Journal Publications

  • Silvernagel M, Tor A, Jun EJ, Clarke SE, Sutherland R, Marshall K, Wu Y, Abdulla MU, Even-Chen N, Nuyujukian P. The curse of dimensionality in motor cortex. (submitted)
  • Tor A, Wu Y, Clarke SE, Yamada L, Weissman T, Nuyujukian P, for the Brain Interfacing Laboratory. Compression detects changes in spiking neural data from cortical lesions. (under revision)
  • Clarke SE, Nuyujukian P, for the Brain Interfacing Laboratory. Neural modes in motor cortex cycle over fast timescales. (under revision)
  • Abdulla MU, Clarke SE, Jun EJ, Nuyujukian P, for the Neural Prosthetic Systems Lab, the Brain Interfacing Laboratory. Stability of neural manifolds at minimal dimensionality despite motor representational drift. (revision submitted)
  • Marshall K, Clarke SE, Nuyujukian P, for the Brain Interfacing Laboratory. Signatures of covert neuron loss in the local field potential of motor cortex. (revision submitted)
  • Ling AS, Silvernagel MP, Clarke SE, Jun EJ, Abdulla MU, Nuyujukian P, for the Brain Interfacing Laboratory. Context-dependent low-dimensional neural dynamics unfold in distinct subspaces, dimensionality, and dynamical strength for natural walking and reaching. (revision submitted)
  • Tor A, Clarke SE, Bray IE, Nuyujukian P, for the Brain Interfacing Laboratory. Material damage to multielectrode arrays after electrolytic lesioning is in the noise. (accepted) eLife
  • Yamada L, Oskotsky T, Nuyujukian P. Compression-enabled joint entropy estimation for seizure detection on human intracortical electroencephalography. (2025) IEEE Transactions on Biomedical Engineering 72 pp. 3440-3452
  • Kauvar IV*, Richman E*, Liu T*, Li C, Vesuna S, Chibukhchyan A, Yamada L, Fogarty A, Solomon E, Choi EY, Mortazavi L, Chau Loo Kung G, Mukunda P, Raja C, Gil-Hernandez D, Patron K, Zhang X, Brawer J, Wrobel S, Lusk Z, Lyu D, Mitra A, Hack L, Luo L, Grosenick L, van Roessel P, Williams LM, Heifets BD, Henderson JH, McNab JA, Rodriguez CI**, Buch V**, Nuyujukian P** Deisseroth K**. Conserved brain-wide emergence of emotional response from sensory experience in humans and mice. (2025) Science 388 (6750) pp. eadt3971
  • Qing C, Von Stein E, Yamada L, Fogarty A, Nuyujukian P. Classifying high-frequency oscillations by morphologic contrast to background, with surgical outcome correlates. (2025) Journal of Clincal Neurophysiology 42 (4) pp. 294-303
  • Bray IE*, Clarke SE*, Casey K, Nuyujukian P, for the Brain Interfacing Laboratory. Neuroelectrophysiology-Compatible Electrolytic Lesioning. (2024) eLife 12 pp. RP84385
  • Yamada L, Oskotsky T, Nuyujukian P, for the Stanford Comprehensive Epilepsy Center, Stanford Pediatric Epilepsy Center. A scalable platform for acquisition of high-fidelity human intracranial EEG with minimal clinical burden. (2024) PLOS ONE 19 (6) pp. 1-18
  • Churchland MM, Nuyujukian P. Krishna V. Shenoy (1968-2023). (2023) Nature Neuroscience 26 pp. 723-724
  • Silvernagel MP*, Ling AS*, Nuyujukian P. A markerless platform for ambulatory systems neuroscience. (2021) Science Robotics 6 (58) pp. eabj7045
  • Peixoto D, Verhein JR, Kiani R, Kao JC, Nuyujukian P, Chandrasekaran C, Brown J, Fong S, Ryu SI, Shenoy KV, Newsome WT. Decoding and perturbing decision states in real time. (2021) Nature 591 (7851) pp. 604-609
