2016) Motor planning, not execution, separates motor memories. Neuron. 92:772-779. pdf
83. Seely J, 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. doi:10.1371/journal.pcbi.1005164 pdf
82. Kaufman MT, Seely J, Ryu SI, Shenoy KV, Churchland MM (2016) The largest response component in motor cortex reflects movement timing but not movement type. eNeuro. 3(4) e0085-16.2016: 1-25. pdf
81. Jarosiewicz B, Sarma AA, Bacher D, Masse NY, Simeral JD, Sorice B, Oakley EM, Blabe C, Pandarinath C, Gilja V, Cash SS, Eskandar E, Friehs G, Henderson JM, Shenoy KV, Donoghue JP, Hochberg LR (2015) Virtual typing by people with tetraplegia using a self-calibrating intracortical brain-computer interface. Science Translational Medicine. 7:1-10. pdf supp mats movie 1
80. Gilja V*, Pandarinath C*, Blabe CH, Nuyujukian P, Simeral JD, Sarma AA, Sorice BL, Perge JA, Jarosiewicz B, Hochberg LR, Shenoy KV**, Henderson JM** (2015) Clinical translation of a high performance neural prosthesis. Nature Medicine. 21:1142-1145. pdf supp mats video 1 video 2 video 3
79. Adamantidis A, Arber S, Bains JS, Bamberg E, Bonci A, Buzsáki G, Cardin JA, Costa RM, Dan Y, Goda Y, Graybiel AM, Häusser M, Hegemann P, Huguenard JR, Insel TR, Janak PH, Johnston D, Josselyn SA, Koch C, Kreitzer AC, Lüscher C, Malenka RC, Miesenböck G, Nagel G, Roska B, Schnitzer MJ, Shenoy KV, Soltesz I, Sternson SM, Tsien RW, Tsien RY, Turrigiano GG, Tye KM, Wilson RI (2015) Nature Neuroscience. 18:1202-1212. pdf editorial intro
78. Kao JC, Nuyujukian P, Cunningham JP, Churchland MM, Ryu SI, Shenoy KV (2015) Single-trial dynamics of motor cortex and their applications to brain-machine interfaces. Nature Communications. 6:7759. doi: 10.1038/ncomms8759. pdf supp mats movie1
77. Blabe C, Gilja V, Chestek CA, Shenoy KV, Anderson K, Henderson JM (2015) Assessment of brain-machine interfaces from the perspective of people with paralysis. Journal of Neural Engineering. 12:043002. pdf
76. Pandarinath C, Gilja V, Blabe CH, Nuyujukian P, Sarma AA, Sorice BL, Eskandar EN, Hochberg LR, Henderson JM*, Shenoy KV* (2015) Neural population dynamics in human motor cortex during movements in people with ALS. eLife. 4:e07436. pdf video1
75. 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. 18:1025-1033. pdf supp figs supp table
74. Kaufman MT, Churchland MM, Ryu SI, Shenoy KV (2015) Vacillation, indecision and hesitation in moment-by-moment decoding of monkey motor cortex. eLife. 4:e04677.  pdf supp mats video1 video2 video3
73. Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV (2015) A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes. Journal of Neural Engineering. 12:036009. pdf supp mats movie1 movie2 JNE video abstract
72. Christie B, Tat D, Irwin Z, Gilja V, Nuyujukian P, Foster J, Ryu SI, Shenoy KV, Thompson D, Chestek CA (2015) Comparison of spike sorting and thresholding of voltage waveforms for intracortical brain-machine interface performance. Journal of Neural Engineering.12:006019. pdf
71. Nuyujukian P, Fan JM, Kao JC, Ryu SI, Shenoy KV (2015) A high-performance keyboard neural prosthesis enabled by task optimization. IEEE Transactions on Biomedical Engineering. 62:21-29. pdf
70. Nuyujukian P, Kao JC, Fan J, Stavisky S, Ryu SI, Shenoy KV (2014) Performance sustaining intracortical neural prostheses. Journal of Neural Engineering. 11:066003. pdf supp mats JNE video abstract
