Byron Yu: Publications

Journal papers

“A posture subspace in primary motor cortex”
by P. J. Marino, L. A. Bahureksa, C. F. Fisac, E. R. Oby, A. L. Smoulder, A. N. Motiwala, A. D. Degenhart, E. M. Grigsby, W. M. Joiner, S. M. Chase*, B. M. Yu*, A. P. Batista*.
bioRxiv.

“A theory of brain-computer interface learning via low-dimensional control”
by J. A. Menéndez, J. A. Hennig, M. D. Golub, E. R. Oby, P. T. Sadtler, A. P. Batista, S. M. Chase, B. M. Yu, P. E. Latham.
bioRxiv.

“Dynamical constraints on neural population activity”
by E. R. Oby†, A. D. Degenhart†, E. M. Grigsby†, A. N. Motiwala, N. T. McClain, P. J. Marino, B. M. Yu*, A. P. Batista*.
Nat Neurosci, in press.

“A neural basis of choking under pressure”
by A. L. Smoulder, P. J. Marino, E. R. Oby, S. E. Snyder, H. Miyata, N. P. Pavlovsky, W. E. Bishop, B. M. Yu, S. M. Chase*, A. P. Batista*.
Neuron, vol. 112 (20), 2024, pp. 3424-3433.

“Automated customization of large-scale spiking network models to neuronal population activity”
by S. Wu, C. Huang, A. C. Synder, M. A. Smith*, B. Doiron*, B. M. Yu*.
Nat Comput Sci, vol. 4, 2024, pp. 690-705.
Supp Mats | Code

“Motor cortex retains and reorients neural dynamics during motor imagery”
by B. M. Dekleva, R. H. Chowdhury, A. P. Batista, S. M. Chase, B. M. Yu, M. L. Boninger, J. L. Collinger.
Nat Hum Behav, vol. 8, 2024, pp. 729-742.

“Learning leaves a memory trace in motor cortex”
by D. M. Losey, J. A. Hennig†, E. R. Oby†, M. D. Golub, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista*, B. M. Yu*, S. M. Chase*.
Curr Biol, vol. 34, 2024, pp. 1519-1531.
Dispatch | Code

“Dimensionality reduction of calcium-imaged neuronal population activity”
by T. Koh, W. E. Bishop, T. Kawashima, B. B. Jeon, R. Srinivasan, Y. Mu, Z. Wei, S. J. Kuhlman, M. B. Ahrens, S. M. Chase*, B. M. Yu*.
Nat Comput Sci, vol. 3, 2023, pp. 71-85.
Supp Mats | Code

“Tracking momentary fluctuations in human attention with a cognitive brain-machine interface”
by A. M. Chinchani*, S. Paliwal*, S. Ganesh, V. Chandrasekhar, B. M. Yu, D. Sridharan
Commun Biol, vol. 5:1346, 2022.
Supp Mats

“Disentangling the flow of signals between populations of neurons”
by E. Gokcen, A. I. Jasper, J. D. Semedo, A. Zandvakili, A. Kohn*, C. K. Machens*, B. M. Yu*.
Nat Comput Sci, vol. 2, 2022, pp. 512-525.
Supp Mats | News & Views | Code

“Feedforward and feedback interactions between visual cortical areas use different population activity patterns”
by J. D. Semedo, A. I. Jasper, A. Zandvakili, A. Krishna, A. Aschner, C. K. Machens*, A. Kohn*, B. M. Yu*.
Nat Commun, vol. 13:1099, 2022.
Supp Mats | Code

“A stable population code for attention in prefrontal cortex leads a dynamic attention code in visual cortex”
by A. C. Snyder, B. M. Yu*, M. A. Smith*.
J Neurosci, vol. 41 (44), 2021, pp. 9163-9176.

“How learning unfolds in the brain: toward an optimization view”
by J. A. Hennig, E. R. Oby, D. M. Losey, A. P. Batista*, B. M. Yu*, S. M. Chase*.
Neuron, vol. 109 (23), 2021, pp. 3720-3735.

“Bridging neuronal correlations and dimensionality reduction”
by A. Umakantha†, R. Morina†, B. R. Cowley†, A. C. Snyder, M. A. Smith*, B. M. Yu*.
Neuron, vol. 109 (17), 2021, pp. 2740-2754.
Code (simulations in paper) | Code (apply to your own data)

“Learning is shaped by abrupt changes in neural engagement”
by J. A. Hennig, E. R. Oby, M. D. Golub, L. A. Bahureksa, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista*, S. M. Chase*, B. M. Yu*.
Nat Neurosci, vol. 24, 2021, pp. 727-736.
Code (analyses in paper) | Code (apply to your own data)

“Statistical methods for dissecting interactions between brain areas”
by J. D. Semedo*, E. Gokcen*, C. K. Machens, A. Kohn, B. M. Yu.
Curr Opin Neurobiol, vol. 65, 2020, pp. 59-69.

“Slow drift of neural activity as a signature of impulsivity in macaque visual and prefrontal cortex”
by B. R. Cowley, A. C. Snyder, K. Acar, R. C. Williamson, B. M. Yu*, M. A. Smith*.
Neuron, vol. 108 (3), 2020, pp. 551-567.

“Principles of corticocortical communication: proposed schemes and design considerations”
by A. Kohn, A. I. Jasper, J. D. Semedo, E. Gokcen, C. K. Machens, B. M. Yu.
Trends Neurosci, vol. 43 (9), 2020, pp. 725-737.

“Stabilization of a brain-computer interface via the alignment of low-dimensional spaces of neural activity”
by A. D. Degenhart†, W. E. Bishop†, E. R. Oby, E. C. Tyler-Kabara, S. M. Chase*, A. P. Batista*, B. M. Yu*.
Nat Biomed Eng, vol. 4, 2020, pp. 672-685.
Supp Mats | News & Views | Code

“New neural activity patterns emerge with long-term learning”
by E. R. Oby, M. D. Golub, J. A. Hennig, A. D. Degenhart, E. C. Tyler-Kabara, B. M. Yu*, S. M. Chase*, A. P. Batista*.
Proc Natl Acad Sci, vol. 116 (30), 2019, pp. 15210-15215.
Supp Mats | Commentary

“Cortical areas interact through a communication subspace”
by J. D. Semedo, A. Zandvakili, C. K. Machens*, B. M. Yu*, A. Kohn*.
Neuron, vol. 102, 2019, pp. 249-259.
Code | Additional Figures

“Bridging large-scale neuronal recordings and large-scale network models using dimensionality reduction”
by R. C. Williamson, B. Doiron, M. A. Smith, B. M. Yu.
Curr Opin Neurobiol, vol. 55, 2019, pp. 40-47.

“Distinct population codes for attention in the absence and presence of visual stimulation”
by A. C. Snyder, B. M. Yu*, M. A. Smith*.
Nat Commun, 2018; 9(1):4382.
Supp Mats

“Constraints on neural redundancy”
by J. A. Hennig, M. D. Golub, P. J. Lund, P. T. Sadtler, E. R. Oby, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista*, B. M. Yu*, S. M. Chase*.
eLife, 2018; 7:e36774.
Spotlight | Code

“Learning by neural reassociation”
by M. D. Golub, P. T. Sadtler, E. R. Oby, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista, S. M. Chase*, B. M. Yu*.
Nat Neurosci, vol. 21, 2018, pp. 607-616.
Supp Mats | News & Views | Code

“Computational neuroscience: mathematical and statistical perspectives”
by R. E. Kass, S. Amari, K. Arai, E. N. Brown, C. O. Diekman, M. Diesmann, B. Doiron, U. T. Eden, A. L. Fairhall, G. M. Fiddyment, T. Fukai, S. Grün, M. T. Harrison, M. Helias, H. Nakahara, J. Teramae, P. J. Thomas, M. Reimers, J. Rodu, H. G. Rotstein, E. Shea-Brown, H. Shimazaki, S. Shinomoto, B. M. Yu, M. A. Kramer.
Annu Rev Stat Appl, vol. 5, 2018, pp. 183-214.

“A path to understanding how motor cortex influences muscle activity”
by E. R. Oby and B. M. Yu.
Neuron, vol. 95, 2017, pp. 476-478.