  • Vesuna S*, Kauvar IV*, Richman E, Gore F, Oskotsky T, Sava-Segal C, Luo L, Malenka RC, Henderson JM, Nuyujukian P, Parvizi J, Deisseroth K. Deep posteromedial cortical rhythm in dissociation. (2020) Nature 586 (7827) pp. 87-94
  • Nuyujukian P*, Albites Sanabria J*, Saab J*, Pandarinath C, Jarosiewicz B, Blabe CH, Franco B, Mernoff ST, Eskandar EN, Simeral J D, Hochberg LR, Shenoy KV, Henderson JM. Cortical control of a tablet computer by people with paralysis. (2018) PLoS One 13 (11) pp. e0204566
  • Stavisky D, Kao JC, Nuyujukian P, Pandarinath C, Blabe CH, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV. Brain-machine interface cursor position only weakly affects monkey and human motor cortical activity in the absence of arm movements. (2018) Scientific Reports 8 (1) pp. 16357
  • Vyas S, Even-Chen N, Stavisky SD, Ryu SI, Nuyujukian P, Shenoy KV. Neural population dynamics underlying motor learning transfer. (2018) Neuron 97 (5) pp. 1177-1186
  • Even-Chen N, Stavisky SD, Pandarinath C, Nuyujukian P, Blabe CH, Hochberg LR, Henderson JM, Shenoy KV. Feasibility of automatic error detect-and-undo system in human intracortical brain-computer interfaces. (2017) IEEE Transactions on Biomedical Engineering PP (99) pp. 1-1
  • Kao JC*, Nuyujukian P*, Ryu SI, Shenoy KV. A high-performance neural prosthesis incorporating discrete state seletion with hidden Markov models. (2017) IEEE Transactions on Biomedical Engineering 64 (4) pp. 935-945
  • Pandarinath C*, Nuyujukian P*, Blabe CH, Sorice BL, Saab J, Willett FR, Hochberg LR, Shenoy KV, Henderson JM. High performance communication by people with paralysis using an intracortical brain-computer interface. (2017) eLife 6 pp. e18554
  • Nuyujukian P, Kao JC, Ryu SI, Shenoy KV. A non-human primate brain-computer typing interface. (2017) Proceedings of the IEEE 105 (1) pp. 66-72
  • Gilja V*, Pandarinath C*, Blabe CH, Nuyujukian P, Simeral JD, Sarma AA, Sorice BL, Perge JA, Jarosiewicz B, Hochberg LR, Shenoy KV**, Henderson JM**. Clinical translation of a high performance neural prosthesis. (2015) Nature Medicine 21 (10) pp. 1142-1145
  • Kao JC, Nuyujukian P, Cunningham JP, Churchland MM, Ryu SI, Shenoy KV. Single-trial dynamics of motor cortex and their applications to brain-machine interfaces. (2015) Nature Communications 6 pp. 7759
  • Pandarinath C, Gilja V, Blabe CH, Nuyujukian P, Sarma AA, Sorice BL, Eskandar EN, Hochberg LR, Henderson JM, Shenoy KV. Neural population dynamics in human motor cortex during movements in people with ALS. (2015) eLife 4
  • Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV. A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes. (2015) Journal of Neural Engineering 12 (3) pp. 036009
  • Christie BP, Tat DM, Irwin ZT, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Thompson DE, Chestek CA. Comparison of spike sorting and thresholding of voltage waveforms for intracortical brain-machine interface performance. (2015) Journal of Neural Engineering 12 (1) pp. 016009
  • Nuyujukian P, Fan JM, Kao JC, Ryu SI, Shenoy KV. A high-performance keyboard neural prosthesis enabled by task optimization. (2015) IEEE Transactions on Biomedical Engineering 62 (1) pp. 21-29
  • Nuyujukian P, Kao JC, Fan JM, Stavisky SD, Ryu SI, Shenoy KV. Performance sustaining intracortical neural prostheses. (2014) Journal of Neural Engineering 11 (6) pp. 066003
  • Foster JD, Nuyujukian P, Freifeld O, Gao H, Walker R, Ryu SI, Meng TH, Murmann B, Black MJ, Shenoy KV. A freely-moving monkey treadmill model. (2014) Journal of Neural Engineering 11 (4) pp. 046020