69. Foster JD, Nuyujukian P, Freifeld O, Gao H, Walker R, Ryu SI, Meng TH, Murmann B, Black MJ, Shenoy KV (2014) A freely-moving monkey treadmill model. Journal of Neural Engineering. 11:046020. pdf supp mats JNE video abstract
68. Bishop WE, Chestek CA, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Yu BM (2014) Self-recalibrating classifiers for intracortical brain computer interfaces. Journal of Neural Engineering. 11:026001. pdf
67. Kaufman MT, Churchland MM, Ryu SI, Shenoy KV (2014) Cortical activity in the null space: permitting preparation without movement. Nature Neuroscience. 17:440-448. pdf supp mats
Sanger TD, Kalaska JF (2014) News & Views: "Crouching Tiger, Hidden Dimensions." Nature Neurocience. 17:338-340. pdf
66. Ames KC, Ryu SI, Shenoy KV (2014) Neural dynamics of reaching following incorrect or absent motor preparation. Neuron. 81:438-451. pdf supp mats movie1 movie2 movie3
65. Fan JM, Nuyujukian P, Kao JC, Chestek CA, Ryu SI, Shenoy KV (2014) Intention estimation in brain-machine interfaces. Journal of Neural Engineering. 11:016004. pdf
64. Shenoy KV, Carmena JM (2014) Combining decoder design and neural adaptation in brain-machine interfaces. Neuron. 84:665-680. pdf
​​Video abstract by Neuron: "Shenoy and Carmena introduce the concept of a brain-machine interface, how to desigin a decoder algorithm to convert neural activity into prosthetic control signals, and how to engage neural adaptation and plasticity. Combining decoder design and neural adaptation may lead to better BMI performance, robustness, and generalization." 
63. Kao JC, Stavisky SD, Sussillo D, Nuyujukian P, Shenoy KV (2014) Information systems opportunities in brain-machine interface decoders. Proceedings of the IEEE. 102:666-682. pdf  Review Article
62. Shenoy KV (2014) Prostheses: hopes & hurdles. Cell. Voices article on "Studying circuits with therapy in mind," by Shenoy KV, Mayberg H, Brown P, Delp S, Nirenberg S, Walsh V, Shannon RV. 156:861-863. pdf  Review Article
61. Mante V*, Sussillo D*, Shenoy KV, Newsome WT (2013) Context-dependent computation by recurrent dynamics in prefrontal cortex. Nature. 503:78-84. pdf supp mats
Erlich JC, Brody CD (2013) News & Views: "What to do and how." Nature. 503:45-47. pdf
60. 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. pdf
59. Kaufman MT, Churchland MM, Shenoy KV (2013) The roles of monkey M1 neuron classes in movement preparation and execution. Journal of Neurophysiology. 110:817-825. pdf
58. Ozden I, Wang J, Lu Y, May T, Lee J, Goo W, O’Shea DJ, Kalanithi P, Diester I, Diagne M, Deisseroth K, Shenoy KV, Nurmikko AV (2013) A Coaxial Optrode As Multifunction Write-Read Probe for Optogenetic Studies in Non-Human Primates. Journal of Neuroscience Methods. 291:142-154. pdf
57. Dethier J*, Nuyujukian P*, Ryu SI, Shenoy KV, Boahen K (2013) Design and validation of a real-time spiking-neural-network decoder for brain-machine interfaces. Journal of Neural Engineering. 10:036008 (12pp). pdf
56. Chestek CA, Gilja V, Blabe CH, Foster BL, Shenoy KV, Parvizi J, Henderson JM (2013) Hand posture classification using electrocorticography signals in the gamma band over human sensorimotor brain areas. Journal of Neural Engineering. 10:02602 (11pp). pdf
55. Shenoy KV, Sahani M, Churchland MM (2013) Cortical control of arm movements: A dynamical systems perspective. Annual Review of Neuroscience. 36:337-359. pdf  Review Article