“Population activity structure of excitatory and inhibitory neurons”
by S. R. Bittner, R. C. Williamson, A. C. Snyder, A. Litwin-Kumar, B. Doiron, S. M. Chase*, M. A. Smith*, B. M. Yu*.
PLoS One, 12(8): e0181773, 2017.

“Stimulus-driven population activity patterns in macaque primary visual cortex”
by B. R. Cowley, M. A. Smith, A. Kohn, B. M. Yu.
PLoS Comput Biol, 12(12): e1005185, 2016.

“Scaling properties of dimensionality reduction for neural populations and network models”
by R. C. Williamson, B. R. Cowley, A. Litwin-Kumar, B. Doiron, A. Kohn, M. A. Smith*, B. M. Yu*.
PLoS Comput Biol, 12(12): e1005141, 2016.

“Fault tolerance in the brain”
by B. M. Yu.
Nature, vol. 532, 2016, pp. 449-450.

“Brain-computer interfaces for dissecting cognitive processes underlying sensorimotor control”
by M. D. Golub, S. M. Chase, A. P. Batista, B. M. Yu.
Curr Opin Neurobiol, vol. 37, 2016, pp. 53-58.

“Internal models for interpreting neural population activity during sensorimotor control”
by M. D. Golub, B. M. Yu*, S. M. Chase*.
eLife, 2015; 4:e10015.
Code

“Extracting low-dimensional latent structure from time series in the presence of delays”
by K. C. Lakshmanan, P. T. Sadtler, E. C. Tyler-Kabara, A. P. Batista, B. M. Yu.
Neural Comput, vol. 27, 2015, pp. 1825-1856.
Code

“Brain-computer interface control along instructed paths”
by P. T. Sadtler, S. I. Ryu, E. C. Tyler-Kabara, B. M. Yu*, A. P. Batista*.
J Neural Eng, vol. 12 (016015), 2015.
Supp Mats

“Neural constraints on learning”
by P. T. Sadtler, K. M. Quick, M. D. Golub, S. M. Chase, S. I. Ryu, E. C. Tyler-Kabara, B. M. Yu*, A. P. Batista*.
Nature, vol. 512, 2014, pp. 423-426. (cover article)
Research highlight

“Dimensionality reduction for large-scale neural recordings”
by J. P. Cunningham and B. M. Yu.
Nat Neurosci, vol. 17, 2014, pp. 1500-1509.

“Shedding light on learning”
by B. M. Yu and S. M. Chase.
Nat Neurosci, vol. 17, 2014, pp. 746-747.

“Motor cortical control of movement speed with implications for brain-machine interface control”
by M. D. Golub, B. M. Yu, A. B. Schwartz, S. M. Chase.
J Neurophysiol, vol. 112, 2014, pp. 411-429.

“Self-recalibrating classifiers for intracortical brain computer interfaces“
by W. E. Bishop, C. A. Chestek, V. Gilja, P. Nuyujukian, J. D. Foster, S. I. Ryu, K. V. Shenoy, B. M. Yu.
J Neural Eng, vol. 11 (026001), 2014.

“DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural activity”
by B. R. Cowley, M. T. Kaufman, Z. S. Butler, M. M. Churchland, S. I. Ryu, K. V. Shenoy, B. M. Yu.
J Neural Eng, vol. 10 (066012), 2013.
Code

“A high-performance neural prosthesis enabled by control algorithm design”
by V. Gilja*, P. Nuyujukian*, C. A. Chestek, J. P. Cunningham, B. M. Yu, J. M. Fan, M. M. Churchland, M. T. Kaufman, J. C. Kao, S. I. Ryu, K. V. Shenoy.
Nat Neurosci, vol. 15, 2012, pp. 1752-1757.
Supp Mats | Video 1 | Video 2 | Video 3 | Video 4 | Video 5 | Video 6

“Single-trial neural correlates of arm movement preparation”
by A. Afshar, G. Santhanam, B. M. Yu, S. I. Ryu, M. Sahani, K. V. Shenoy.
Neuron, vol. 71, 2011, pp. 555-564.
Supp Mats

“The roles of monkey premotor neuron classes in movement preparation and execution”
by M. T. Kaufman, M. M. Churchland, G. Santhanam, B. M. Yu, A. Afshar, S. I. Ryu, K. V. Shenoy.
J Neurophysiol, vol. 104, 2010, pp. 799-810.

“Stimulus onset quenches neural variability: a widespread cortical phenomenon”
by M. M. Churchland*, B. M. Yu*, J. P. Cunningham, L. P. Sugrue, M. R. Cohen, G. S. Corrado, W. T. Newsome, A. M. Clark, P. Hosseini, B. B. Scott, D. C. Bradley, M. A. Smith, A. Kohn, J. A. Movshon, K. M. Armstrong, T. Moore, S. W. Chang, L. H. Snyder, S. G. Lisberger, N. J. Priebe, I. M. Finn, D. Ferster, S. I. Ryu, G. Santhanam, M. Sahani, K. V. Shenoy.
Nat Neurosci, vol. 13, 2010, pp. 369-378.
Supp Notes | Video 1 | Video 2 | Video 3 | Video 4 | Historical News & Views

“Factor-analysis methods for higher-performance neural prostheses”
by G. Santhanam, B. M. Yu, V. Gilja, S. I. Ryu, A. Afshar, M. Sahani, K. V. Shenoy.
J Neurophysiol, vol. 102, 2009, pp. 1315-1330.

“Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy*, M. Sahani*.
J Neurophysiol, vol. 102, 2009, pp. 614-635.
Code

“Toward optimal target placement for neural prosthetic devices”
by J. P. Cunningham, B. M. Yu, V. Gilja, S. I. Ryu, K. V. Shenoy.
J Neurophysiol, vol. 100, 2008, pp. 3445-3457.

“Detecting neural state transitions using hidden Markov models for motor cortical prostheses”
by C. Kemere, G. Santhanam, B. M. Yu, A. Afshar, S. I. Ryu, T. H. Meng, K. V. Shenoy.
J Neurophysiol, vol. 100, 2008, pp. 2441-2452.

“Cortical neural prosthesis performance improves when eye position is monitored”
by A. P. Batista, B. M. Yu, G. Santhanam, S. I. Ryu, A. Afshar, K. V. Shenoy.
IEEE Trans Neural Syst Rehabil Eng, vol. 16, no. 1, 2008, pp. 24-31.

“Signal processing challenges for neural prostheses”
by M. D. Linderman, G. Santhanam, C. T. Kemere, V. Gilja, S. O'Driscoll, B. M. Yu, A. Afshar, S. I. Ryu, K. V. Shenoy, T. H. Meng.
IEEE Signal Processing Magazine, vol. 25, no. 1, 2008, pp. 18-28.

“Techniques for extracting single-trial activity patterns from large-scale neural recordings”
by M. M. Churchland, B. M. Yu, M. Sahani, K. V. Shenoy.
Current Opinion in Neurobiology, vol. 17, no. 5, Oct. 2007, pp. 609-618.

“Single-neuron stability during repeated reaching in macaque premotor cortex”
by C. A. Chestek*, A. P. Batista*, G. Santhanam, B. M. Yu, A. Afshar, J. P. Cunningham, V. Gilja, S. I. Ryu, M. M. Churchland, K. V. Shenoy.
J Neurosci, vol. 27, no. 40, 2007, pp. 10742-10750.
Supp Data

“Free paced high-performance brain-computer interfaces”
by N. Achtman*, A. Afshar*, G. Santhanam, B. M. Yu, S. I. Ryu, K. V. Shenoy.
J Neural Eng, vol. 4, 2007, pp. 336-347.

“Reference frames for reach planning in macaque dorsal premotor cortex”
by A. P. Batista, G. Santhanam, B. M. Yu, S. I. Ryu, A. Afshar, K. V. Shenoy.
J Neurophysiol, vol. 98, 2007, pp. 966-983.