  • Kao JC, Stavisky SD, Sussillo D, Nuyujukian P, Shenoy KV. Information Systems Opportunities in Brain-Machine Interface Decoders. (2014) Proceedings of the IEEE 102 (5) pp. 666-682
  • Fan JM, Nuyujukian P, Kao JC, Chestek CA, Ryu SI, Shenoy KV. Intention estimatation in brain machine interfaces. (2014) Journal of Neural Engineering 11 (1) pp. 016004
  • Bishop W, Chestek CA, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Yu BM. Self-recalibrating classifiers for intracortical brain-computer interfaces. (2014) Journal of Neural Engineering 11 (2) pp. 026001
  • Dethier J*, Nuyujukian P*, Ryu SI, Shenoy KV, Boahen K. Design and validation of a real-time spiking-neural-network decoder for brain-machine interfaces. (2013) Journal of Neural Engineering 10 (3) pp. 036008
  • Gilja V*, Nuyujukian P*, Chestek C A, Cunningham J P, Yu B M, Fan J M, Churchland M M, Kaufman M T, Kao J C, Ryu S I, Shenoy K V. A high-performance neural prosthesis enabled by control algorithm design. (2012) Nature Neuroscience 15 pp. 1752-1757
  • Sussillo D, Nuyujukian P, Fan JM, Kao JC, Stavisky SD, Ryu SI, Shenoy KV. A recurrent neural network for closed-loop intracortical brain-machine interface decoders. (2012) Journal of Neural Engineering 9 (2) pp. 026027
  • Churchland MM*, Cunningham JP*, Kaufman MT, Foster JD, Nuyujukian P, Ryu SI, Shenoy KV. Neural population dynamics during reaching. (2012) Nature 487 pp. 51-56
  • Gao H, Walker RM, Nuyujukian P, Makinwa KAA, Shenoy KV, Murmann B, Meng TH. HermesE: A 96-Channel Full Data Rate Direct Neural Interface in 0.13 um CMOS. (2012) IEEE Journal of Solid-State Circuits 47 (4) pp. 1043-1055
  • 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. (2011) Journal of Neural Engineering 8 (4) pp. 045005
  • 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. (2010) Journal of Neurophysiolgy 105 (4) pp. 1932-1949
  • Gilja V, Chestek CA, Nuyujukian P, Foster JD, Shenoy KV. Autonomous head-mounted electrophysiology systems for freely behaving primates. (2010) Current Opinion Neurobiology 20 (5) pp. 676-686
  • Farshchi S, Pesterev A, Nuyujukian P, Guenterberg E, Mody I, Judy JW. Embedded neural recording with TinyOS-based wireless-enabled processor modules. (2010) IEEE Transactions on Neural Systems and Rehabilitation Engineering 18 (2) pp. 134-141
  • Chestek CA, Gilja V, Nuyujukian P, Kier RJ, Solzbacher F, Ryu SI, Harrison RR, Shenoy KV. HermesC: low-power wireless neural recording system for freely moving primates. (2009) IEEE Transactions on Neural Systems and Rehabilitation Engineering 17 (4) pp. 330-338
  • Harrison RR, Kier RJ, Chestek CA, Gilja V, Nuyujukian P, Ryu SI, Greger B, Solzbacher F, Shenoy KV. Wireless neural recording with single low-power integrated circuit. (2009) IEEE Transactions on Neural Systems and Rehabilitation Engineering 17 (4) pp. 322-329
  • Farshchi S, Pesterev A, Nuyujukian P, Mody I, Judy JW. Bi-Fi: an embedded sensor/system architecture for remote biological monitoring. (2007) IEEE Transactions on Information Technology in Biomedicine 11 (6) pp. 611-618
  • Farshchi S, Nuyujukian P, Pesterev A, Mody I, Judy JW. A TinyOS-enabled MICA2-based wireless neural interface. (2006) IEEE Transactions on Biomedical Engineering 53 (7) pp. 1416-1424


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