54. Gilja V*, Nuyujukian P*, Chestek CA, Cunningham JP, Yu BM, Fan JM, Churchland MM, Kaufman MT, Kao JC, Ryu SI, Shenoy KV (2012) A high-performance neural prosthesis enabled by control algorithm design. Nature Neuroscience. 15:1752-1757. pdf supp matsmovie 1 movie 2 movie 3 movie 4 movie 5 movie 6
53. Churchland MM*, Cunningham JP*, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV (2012) Neural population dynamics during reaching. Nature. 487:51-56. pdf supp mats movie 1 movie 2 movie 3 movie 4 movie 5
52. Gao H, Walker RM, Nuyujukian P, Makinwa KAA, Shenoy KV, Murmann B, Meng TH (2012) HermesE: A 96-channel full data rate direct neural interface in 0.13 um CMOS. IEEE Journal of Solid State Circuits. 47:1043-1054. pdf
51. Zhao M, Batista AP, Cunningham JP, Chestek CA, Rivera-Alvidrez Z, Kalmar R, Ryu SI, Shenoy KV, Iyengar S (2012) An L1-regularized logistic model for detecting short-term neuronal interactions. Journal of Computational Neuroscience. 32:479-497. pdf
50. Sussillo D, Nuyujukian P, Fan JM, Kao JC, Stavisky SD, Ryu SI, Shenoy KV (2012) A recurrent neural network for closed-loop intracortical brain-machine interface decoders. Journal of Neural Engineering. 9:026027. pdf supp mats Movie 1 ("Movie demonstrating the quality of the FORCE decoder. Monkey J, 2/4/2011.")  Movie 2 ("Movie demonstrating the quality of the FORCE decoder. Monkey L, 2/10/2011.")
49. Shenoy KV, Nurmikko AV (2012) Brain models enabled by next-generation neurotechnology. Pulse Magazine, IEEE Engineering in Medicine and Biology Society. 3: 31-36. pdf
Schnitzer JJ (2012) 2010 DARPA neural engineering, science, and technology forum [Guest Editorial]. Pulse Magazine, IEEE EMBS. 3:10. pdf  Review Article
48. Afshar A, Santhanam G, Yu BM, Ryu SI, Sahani M*, Shenoy KV* (2011) Single-trial neural correlates of arm movement preparation. Neuron. 71:555-564. pdf supp mats
Previews: Graziano MSA (2011) New insights into motor cortex. Neuron. 71:387-388. pdf
47.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. 8:045005pdf
46. O'Driscoll S, Shenoy KV, Meng TH (2011) Adaptive resolution ADC array for an implantable neural sensor. IEEE Transactions on Biomedical Circuits and Systems. 5:120-130. pdf
45. Cunningham JP, Nuyujukian P, Gilja V, Chestek CA, Ryu SI, Shenoy KV (2011) A closed-loop human simulator for investigating the role of feedback-control in brain-machine interfaces. Journal of Neurophysiology. 105:1932-1949. pdf
44. 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. 14:387-397. pdf supp mats
43. Gilja V, Chestek CA, Diester I, Henderson JM, Deisseroth K, Shenoy KV (2011) Challenges and opportunities for next-generation intra-cortically based neural prostheses. IEEE Transactions on Biomedical Engineering. 58:1891-1899. pdf   Review Article
42. 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. pdf
41. 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. pdf
40. Miranda H, Gilja V, Chestek CA, Shenoy KV, Meng TH (2010) HermesD: A high-rate long-range wireless transmission system for simultaneous multichannel neural recording applications. IEEE Transactions on Biomedical Circuits and Systems. 4:181-191. pdf
39. 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, Moore T, Chang SW, Snyder LH, Lisberger SG, Priebe NJ, Finn IM, Ferster D, Ryu SI, Santhanam G, Sahani M, Shenoy KV (2010) Stimulus onset quenches neural variability: a widespread cortical phenomenon. Nature Neuroscience. 13:369-378. pdf supp mats supp video 1 supp video 2 supp video 3 supp video 4