“Mixture of trajectory models for neural decoding of goal-directed movements”
by B. M. Yu, C. Kemere, G. Santhanam, A. Afshar, S. I. Ryu, T. H. Meng, M. Sahani*, K. V. Shenoy*.
J Neurophysiol, vol. 97, 2007, pp. 3763-3780.
Issue cover

“A high-performance brain-computer interface”
by G. Santhanam*, S. I. Ryu*, B. M. Yu, A. Afshar, K. V. Shenoy.
Nature, vol. 442, 2006, pp. 195-198.
Supp Notes | Video 1 | Video 2 | Video 3

“Neural variability in premotor cortex provides a signature of motor preparation”
by M. M. Churchland, B. M. Yu, S. I. Ryu, G. Santhanam, K. V. Shenoy.
J Neurosci, vol. 26, no. 14, Apr. 2006, pp. 3697-3712.

Conference papers

“MiSO: Optimizing brain stimulation to create neural activity states”
by Y. Minai, J. Soldado Magraner, M. A. Smith*, B. M. Yu*.
In Advances in Neural Information Processing Systems 37, 2024, in press.

“Uncovering motifs of concurrent signaling across multiple neuronal populations”
by E. A. Gokcen, A. I. Jasper, A. Xu, A. Kohn*, C. K. Machens*, B. M. Yu*.
In Advances in Neural Information Processing Systems 36, 2023, pp. 34711-34722.
Supp Mats | Code

“Adaptive stimulus selection for optimizing neural population responses”
by B. R. Cowley, R. C. Williamson, K. Acar, M. A. Smith*, B. M. Yu*.
In Advances in Neural Information Processing Systems 30, 2017, pp. 1395-1405.

“Distance covariance analysis”
by B. R. Cowley, J. D. Semedo, A. Zandvakili, M. A. Smith, A. Kohn, B. M. Yu.
In Artificial Intelligence and Statistics (AISTATS), vol. 54, 2017, pp. 242-251.
Supp Mats | Code

“Deterministic symmetric positive semidefinite matrix completion”
by W. E. Bishop and B. M. Yu.
In Advances in Neural Information Processing Systems 27, 2014, pp. 2762-2770.
Supp Mats

“Extracting latent structure from multiple interacting neural populations”
by J. D. Semedo, A. Zandvakili, A. Kohn, C. K. Machens*, B. M. Yu*.
In Advances in Neural Information Processing Systems 27, 2014, pp. 2942-2950.

“Learning an internal dynamics model from control demonstration”
by M. D. Golub, S. M. Chase*, B. M. Yu*.
In International Conference on Machine Learning (ICML), vol. 28, 2013, pp. 606-614.
Code

“Internal models engaged by brain-computer interface control”
by M. D. Golub, B. M. Yu*, S. M. Chase*.
In Proc 34th Annual Conf IEEE EMBS, 2012, pp. 1327-1330. Talk.

“DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural activity”
by B. R. Cowley, M. T. Kaufman, M. M. Churchland, S. I. Ryu, K. V. Shenoy, B. M. Yu.
In Proc 34th Annual Conf IEEE EMBS, 2012, pp. 4607-4610.
Code

“A brain machine interface control algorithm designed from a feedback control perspective”
by V. Gilja, P. Nuyujukian, C. A. Chestek, J. P. Cunningham, B. M. Yu, J. M. Fan, S. I. Ryu, K. V. Shenoy.
In Proc 34th Annual Conf IEEE EMBS, 2012, pp. 1318-1322. Talk.

“Empirical models of spiking in neural populations”
by J. Macke, L. Buesing, J. P. Cunningham, B. M. Yu, K. V. Shenoy, M. Sahani.
In Advances in Neural Information Processing Systems 24, 2011, pp. 1350-1358. Talk.

“Dynamical segmentation of single trials from population neural data”
by B. Petreska, B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, M. Sahani.
In Advances in Neural Information Processing Systems 24, 2011, pp. 756-764.

“High-performance neural prosthetic control along instructed paths”
by P. T. Sadtler, S. I. Ryu, B. M. Yu, A. P. Batista.
In Proc 5th IEEE EMBS Neural Eng, 2011, pp. 601-604.

“Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, M. Sahani.
In Advances in Neural Information Processing Systems 21, 2009, pp. 1881-1888.

“An efficient approximation for the real-time implementation of the mixture of trajectory models decoder”
by W. Bishop, B. M. Yu, G. Santhanam, A. Afshar, S. I. Ryu, K. V. Shenoy.
In Proc IEEE Biomedical Circuits and Systems Conference, 2008, pp. 133-136.

“The use of a virtual integration environment for the real-time implementation of neural decode algorithms”
by W. Bishop, B. M. Yu, G. Santhanam, A. Afshar, S. I. Ryu, K. V. Shenoy, J. Vogelstein, J. Beaty, S. Harshbarger.
In Proc 30th Annual Conf IEEE EMBS, 2008, pp. 628-633.

“A factor-analysis decoder for high-performance neural prostheses”
by G. Santhanam, B. M. Yu, V. Gilja, S. I. Ryu, A. Afshar, M. Sahani, K. V. Shenoy.
In Proc. IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP), 2008, pp. 5208-5211.

“Inferring neural firing rates from spike trains using Gaussian processes”
by J. P. Cunningham, B. M. Yu, K. V. Shenoy, M. Sahani.
In Advances in Neural Information Processing Systems 20, 2008, pp. 329-336.

“Neural decoding of movements: From linear to nonlinear trajectory models”
by B. M. Yu, J. P. Cunningham, K. V. Shenoy, M. Sahani.
In Neural Information Processing (ICONIP 2007), Part I, vol. 4984, (M. Ishikawa, K. Doya, H. Miyamoto, and T. Yamakawa, eds.), Springer, 2008, pp. 586-595. Talk.

“Optimal target placement for neural communication prostheses”
by J. P. Cunningham, B. M. Yu, K. V. Shenoy.
In Proc 28th Annual Conf IEEE EMBS, 2006, pp. 2912-2915.

“Increasing the performance of cortically-controlled prostheses”
by K. V. Shenoy, G. Santhanam, S. I. Ryu, A. Afshar, B. M. Yu, V. Gilja, M. D. Linderman, R. S. Kalmar, J. P. Cunningham, C. T. Kemere, A. P. Batista, M. M. Churchland, T. H. Meng.
In Proc 28th Annual Conf IEEE EMBS, 2006, pp. 6652-6656.

“Expectation propagation for inference in non-linear dynamical models with Poisson observations”
by B. M. Yu, K. V. Shenoy, M. Sahani.
In Proc IEEE Nonlinear Statistical Signal Processing Workshop, 2006.

“Extracting dynamical structure embedded in neural activity”
by B. M. Yu, A. Afshar, G. Santhanam, S. I. Ryu, K. V. Shenoy, M. Sahani.
In Advances in Neural Information Processing Systems 18, 2006, pp. 1545-1552. Talk.

“A high performance neurally-controlled cursor positioning system”
by G. Santhanam, S. I. Ryu, B. M. Yu, A. Afshar, K. V. Shenoy.
In Proc 2nd IEEE EMBS Neural Eng, 2005, pp. 494-500.

“Model-based decoding of reaching movement for prosthetic systems”
by C. Kemere, G. Santhanam, B. M. Yu, S. I. Ryu, T. H. Meng, K. V. Shenoy.
In Proc 26th Annual Conf IEEE EMBS, 2004, pp. 4524-4528.

“Improving neural prosthetic system performance by combining plan and peri-movement activity”
by B. M. Yu, S. I. Ryu, G. Santhanam, M. M. Churchland, K. V. Shenoy.
In Proc 26th Annual Conf IEEE EMBS, 2004, pp. 4516-4519. Talk.

“Influence of movement speed on plan activity in monkey pre-motor cortex and implictions for high-performance neural prosthetic systems design”
by K. V. Shenoy, M. M. Churchland, G. Santhanam, B. M. Yu, S. I. Ryu.
In Proc 25th Annual Conf IEEE EMBS, 2003, pp. 1897-1900.

“Decoding of plan and peri-movement neural signals in prosthetic systems”
by C. T. Kemere, G. Santhanam, B. M. Yu, K. V. Shenoy, T. H. Meng.
In IEEE Workshop on Signal Processing Systems, Oct. 2002, pp. 276-283.

“Power-efficient multiple-subcarrier modulation scheme for optical wireless communications”
by B. Yu, J. M. Kahn, R. You.
In Proc SPIE ITCom, 2002, pp. 41-53.

Book chapters

“Brain-machine interfaces”
by K. V. Shenoy and B. M. Yu.
In Principles of Neural Science, (E. R. Kandel, J. D. Koester, S. H. Mack, S. A. Siegelbaum, eds.), McGraw Hill, 6th edition, 2021, Chapter 39 (entirely new chapter).

“Intracortical brain-machine interfaces”
by E. R. Oby, J. A. Hennig, A. P. Batista, B. M. Yu, S. M. Chase.
In Neural Engineering, (B. He, ed.), Springer, 2020, pp. 185-221.

“Neural decoding for motor and communication prostheses”
by B. M. Yu, G. Santhanam, M. Sahani, K. V. Shenoy.
In Statistical Signal Processing for Neuroscience, (K. G. Oweiss, ed.), Academic Press, 2010. ISBN: 978-0-12-375027-3.

Thesis

“Neural dynamics of motor preparation and execution”
by B. M. Yu.
Ph.D. dissertation, Stanford University, 2007.

Technical reports

“Factor analysis with Poisson output”
by G. Santhanam, B. M. Yu, K. V. Shenoy, M. Sahani.
Technical report, 2006.

“Derivation of Kalman filtering and smoothing equations”
by B. M. Yu, K. V. Shenoy, M. Sahani.
Technical report, 2004.

“Derivation of extended Kalman filtering and smoothing equations”
by B. M. Yu, K. V. Shenoy, M. Sahani.
Technical report, 2004.

Abstracts

2024

“Probing movement preparation dynamics using BCI-based causal perturbations”
by A. N. Motiwala, E. R. Oby, E. M. Grigsby, J. Couras, A. D. Degenhart, A. P. Batista, B. M. Yu.
Cosyne Abstracts, 2024. Talk.

“Diverse signals mediate feedforward and feedback communication in early visual cortex”
by F. Mastrogiuseppe, J. Carmona, B. M. Yu, A. Kohn, C. K. Machens.
Cosyne Abstracts, no. 1-045, 2024.

“Reward and perceptual difficulty drive distinct changes in behavior and motor cortical activity”
by A. N. Chandrasekaran, M. E. McDonnell, C. S. Ki, A. L. Smoulder, B. M. Yu, A. P. Batista, M. A. Smith, S. M. Chase.
Cosyne Abstracts, no. 1-143, 2024.

“Network models for distinguishing population-level learning mechanisms”
by J. Sacks, E. R. Oby, J. A. Hennig, A. D. Degenhart, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, S. M. Chase, B. M. Yu, A. P. Batista, M. D. Golub.
Cosyne Abstracts, no. 2-007, 2024.

“Uncovering motifs of concurrent signaling across multiple neuronal populations”
by E. A. Gokcen, A. I. Jasper, A. Xu, A. Kohn, C. K. Machens, B. M. Yu.
Cosyne Abstracts, no. 2-091, 2024.

“A posture subspace in primary motor cortex”
by P. J. Marino, L. A. Bahureksa, C. F. Fisac, E. R. Oby, A. L. Smoulder, A. N. Motiwala, A. D. Degenhart, E. M. Grigsby, W. M. Joiner, S. M. Chase, B. M. Yu, A. P. Batista.
Cosyne Abstracts, no. 2-099, 2024.

“A causal test of the interactions between brain areas”
by S. E. Snyder, E. R. Oby, M. A. Smith, S. M. Chase, B. M. Yu, A. P. Batista.
Cosyne Abstracts, no. 2-146, 2024.

“How noise sources shape cortical inter-areal communication”
by J. Carmona, F. Mastrogiuseppe, B. M. Yu, A. Kohn, C. K. Machens.
Cosyne Abstracts, no. 3-071, 2024.

“A link between the memory trace in motor cortex and savings”
by J. Couras, E. R. Oby, A. N. Motiwala, S. E. Snyder, D. M. Losey, J. A. Hennig, B. M. Yu, S. M. Chase, A. P. Batista.
Cosyne Abstracts, no. 3-146, 2024.

2023

“A link between memory traces in motor cortex and savings”
by J. Couras, E. R. Oby, A. N. Motiwala, S. E. Snyder, D. M. Losey, J. A. Hennig, B. M. Yu*, S. M. Chase*, A. P. Batista*.
Soc Neurosci Abstr, no. 349.09, 2023.

“A causal test of the flexibility of interactions between cortical areas”
by S. E. Snyder, E. R. Oby, M. A. Smith*, S. M. Chase*, B. M. Yu*, A. P. Batista*.
Soc Neurosci Abstr, no. 552.09, 2023.

“Interpreting area-to-area differences in spiking variability using spiking network models”
by S. Wu, A. C. Snyder, C. Huang*, M. A. Smith*, B. M. Yu*, B. Doiron*.
Soc Neurosci Abstr, no. 577.06, 2023.

“Dissecting multi-population interactions across cortical areas and layers”
by E. A. Gokcen†, A. I. Jasper†, A. Xu, B. M. Yu*, C. K. Machens*, A. Kohn*.
Cosyne Abstracts, no. 1-041, 2023.

“Robustness of PFC networks under inter and intra-hemispheric patterned microstimulation perturbations”
by J. Soldado Magraner, Y. Minai, M. A. Smith*, B. M. Yu*.
Cosyne Abstracts, no. 1-068, 2023.

2022

“A brain-computer interface in the prefrontal cortex that suppresses neural variability”
by R. C. Williamson†, A. Umakantha†, C. S. Ki†, B. M. Yu*, M. A. Smith*.
Soc Neurosci Abstr, no. 058.16, 2022.

“Exceptionally large rewards collapse task information in neural population activity”
by A. L. Smoulder, P. J. Marino, N. P. Pavlovsky, E. R. Oby, S. E. Snyder, W. E. Bishop, B. M. Yu, S. M. Chase, A. P. Batista.
Soc Neurosci Abstr, no. 217.16, 2022.

“Distinct neural modes are associated with static and dynamic grasping force”
by G. H. Blumenthal, B. M. Dekleva, A. P. Batista, M. L. Boninger, S. M. Chase, R. A. Gaunt, J. A. Gonzalez-Martinez, B. M. Yu, J. L. Collinger.
Soc Neurosci Abstr, no. 218.10, 2022.

“Posture and motor signals are organized in primary motor cortex”
by P. J. Marino, L. A. Bahureksa, C. F. Fisac, E. R. Oby, A. N. Motiwala, E. M. Grigsby, A. L. Smoulder, A. D. Degenhart, W. M. Joiner, S. M. Chase*, B. M. Yu*, A. P. Batista*.
Soc Neurosci Abstr, no. 301.01, 2022.

“Coordinated variability in prefrontal cortex reflects global and local neuronal processing”
by A. Umakantha†, R. C. Williamson†, M. E. McDonnell†, B. M. Yu*, M. A. Smith*.
Soc Neurosci Abstr, no. 389.18, 2022.

“Constraints on the temporal sequencing of neural population activity”
by A. D. Degenhart†, E. M. Grigsby†, E. R. Oby†, A. N. Motiwala, N. T. McClain, P. J. Marino, A. P. Batista*, B. M. Yu*.
Soc Neurosci Abstr, no. 390.17, 2022.

“Characterizing neural population dynamics in primary motor cortex in the absence of arm movement”
by A. N. Motiwala, E. R. Oby, E. M. Grigsby, A. D. Degenhart, N. T. McClain, A. P. Batista*, B. M. Yu*.
Soc Neurosci Abstr, no. 390.18, 2022.

“Learning alters neural activity to simultaneously support memory and action”
by D. M. Losey, J. A. Hennig, E. R. Oby, M. D. Golub, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista*, B. M. Yu*, S. M. Chase*.
Soc Neurosci Abstr, no. 428.03, 2022. Talk.

“Neuronal population signal flow between macaque visual cortical areas under different temporal contexts”
by A. Krishna, B. M. Yu, C. K. Machens, A. Kohn.
Soc Neurosci Abstr, no. 545.12, 2022.