38. Gilja V*, Chestek CA*, Nuyujukian P, Foster JD, Shenoy KV (2010) Autonomous head-mounted electrophysiology systems for freely-behaving primates. Current Opinion in Neurobiology. 20:676-686. pdf  Review Article
Schuman E, Zhuang X, (2010) Editorial overview -- Special section on New Technologies. Current Opinion in Neurobiology. 20:608-609. pdf  Review Article
37. Cunningham JP, Gilja V, Ryu SI, Shenoy KV (2009) Methods for estimating neural firing rates and their application to brain-machine interfaces. Neural Networks, special issue on brain-machine interfaces. 22:1235-1246. pdf
36. Chestek CA*, Gilja V*, Nuyujukian P, Kier R, Solzbacher F, Ryu SI, Harrison RA, Shenoy KV (2009) HermesC: Low-power wireless neural recording system for freely moving primates. IEEE TNSRE, special issue on wireless neurotechnology. 17:330-338. pdf
Judy JW, Markovic D (2009) Guest Editorial -- Special section on wireless neural interfaces. IEEE TNSRE. 17:309-311. pdf  Review Article
35. Harrison RR, Kier RJ, Chestek CA, Gilja V, Nuyujukian P, Ryu SI, Gregor B, Solzbacher F, Shenoy KV (2009) Wireless neural recording with single low-power integrated circuit. IEEE TNSRE, special issue on wireless neurotechnology. 17:322-329. pdf
Judy JW, Markovic D (2009) Guest Editorial -- Special section on wireless neural interfaces. IEEE TNSRE. 17:309-311pdf  Review Article
34. Santhanam G, Yu BM, Gilja V, Afshar A, Ryu SI, Sahani M, Shenoy KV (2009) Factor-analysis methods for higher-performance neural prostheses. Journal of Neurophysiology. 102:1315-1330. pdf
33. Yu BM, Cunningham JP, Santhanam G, Ryu SI, Shenoy KV*, Sahani M* (2009) Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity. Journal of Neurophysiology. 102:614-635. pdf
32. Ryu SI, Shenoy KV (2009) Human cortical prostheses: Lost in translation? Neurosurgical Focus, special issue on advances in brain-machine interfaces, Parag Patil guest editor. 27:E5. pdf  Review Article
31. Cunningham JP, Yu BM, Gilja V, Ryu SI, Shenoy KV (2008) Toward optimal target placement for neural prosthetic devices. Journal of Neurophysiology. 100::3445-3457. pdf
30. Kemere C, Santhanam G, Yu BM, Afshar A, Ryu SI, Meng TH, Shenoy KV (2008) Detecting neural state transitions using hidden Markov models for motor cortical prostheses. Journal of Neurophysiology. 100:2441-2452pdf
29. Batista AP, Yu BM, Santhanam G, Ryu SI, Afshar A, Shenoy KV (2008) Cortical neural prosthesis performance improves when eye position is monitored. IEEE Transactions in Neural Systems and Rehabilitation Engineering. 16:24-31. pdf
28. Linderman MD, Santhanam G, Kemere CT, Gilja V, O'Driscoll S, Yu BM, Afshar A, Ryu SI, Shenoy KV, Meng TH (2008) Signal processing challenges for neural prostheses. IEEE Signal Processing Magazine, special issue on brain-computer interfaces. 25:18-28. pdf
​​Sajda P, Muller K-R, Shenoy KV (2008) Brain-computer interfaces [from the guest editors]. IEEE Signal Processing Magazine. 25:16-17pdf  Review Article
27. Santhanam G*, Linderman MD*, Gilja V, Afshar A, Ryu SI, Meng TH, Shenoy KV (2007) HermesB: A continuous neural recording system for freely behaving primates. IEEE Transactions in Biomedical Engineering. 54:2037-2050. pdf