“Early and midlevel visual areas interact via distinct communication subspaces”
by A. I. Jasper, A. Xu, C. K. Machens, B. M. Yu, A. Kohn.
Soc Neurosci Abstr, no. 545.15, 2022.

“Inter-areal patterned microstimulation selectively drives PFC population activity across behavioral tasks”
by J. Soldado Magraner, Y. Minai, W. E. Bishop, M. A. Smith*, B. M. Yu*.
Soc Neurosci Abstr, no. 736.09, 2022.

“Inter-areal patterned microstimulation selectively drives PFC activity and behavior in a memory task”
by J. Soldado Magraner, Y. Minai, W. E.Bishop, M. A. Smith*, B.M. Yu*.
Cosyne Abstracts, no. 1-027, 2022.

“Exceptionally large rewards lead to a collapse in neural information about upcoming movements”
by A. L. Smoulder, P. J. Marino, N. P. Pavlovsky, E. R. Oby, S. E. Snyder, W. E. Bishop, B. M. Yu, S. M. Chase*, A. P. Batista*.
Cosyne Abstracts, no. 2-001, 2022.

“A brain-computer interface in prefrontal cortex that suppresses neural variability”
by R. C. Williamson†, A. Umakantha†, C. S. Ki†, B. M. Yu*, M. A. Smith*.
Cosyne Abstracts, no. 2-124, 2022.

2021

“Neuronal population representations within and across cortical areas during perceptual decision making”
by A. I. Jasper, C. K. Machens, B. M. Yu, A. Kohn.
Soc Neurosci Abstr, no. 466.01, 2021.

“The time course of neural population activity is constrained”
by A. D. Degenhart, E. M. Grigsby, E. R. Oby, A. N. Motiwala, N. T. McClain, P. J. Marino, A. P. Batista*, B. M. Yu*.
Neural Control of Movement (NCM) Abstr, no. 3-G-72, 2021.

“Learning is shaped by an abrupt change in neural engagement”
by J. A. Hennig, E. R. Oby, M. D. Golub, L. A. Bahureksa, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista*, S. M. Chase*, B. M. Yu*.
Cosyne Abstracts, no. 1-077, 2021.

“The arm’s posture does not alter the time course of population activity in motor cortex”
by P. J. Marino, E. R. Oby, A. N. Motiwala, E. M. Grigsby, A. D. Degenhart, B. M. Yu*, A. P. Batista*.
Cosyne Abstracts, no. 1-092, 2021.

2020

“Dissecting feedforward and feedback interactions between populations of neurons”
by E. A. Gokcen, J. D. Semedo, A. Zandvakili, C. K. Machens*, A. Kohn*, B. M. Yu*.
Cosyne Abstracts, 2020. Talk.

“Evidence of a memory trace in motor cortex after short-term learning”
by D. M. Losey, J. A. Hennig, E. R. Oby, M. D. Golub, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista*, B. M. Yu*, S. M. Chase*.
Cosyne Abstracts, 2020. Talk.

“Simultaneous dimensionality reduction and deconvolution for calcium imaging recordings”
by T. Koh, W. E. Bishop, T. Kawashima, M. B. Ahrens, S. M. Chase*, B. M. Yu*.
Cosyne Abstracts, no. I-29, 2020.

“Slow coordinated activity across hemispheres in PFC predicts pupil size”
by A. Umakantha†, R. C. Williamson†, B. M. Yu*, M. A. Smith*.
Cosyne Abstracts, no. II-2, 2020.

“Automatic fitting of spiking network models to neuronal activity reveals limits of model flexibility”
by S. Wu, C. Huang, A. C. Snyder, M. A. Smith*, B. Doiron*, B. M. Yu*.
Cosyne Abstracts, no. II-105, 2020.

“Constraints on the time course of neural population activity”
by A. D. Degenhart, E. M. Grigsby, N. T. McClain, P. J. Marino, A. N. Motiwala, E. R. Oby, A. P. Batista*, B. M. Yu*.
Cosyne Abstracts, no. III-59, 2020.

“A motor cortical model of brain-machine interface learning, fast and slow”
by J. A. Menendez, J. A. Hennig, M. D. Golub, E. R. Oby, A. P. Batista, S. M. Chase, B. M. Yu, P. E. Latham.
Cosyne Abstracts, no. III-93, 2020.

2019

“Constraints on the time course of neural population activity”
by A. D. Degenhart, E. M. Grigsby, N. T. McClain, E. R. Oby, A. P. Batista*, B. M. Yu*.
Soc Neurosci Abstr, no. 313.15, 2019.

“The influence of object presence on M1 activity during movement planning and execution”
by A. J. Herrera, R. A. Gaunt, M. L. Boninger, A. P. Batista, B. M. Yu, S. M. Chase, J. L. Collinger.
Soc Neurosci Abstr, no. 315.08, 2019.

“A stable population code for attention in prefrontal cortex drives a dynamic code in visual cortex”
by A. C. Snyder, B. M. Yu, M. A. Smith.
Soc Neurosci Abstr, no. 664.21, 2019.

“Low-dimensional interactions between cortical areas”
by J. D. Semedo, A. Zandvakili, A. Aschner, C. K. Machens, A. Kohn, B. M. Yu.
SAND Abstracts, 2019. Talk.

“Simultaneous dimensionality reduction and deconvolution of calcium imaging activity”
by T. Koh, W. E. Bishop, S. M. Chase*, B. M. Yu*.
SAND Abstracts, no. 33, 2019.

“A slow drift of macaque visual and prefrontal cortex: Implications for perceptual decision-making”
by B. R. Cowley, A. C. Snyder, K. Acar, R. C. Williamson, B. M. Yu, M. A. Smith.
Cosyne Abstracts, no. II-86, 2019.

“Temporal dynamics of inter-area neuronal population interactions”
by J. D. Semedo, A. Zandvakili, A. Aschner, C. K. Machens, A. Kohn, B. M. Yu.
Cosyne Abstracts, no. III-31, 2019.

“Tracking attention fluctuations in the human brain with an EEG-based cognitive brain-machine interface”
by A. Chinchani, S. Ganesh, B. M. Yu, D. Sridharan.
Cosyne Abstracts, no. III-101, 2019.

2018

“A slow drift of macaque V4 population activity: Implications for perceptual decision-making”
by B. R. Cowley, A. C. Snyder, K. Acar, R. C. Williamson, B. M. Yu, M. A. Smith.
Soc Neurosci Abstr, no. 017.07, 2018. Talk.

“Temporal dynamics of inter-area neuronal population interactions”
by J. D. Semedo, A. Zandvakili, C. K. Machens, A. Kohn, B. M. Yu.
Soc Neurosci Abstr, no. 141.11, 2018.

“Neural signal stabilization improves human intracortical BCI control”
by A. J. Herrera, A. D. Degenhart, W. E. Bishop, E. R. Oby, E. C. Tyler-Kabara, S. M. Chase, A. P. Batista, B. M. Yu, J. L. Collinger.
Soc Neurosci Abstr, no. 312.19, 2018.

“Learning can generate new patterns of neural population activity”
by E. R. Oby, M. D. Golub, J. A. Hennig, A. D. Degenhart, E. C. Tyler-Kabara, B. M. Yu*, S. M. Chase*, A. P. Batista*.
Cosyne Abstracts, 2018. Talk.

“The relationship between pairwise correlation and dimensionality reduction”
by R. Morina, B. R. Cowley, A. Umakantha, A. C. Snyder, M. A. Smith*, B. M. Yu*.
Cosyne Abstracts, no. I-15, 2018.

“Distinct population codes for attention in the presence and absence of visual stimulation”
by A. C. Snyder, B. M. Yu, M. A. Smith.
Cosyne Abstracts, no. I-44, 2018.

“Leveraging low-dimensional structure in neural population activity to combine neural recordings”
by W. E. Bishop, E. Crowder, A. Zandvakili, X. Zhou, S. M. Chase, A. Kohn, C. R. Olson, B. M. Yu.
Cosyne Abstracts, no. I-69, 2018.

“Adaptive stimulus selection for optimizing neural population responses”
by B. R. Cowley, R. C. Williamson, K. Acar, M. A. Smith*, B. M. Yu*.
Cosyne Abstracts, no. II-23, 2018.

2017

“A diverse neural code gives rise to attentional preparation”
by A. C. Snyder, B. M. Yu, M. A. Smith.
Soc Neurosci Abstr, no. 16.05, 2017. Talk.

“The relationship between pairwise correlation and dimensionality reduction”
by R. Morina, B. R. Cowley, M. A. Smith*, B. M. Yu*.
Soc Neurosci Abstr, no. 148.26, 2017.

“Distance covariance analysis”
by B. R. Cowley, J. D. Semedo, D. A. Ruff, A. Zandvakili, M. R. Cohen, M. A. Smith, A. Kohn, B. M. Yu.
Asilomar Conference on Signals, Systems, and Computers, 2017. Talk.

“Distance covariance analysis”
by B. R. Cowley, J. D. Semedo, D. A. Ruff, A. Zandvakili, M. R. Cohen, M. A. Smith, A. Kohn, B. M. Yu.
Statistical Analysis of Neural Data (SAND) meeting, 2017. Talk.

“Extracting stable representations of neural population state from unstable neural recordings”
by W. E. Bishop*, A. D. Degenhart*, E. R. Oby, E. C. Tyler-Kabara, A. P. Batista, S. M. Chase*, B. M. Yu*
Statistical Analysis of Neural Data (SAND) meeting, 2017. Talk.

“Relationship between pairwise correlation and dimensionality reduction”
by R. Morina, B. R. Cowley, M. A. Smith*, B. M. Yu*.
Statistical Analysis of Neural Data (SAND) meeting, 2017.

“Distance covariance analysis”
by B. R. Cowley, J. D. Semedo, A. Zandvakili, M. A. Smith, A. Kohn, B. M. Yu.
Cosyne Abstracts, 2017.

“Learning by neural reassociation”
by M. D. Golub, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista, S. M. Chase*, B. M. Yu*
Cosyne Abstracts, 2017.

“Predicting neural activity in behaviorally-irrelevant dimensions”
by J. A. Hennig, M. D. Golub, P. J. Lund, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista, B. M. Yu*, S. M. Chase*
Cosyne Abstracts, 2017.

2016

“Self-recalibrating brain-computer interfaces based on population subspace alignment”
by A. D. Degenhart, W. E. Bishop, E. R. Oby, E. C. Tyler-Kabara, A. P. Batista, S. M. Chase*, B. M. Yu*
Soc Neurosci Abstr, no. 334.13, 2016.

“Population-level changes in neural activity during learning”
by M. D. Golub, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista, S. M. Chase*, B. M. Yu*
Soc Neurosci Abstr, no. 486.06, 2016. Talk.

“Moment-to-moment fluctuations of attention in macaque area V4”
by A. Umakantha, A. C. Snyder, B. M. Yu, M. A. Smith
Soc Neurosci Abstr, no. 531.11, 2016.

“Risky reward seeking disrupts coordination of prefrontal cortex and VTA neuronal activity”
by J. Park, A. Del Arco, B. M. Yu, B. Moghaddam
Soc Neurosci Abstr, no. 175.13, 2016.

“Exploring learning-induced changes in neural population activity”
by E. R. Oby, A. D. Degenhart, E. C. Tyler-Kabara, B. M. Yu, S. M. Chase, A. P. Batista
Neural Control of Movement (NCM) Abstr, 2016.

“Effects of excitatory versus inhibitory neuron sampling on outputs of dimensionality reduction”
by S. Bittner, R. C. Williamson, A. C. Snyder, A. Litwin-Kumar, B. Doiron, S. M. Chase*, M. A. Smith*, B. M. Yu*
Cosyne Abstracts, 2016.

“Low trial-to-trial variability in stimulus-encoding dimensions in macaque primary visual cortex”
by B. R. Cowley, D. A. Ruff, M. R. Cohen, T. S. Lee, A. Kohn*, M. A. Smith*, B. M. Yu*
Cosyne Abstracts, 2016.

“Learning engages both high- and low-covariance modes of neural population activity”
by M. D. Golub, P. T. Sadtler, K. M. Quick, S. I. Ryu, E. C. Tyler-Kabara, A. P. Batista, S. M. Chase*, B. M. Yu*
Cosyne Abstracts, 2016.

“Predicting V2 activity from V1 population activity”
by J. D. Semedo, A. Zandvakili, C. K. Machens*, B. M. Yu*, A. Kohn*
Cosyne Abstracts, 2016.

2015

“Characterizing population-level interactions between V1 and V2”
by J. D. Semedo, B. R. Cowley, A. Zandvakili, C. K. Machens, B. M. Yu, A. Kohn
Soc Neurosci Abstr, no. 331.07, 2015.

“Scaling properties of dimensionality reduction for neural populations and network models”
by R. C. Williamson, B. R. Cowley, A. Litwin-Kumar, B. Doiron, A. Kohn, M. A. Smith, B. M. Yu
Soc Neurosci Abstr, no. 59.08, 2015.

“Network constraints dictate the timescale of learning new brain-computer interfaces”
by E. R. Oby, A. D. Degenhart, E. C. Tyler-Kabara, B. M. Yu, A. P. Batista
Soc Neurosci Abstr, no. 201.01, 2015. Talk.

“PFC-VTA neuronal substrates for anxiety-related alteration of motivated behavior”
by J. Park, A. Del Arco, B. M. Yu, B. Moghaddam
Soc Neurosci Abstr, no. 259.04, 2015.

“Characterizing population-level interactions between V1 and V2”
by J. D. Semedo, B. R. Cowley, A. Zandvakili, C. K. Machens, B. M. Yu, A. Kohn
Neural Coding, Computation and Dynamics, 2015. Talk.

“Internal models for interpreting neural population activity during sensorimotor control”
by M. D. Golub, B. M. Yu, S. M. Chase
Cosyne Abstracts, 2015.

“Accounting for time delays in dimensionality reduction of neural population activity”
by K. C. Lakshmanan, P. T. Sadtler, E. C. Tyler-Kabara, A. P. Batista, B. M. Yu
Cosyne Abstracts, 2015.

“Extracting latent structure from multiple interacting neural populations”
by J. D. Semedo, A. Zandvakili, A. Kohn, C. K. Machens, B. M. Yu
Cosyne Abstracts, 2015.

“Single-trial motor and cortical variability are tightly and bi-directionally coupled”
by M. Pachitariu, C. Ames, B. Yu, G. Santhanam, S. Ryu, K. Shenoy, M. Sahani
Cosyne Abstracts, 2015. Talk.

2014

“Neural constraints on learning”
by P. Sadtler, K. Quick, M. Golub, S. Ryu, B. Yu, and A. Batista.
Cosyne Abstracts, 2014. Talk.

“Co-fluctuation patterns of population activity in macaque primary visual cortex”
by B. Cowley, M. Smith, A. Kohn, and B. Yu.
Cosyne Abstracts, no. I-62, 2014.

“A theory of neural dimensionality and measurement”
by P. Gao, E. Trautmann, B. Yu, G. Santhanam, S. Ryu, K. Shenoy, and S. Ganguli.
Cosyne Abstracts, 2014. Talk.

2013

“Neural co-modulation constrains motor learning”
by P. T. Sadtler, K. M. Quick, M. D. Golub, S. I. Ryu, B. M. Yu, and A. P. Batista.
Soc Neurosci Abstr, no. 833.03, 2013.

“Dimensionality in the motor cortical substrate for reaching”
by E. Trautmann, P. Gao, J. Fan, J. Kao, S. Stavisky, P. Nuyujukian, B. Yu, G. Santhanam, S. Ryu, S. Ganguli, and K. Shenoy.
Soc Neurosci Abstr, no. 750.07, 2013.

“Dimensionality, dynamics, and correlations in the motor cortical substrate for reaching”
by P. Gao, E. Trautmann, B. Yu, G. Santhanam, S. Ryu, K. Shenoy, and S. Ganguli.
Cosyne Abstracts, no. III-12, 2013.

2012

“Long-term decoding stability without retraining for intracortical brain-computer interfaces”
by W. Bishop, C. A. Chestek, V. Gilja, P. Nuyujukian, S. I. Ryu, K. V. Shenoy, and B. M. Yu.
Translational and Computational Motor Control (TCMC), 2012.