26. Chestek CA*, Batista AP*, Santhanam G, Yu BM, Afshar A, Cunningham JP, Gilja V, Ryu SI, Churchland MM, Shenoy KV (2007) Single-neuron stability during repeated reaching in macaque premotor cortex. Journal of Neuroscience. 27:10742–10750pdf supp mats
25. Achtman N*, Afshar A*, Santhanam G, Yu BM, Ryu SI, Shenoy KV (2007) Free-paced high-performance brain-computer interfaces. Journal of Neural Engineering. 4:336-347. pdf
24. Batista AP, Santhanam G, Yu BM, Ryu SI, Afshar A, Shenoy KV (2007) Reference frames for reach planning in macaque dorsal premotor cortex. Journal of Neurophysiology. 98:966-983. pdf
23. Churchland MM, Shenoy KV (2007) Temporal complexity and heterogeneity of single-neuron activity in premotor and motor cortex. Journal of Neurophysiology. 97:4235-4257.pdf
22. Yu BM, Kemere C, Santhanam G, Afshar A, Ryu SI, Meng TH, Sahani M*, Shenoy KV* (2007) Mixture of trajectory models for neural decoding of goal-directed movements. Journal of Neurophysiology. 97:3763-3780pdf  Cover article
21. Churchland MM, Shenoy KV (2007) Delay of movement caused by disruption of cortical preparatory activity. Journal of Neurophysiology. 97:348-359. pdf
20. Churchland MM, Yu BM, Sahani M, Shenoy KV (2007) Techniques for extracting single-trial activity patterns from large-scale neural recordings. Current Opinion in Neurobiology, special issue on new technologies. 17:609-618. pdf  Review article
19. Churchland MM, Afshar A, Shenoy KV (2006) A central source of movement variability. Neuron. 52:1085-1096. pdf supp mat
​​NatureNews & Views section --- Dell H (2007) Hit and miss. Nature. 445:36. url
News articles lists selected items (e.g., Scientific AmericanBBC NewsNew Scientist)
18. Churchland MM, Santhanam G, Shenoy KV (2006) Preparatory activity in premotor and motor cortex reflects the speed of the upcoming reach. Journal of Neurophysiology. 96:3130-3146pdf
​​Cisek P (2006) Preparing for speed. Focus on: "Preparatory activity in premotor and motor cortex reflects the speed of the upcoming reach." Journal of Neurophysiology. 96:2842-2843pdf
17. Santhanam G*, Ryu SI*, Yu BM, Afshar A, Shenoy KV (2006) A high-performance brain-computer interface. Nature. 442:195-198. pdf supp mats video1 video2 video3
​​NATURE WEB FOCUS (url) -- Brain-Machine Interfaces introduction: "Brain-machine interfaces promise to aid paralyzed patients by re-routing movement-related signals around damaged parts of the nervous system. A new study in Nature demonstrates a human with spinal injury manipulating a screen cursor and robotic devices by thought alone (Hochberg et al. Nature 442:164-171, 2006). Implanted electrodes in his motor cortex recorded neural activity, and translated it into movement commands. A second study, in monkeys, shows that brain-machine interfaces can operate at high speed, greatly increasing their clinical potential (Santhanam et al. Nature 442:195-198, 2006). This Nature Web Focus includes exclusive interviews and video footage of experiments, alongside papers that paved the way for these recent advances."Nature News & Views -- Scott SH (2006) Neuroscience: Converting thoughts into action. Nature 442:141-142. pdf
Nature News Features -- Abbott A (2006) Neuroprosthetics: In search of the sixth sense. Nature 442:125-127. pdf 
Nature Editorial -- Is this the bionic man? Nature 442:109, 2006. pdf
Nature News -- Hopkin M (2006) Bionic brains become a reality html
Nature Video Streaming -- Brain Machine Interfaces. videos