“Internal models engaged by brain-computer interface control”
by M. D. Golub, B. M. Yu, and S. M. Chase.
Translational and Computational Motor Control (TCMC), 2012. Talk.

“Internal models engaged by brain-computer interface control”
by M. D. Golub, B. M. Yu, and S. M. Chase.
Soc Neurosci Abstr, no. 275.01, 2012.

“Enhanced stability of cursor stopping in brain-computer interfaces”
by M. D. Golub, B. M. Yu, A. B. Schwartz, and S. M. Chase.
34th Annual Conf IEEE EMBS, 2012. Talk.

“Internal model estimation for closed-loop brain-computer interfaces”
by M. D. Golub, S. M. Chase, and B. M. Yu.
Statistical Analysis of Neural Data (SAND) meeting, 2012. Talk.

“Internal model estimation for feedback control in brain-computer interfaces”
by M. D. Golub, S. M. Chase, and B. M. Yu.
Janelia Conference: Machine Learning, Statistical Inference, and Neuroscience, 2012.

“Internal model estimation for feedback control in brain-computer interfaces”
by M. D. Golub, S. M. Chase, and B. M. Yu.
Cosyne Abstracts, no. I-8, 2012.

“Long-term decoding stability without retraining for intracortical brain computer interface”
by W. E. Bishop, C. A. Chestek, V. Gilja, P. Nuyujukian, S. I. Ryu, K. V. Shenoy, and B. M. Yu.
Cosyne Abstracts, no. III-40, 2012.

2011

“DataHigh: Graphical user interface for visualizing and interacting with high-dimensional neural trajectories”
by B. R. Cowley, M. T. Kaufman, M. M. Churchland, S. I. Ryu, K. V. Shenoy, and B. M. Yu.
Soc Neurosci Abstr, no. 591.16, 2011.

“Estimating shared firing rate fluctuations in neural populations”
by B. M. Yu, A. Kohn, and M. A. Smith.
Soc Neurosci Abstr, no. 483.18, 2011.

“High-performance neural prosthetic control along instructed paths”
by P. T. Sadtler, K. M. Wilson, S. I. Ryu, B. M. Yu, and A. P. Batista.
Soc Neurosci Abstr, no. 142.13, 2011.

“Sources of within-session performance variability for closed-loop brain-computer interfaces”
by K. M. Wilson, P. T. Sadtler, S. I. Ryu, A. P. Batista, and B. M. Yu.
Soc Neurosci Abstr, no. 142.11, 2011.

“Improving cursor stops in closed-loop brain-computer interfaces by leveraging trajectory curvature”
by M. D. Golub, B. M. Yu, A. B. Schwartz, and S. M. Chase.
Soc Neurosci Abstr, no. 142.18, 2011.

“Low-dimensional dynamical segmentation of single-trial array recordings”
by B. Petreska, B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Soc Neurosci Abstr, no. 123.04, 2011. Talk.

“Modeling neural population recordings: Latent dynamics or directed couplings?”
by J. Macke, L. Buesing, J. P. Cunningham, B. M. Yu, K. V. Shenoy, and M. Sahani.
BC11: Computational Neuroscience & Neurotechnology Bernstein Conference & Neurex Annual Meeting, 2011.

“Estimating shared firing rate fluctuations in neural populations”
by B. M. Yu, A. Kohn, and M. A. Smith.
Nature Precedings: Computational and Systems Neuroscience (Cosyne) meeting, 2011. Talk.

“High-performance neural prosthetic control along instructed paths”
by P. T. Sadtler, S. I. Ryu, B. M. Yu, and A. P. Batista.
Nature Precedings: Computational and Systems Neuroscience (Cosyne) meeting, no. II-67, 2011.

“Detecting changes in neural dynamics within single trials”
by B. Petreska, B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Nature Precedings: Computational and Systems Neuroscience (Cosyne) meeting, no. I-33, 2011.

“Modelling low-dimensional dynamics in recorded spiking populations”
by J. Macke, L. Busing, J. P. Cunningham, B. M. Yu, K. V. Shenoy, and M. Sahani.
Nature Precedings: Computational and Systems Neuroscience (Cosyne) meeting, no. I-34, 2011.

“High-performance neural prosthetic control along instructed paths”
by P. T. Sadtler, S. I. Ryu, B. M. Yu, and A. P. Batista.
Emerging System Theories in BMI Neuroscience (Cosyne Workshop), 2011. Talk.

2010

“A high-performance continuous cortically-controlled prosthesis enabled by feedback control design”
by V. Gilja, P. Nuyujukian, C. A. Chestek, J. P. Cunningham, B. M. Yu, S. I. Ryu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 20.6, 2010. Talk.

“Generalization and robustness of a continuous cortically-controlled prosthesis enabled by feedback control design”
by P. Nuyujukian, V. Gilja, C. A. Chestek, J. P. Cunningham, J. M. Fan, B. M. Yu, S. I. Ryu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 20.7, 2010. Talk.

“A high-performance cortically-controlled motor prosthesis enabled by a feedback control perspective”
by V. Gilja, P. Nuyujukian, C. A. Chestek, J. P. Cunningham, B. M. Yu, S. I. Ryu, and K. V. Shenoy.
Proc of the Neural Interfaces Conference, Long Beach, CA, 2010. Poster F10.

“High-performance continuous neural cursor control enabled by a feedback control perspective”
by V. Gilja, P. Nuyujukian, C. A. Chestek, J. P. Cunningham, B. M. Yu, S. I. Ryu, and K. V. Shenoy.
Frontiers in System Neuroscience: Computational and Systems Neuroscience (Cosyne) meeting, 2010.

2009

“Low-dimensional single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Dimensionality reduction for multi-channel neural recordings (Cosyne Workshop), 2009. Talk.

“Gaussian-process factor analysis for low-d single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Frontiers in System Neuroscience: Computational and Systems Neuroscience (Cosyne) meeting, 2009.

“Stimulus onset quenches neural variability: a widespread cortical phenomenon”
by M. M. Churchland, B. M. Yu, J. P. Cunningham, L. P. Sugrue, M. R. Cohen, G. S. Corrado, W. T. Newsome, A. M. Clark, P. Hosseini, B. B. Scott, D. C. Bradley, M. A. Smith, A. Kohn, J. A. Movshon, K. M. Armstrong, T. Moore, S. W. Chang, L. H. Snyder, S. I. Ryu, G. Santhanam, M. Sahani, and K. V. Shenoy.
Frontiers in System Neuroscience: Computational and Systems Neuroscience (Cosyne) meeting, 2009.

2008

“Low-dimensional single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Statistical Analysis and Modeling of Response Dependencies in Neural Populations (NIPS Workshop), 2008. Talk.

“Single-trial analysis of neural population activity during motor preparation”
by B. M. Yu, J. P. Cunningham, M. M. Churchland, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Proceedings of the Annual Symposium: Advances in Computational Motor Control (Pre-SFN Symposium), (Emanuel Todorov and Reza Shadmehr, eds.), vol. 7, 2008. Talk.

“Low-dimensional single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Dynamical Neuroscience XVI: Neuronal Variability and Its Functional Significance (Pre-SFN Symposium), 2008.

“Gaussian process factor analysis for low-dimensional single-trial analysis of neural population activity”
by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Soc Neurosci Abstr, no. 319.9, 2008. Talk.

“Evidence for smooth and inertial dynamics in the evolution of neural state”
by A. Afshar, B. M. Yu, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Soc Neurosci Abstr, no. 319.8, 2008.

“Factor analysis based BCI decoding from spikes and LFP”
by V. Gilja, B. M. Yu, G. Santhanam, A. Afshar, S. I. Ryu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 779.2, 2008.

“Towards optimal estimates of neural firing rates from spike trains”
by J. P. Cunningham, B. M. Yu, V. Gilja, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Soc Neurosci Abstr, no. 862.10, 2008.

“Neural decoding of goal-directed reaches: scaling up the number of reach goals”
by Z. Rivera Alvidrez, R. S. Kalmar, B. M. Yu, S. I. Ryu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 862.17, 2008.