Nature Podcast -- Smith C & Lacey A (2006) audio transcript
News articles lists selected items (e.g., NY TimesThe Economist, NPR Talk of the Nation Science Friday)
Barton S (2006) Neurological disorders: Mind over machine. Nature Reviews Neuroscience 7:682-683. pdf
16. Churchland MM, Yu BM, Ryu SI, Santhanam G, Shenoy KV (2006) Neural variability in premotor cortex provides a signature of motor preparation. Journal of Neuroscience. 26(14):3697-3712pdf supp mats
15. Zumsteg ZS, Kemere C, O'Driscoll S, Santhanam G, Ahmed RE, Shenoy KV, Meng TH (2005) Power feasibility of implantable digital spike sorting circuits for neural prosthetic systems. IEEE Transactions in Neural Systems and Rehabilitation Engineering. 13:272-279 pdf
14. Kemere C, Shenoy KV, Meng TH (2004) Model-based neural decoding of reaching movements: a maximum likelihood approach. IEEE Transactions on Biomedical Engineering. 51:925-932 pdf
13. Shenoy KV, Meeker D, Cao S, Kureshi SA, Pesaran B, Mitra P, Buneo C A, Batista AP, Burdick JW, Andersen RA (2003) Neural prosthetic control signals from plan activity. NeuroReport 14:591-596. pdf
12. Shenoy KV, Crowell JA, Andersen RA (2002) Pursuit-Speed Compensation in Cortical Area MSTd. Journal of Neurophysiology.88:2630-2647. pdf
11. Sugihara H, Murakami I, Shenoy KV, Andersen RA, Komatsu H (2002) Response of MSTd neurons to simulated 3D-orientation of rotating planes. Journal of Neurophysiology 87:273-285. pdf
10. Shenoy KV, Bradley DC, Andersen RA (1999) Influence of gaze rotation on the visual response of primate MSTd neurons. Journal of Neurophysiology 81:2764-2786. pdf
9. Crowell JA, Banks MS, Shenoy KV, Andersen RA (1998) Visual self-motion perception during head turns. Nature Neuroscience 1:732-737. pdf
Nature Neuroscience​​News & Views -- Warren WH (1998) Perception of heading is a brain in the neck. Nature Neuroscience 1:647-649. pdf
8. Wang H, Luo J, Shenoy KV, Fonstad Jr. CG, Psaltis D (1997) Monolithic integration of SEEDs and VLSI GaAs circuits by epitaxy on electronics. IEEE Photon. Technol. Lett. 9:607-609. pdf
7. Bradley DC, Maxwell M, Andersen RA, Banks MS, Shenoy KV (1996) Neural mechanisms for heading perception in primate visual cortex. Science 273:1544-1547. pdf
​​Science -- Barinaga M (1996) Neuroscience: Researchers find neurons that may help us navigate. Science 273:1489-1490. pdf
6. Braun EK, Shenoy KV, Fonstad Jr. CG, Mikkelson JM (1996) Elevated temperature stability of GaAs digital integrated circuits. IEEE Electron Device Lett. 17:37-39. pdf
5. Shenoy KV, Fonstad Jr. CG, Grot AC, Psaltis D (1995) Monolithic optoelectronic circuit design and fabrication by epitaxial growth on commercial VLSI GaAs MESFETs. IEEE Photon. Technol. Lett. 7:508-510. pdf
4. Grot AC, Psaltis D, Shenoy KV, Fonstad Jr. CG (1994) Integration of LEDs and GaAs circuits by MBE regrowth. IEEE Photon. Technol. Lett. 6:819-821. pdf
3. Shenoy KV, Fonstad Jr. CG, Mikkelson JM (1994) High temperature stability of refractory-metal VLSI GaAs MESFETs. IEEE Electron Device Lett. 15:106-108. pdf
2. McGrann JV, Shaw GL, Shenoy KV, Matthews RB (1994) Computation by symmetry operations in a highly structured model of the brain. Phys. Rev. E 49:5830-5839. pdf
1. Shenoy KV, Kaufman J, McGrann JV, Shaw GL (1993) Learning by selection in the Trion model of cortical organization. Cerebral Cortex 3:239-248. pdf


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