“Absence of fast-timescale correlations in macaque dorsal premotor cortex”
by C. A. Lehocky, G. Santhanam, A. Afshar, B. M. Yu, S. I. Ryu, J. P. Cunningham, V. Gilja, K. V. Shenoy, and A. P. Batista.
Soc Neurosci Abstr, no. 262.12, 2008.

“Ensemble recordings of neural activity in the prefrontal cortex during oculomotor choice behavior”
by J. B. Reppas, R. S. Kalmar, D. L. Kimmel, B. M. Yu, S. I. Ryu, K. V. Shenoy, and W. T. Newsome.
Research in Encoding And Decoding of Neural Ensembles (AREADNE), 2008.

“Single-trial representation of uncertainty about reach goals in macaque PMd”
by Z. Rivera Alvidrez, R. Kalmar, A. Afshar, G. Santhanam, B. M. Yu, S. I. Ryu, and K. V. Shenoy.
Computational and Systems Neuroscience (Cosyne) meeting, no. III-52, 2008.

2007

“Extracting low-dimensional trajectories from multiple spike trains”
by B. M. Yu, J. P. Cunningham, K. V. Shenoy, and M. Sahani.
Coherent Behavior in Neuronal Networks (CoBeNN), 2007.

“Extracting dynamical structure embedded in premotor cortical activity”
by K. V. Shenoy, B. M. Yu, A. Afshar, M. M. Churchland, J. P. Cunningham, and M. Sahani.
Neural Coding, Computation and Dynamics (NCCD), 2007.

“Inferring neural firing rates from spike trains using Gaussian processes”
by J. P. Cunningham, B. M. Yu, M. Sahani, and K. V. Shenoy.
Neural Coding, Computation and Dynamics (NCCD), 2007.

2006

“Optimal target placement for neural communication prostheses”
by J. P. Cunningham, B. M. Yu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 256.21, 2006.

“Influence of eye position on end-point decoding accuracy in dorsal premotor cortex”
by A. P. Batista, B. M. Yu, G. Santhanam, S. I. Ryu, A. Afshar, and K. V. Shenoy.
Soc Neurosci Abstr, no. 148.8, 2006.

“Hidden Markov models for spatial and temporal estimation for prosthetic control”
by C. Kemere, B. M. Yu, G. Santhanam, S. I. Ryu, A. Afshar, T. H. Meng, and K. V. Shenoy.
Soc Neurosci Abstr, no. 256.17, 2006.

“The relationship between PMd neural activity and reaching behavior is stable in highly trained macaques”
by C. A. Chestek, A. P. Batista, B. M. Yu, G. Santhanam, S. I. Ryu, A. Afshar, and K. V. Shenoy.
Soc Neurosci Abstr, no. 148.5, 2006.

“Heterogeneous reference frames for reaching in macaque PMd”
by A. P. Batista, G. Santhanam, B. M. Yu, S. I. Ryu, A. Afshar, and K. V. Shenoy.
Neural Control of Movement Annual Meeting, no. F-12, 2006.

2005

“Extracting dynamical structure embedded in motor preparatory activity”
by B. M. Yu, A. Afshar, G. Santhanam, S. I. Ryu, K. V. Shenoy, and M. Sahani.
Computational and Systems Neuroscience (Cosyne) meeting, no. 290, 2005.

“Feedback-directed state transition for recursive Bayesian estimation of goal-directed trajectories”
by B. M. Yu, G. Santhanam, S. I. Ryu, and K. V. Shenoy.
Computational and Systems Neuroscience (Cosyne) meeting, no. 291, 2005.

“Neural variability in premotor cortex provides a signature of motor preparation”
by M. M. Churchland, B. M. Yu, S. I. Ryu, G. Santhanam, and K. V. Shenoy.
Computational and Systems Neuroscience (Cosyne) meeting, no. 13, 2005.

“Mixture of trajectory models for neural decoding of goal-directed movements”
by B. M. Yu, C. Kemere, G. Santhanam, A. Afshar, S. I. Ryu, T. H. Meng, M. Sahani, and K. V. Shenoy.
Soc Neurosci Abstr, no. 520.18, 2005.

“Extracting dynamical structure embedded in neural activity”
by M. Sahani, B. M. Yu, A. Afshar, G. Santhanam, S. I. Ryu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 689.14, 2005.

“Intra-cortical communication prosthesis design”
by G. Santhanam, S. I. Ryu, B. M. Yu, A. Afshar, and K. V. Shenoy.
Soc Neurosci Abstr, no. 519.19, 2005.

“Free-paced target estimation in a delayed-reach task”
by A. Afshar, N. Achtman, G. Santhanam, S. I. Ryu, B. M. Yu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 401.13, 2005.

“Heterogeneous coordinate frames for reaching in macaque PMd”
by A. P. Batista, G. Santhanam, B. M. Yu, S. I. Ryu, A. Afshar, and K. V. Shenoy.
Soc Neurosci Abstr, no. 363.12, 2005.

“PMd delay activity during rapid sequential-movement plans”
by R. S. Kalmar, V. Gilja, G. Santhanam, S. I. Ryu, B. M. Yu, A. Afshar, and K. V. Shenoy.
Soc Neurosci Abstr, no. 519.17, 2005.

“Trial-by-trial mean normalization improves plan period reach target decoding”
by V. Gilja, R. S. Kalmar, G. Santhanam, S. I. Ryu, B. M. Yu, A. Afshar, and K. V. Shenoy.
Soc Neurosci Abstr, no. 519.18, 2005.

“Motor preparation and settling activity in PMd”
by M. M. Churchland, B. M. Yu, S. I. Ryu, G. Santhanam, and K. V. Shenoy.
Neural Control of Movement Annual Meeting, no. E-13, 2005.

2004

“Improving neural prosthetic system performance for a fixed number of neurons”
by B. M. Yu, S. I. Ryu, M. M. Churchland, and K. V. Shenoy.
Computational and Systems Neuroscience (Cosyne) meeting, no. 219, 2004.

“Improving classification performance of neural prosthetic systems by combining plan and peri-movement activity”
by B. M. Yu, S. I. Ryu, G. Santhanam, M. M. Churchland, and K. V. Shenoy.
Soc Neurosci Abstr, no. 884.11, 2004.

“Time-course of PMd processing predicts reaction time”
by M. M. Churchland, B. M. Yu, S. I. Ryu, G. Santhanam, and K. V. Shenoy.
Soc Neurosci Abstr, no. 603.5, 2004.

“Coordinate frames for reaching in macaque dorsal premotor cortex (PMd)”
by A. P. Batista, B. M. Yu, G. Santhanam, S. I. Ryu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 191.7, 2004.

“High speed neural prosthetic icon positioning”
by S. I. Ryu, G. Santhanam, B. M. Yu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 263.1, 2004.

“High information transmission rates in a neural prosthetic system”
by G. Santhanam, S. I. Ryu, B. M. Yu, and K. V. Shenoy.
Soc Neurosci Abstr, no. 263.2, 2004.

“Reconstruction of arm trajectories from plan and peri-movement motor cortical activity”
by C. Kemere, G. Santhanam, S. I. Ryu, B. M. Yu, T. H. Meng, and K. V. Shenoy.
Soc Neurosci Abstr, no. 884.12, 2004.

“Reconstruction of arm trajectories from plan and peri-movement motor cortical activity”
by C. Kemere, G. Santhanam, S. I. Ryu, B. M. Yu, T. H. Meng, and K. V. Shenoy.
Annual Neural Prosthesis Program Meeting, National Institutes of Health, 2004.

“The speed at which reach movement plans can be decoded from the cortex and its implications for high performance neural prosthetic arm systems”
by S. I. Ryu, G. Santhanam, B. M. Yu, and K. V. Shenoy.
Annual Meeting Congress of Neurological Surgeons (CNS), vol. 55, no. 2, 2004. Article ID: 785.

“Premotor cortex plan activity used to decode upcoming reach speed for high-performance neural prosthetic system design”
by S. I. Ryu, B. M. Yu, M. M. Churchland, and K. V. Shenoy.
Annual Meeting American Association of Neurological Surgeons (AANS), 2004. Article ID: 19873.