“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, and
B. M. Yu.

*Neural Comput*, in press.

“Brain-computer interface control along instructed paths”

by P. T. Sadtler, S. I. Ryu, E. C. Tyler-Kabara, B. M. Yu*, and
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*, and A. P. Batista*.

*Nature*, vol. 512, 2014,
pp. 423-426. (cover article)

Research highlight in *Nat Rev Neurosci*: "Putting limits on learning"

“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, and 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, and 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, and B. M. Yu.

*J Neural Eng*, vol. 10 (066012), 2013.

“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, and K. V. Shenoy.

*Nat Neurosci*, vol. 15, 2012, pp. 1752-1757.

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“Single-trial neural correlates of arm movement preparation”

by A. Afshar, G. Santhanam, B. M. Yu, S. I. Ryu, M. Sahani, and K. V. Shenoy.

*Neuron*, vol. 71, 2011, pp. 555-564.

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“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, and 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, and K. V. Shenoy.

*Nat Neurosci*, vol. 13, 2010, pp. 369-378.

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4

“Factor-analysis methods for higher-performance neural
prostheses”

by G. Santhanam, B. M. Yu, V. Gilja, S. I. Ryu, A. Afshar, M. Sahani, and 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*, and M. Sahani*.

*J Neurophysiol*, vol. 102, 2009, pp. 614-635.

“Toward optimal target placement for neural prosthetic
devices”

by J. P. Cunningham, B. M. Yu, V. Gilja, S. I. Ryu, and 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, and 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, and
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, and 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, and 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, and 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, and 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, and
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*, and 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, and K. V.
Shenoy.

*Nature*, vol. 442, 2006, pp. 195-198.

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3

“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.

*J Neurosci*, vol. 26, no. 14, Apr. 2006, pp. 3697-3712.

“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.

“Extracting latent structure from multiple interacting neural populations”

by J. D. Semedo, A. Zandvakili, A. Kohn, C. K. Machens*, and 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*, and B. M. Yu*.

In *International Conference on Machine Learning*, 2013, pp. 606-614.

“Internal models engaged by brain-computer interface control”

by M. D. Golub, B. M. Yu*, and 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, and B. M. Yu.

In *Proc 34th Annual Conf IEEE EMBS*, 2012, pp. 4607-4610.

“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, and 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, and 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, and 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, and 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, and 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, and 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, and 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, and 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, and M. Sahani.

In *Advances in Neural Information Processing Systems 20*,
2008, pp. 329-336.

“Optimal target placement for neural communication
prostheses”

by J. P. Cunningham, B. M. Yu, and 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, and 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, and 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, and 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, and 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, and 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, and 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, and 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, and 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, and R. You.

In *Proc SPIE ITCom*, 2002, pp. 41-53.

“Neural decoding for motor and communication prostheses”

by B. M. Yu, G. Santhanam, M. Sahani, and K. V. Shenoy.

In *Statistical Signal Processing for Neuroscience*, (K. G. Oweiss, ed.), Academic Press, 2010. ISBN: 978-0-12-375027-3.

“Neural decoding of movements: From linear to nonlinear
trajectory models”

by B. M. Yu, J. P. Cunningham, K. V. Shenoy, and 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.

**“Neural dynamics of motor preparation and
execution”**

by B. M. Yu.

Ph.D. dissertation, Stanford University, 2007.

“Factor analysis with Poisson output”

by G. Santhanam, B. M. Yu, K. V. Shenoy, and M. Sahani.

Technical report, 2006.

“Derivation of Kalman filtering and smoothing
equations”

by B. M. Yu, K. V. Shenoy, and M. Sahani.

Technical report, 2004.

“Derivation of extended Kalman filtering and smoothing
equations”

by B. M. Yu, K. V. Shenoy, and M. Sahani.

Technical report, 2004.

**“Internal models for interpreting neural population activity during sensorimotor control”**

by M. D. Golub, B. M. Yu, and 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.

**“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

*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.

**“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.

**“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.

**“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.

**“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.

*Soc Neurosci Abstr*, no. 583.03, 2012.

**“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.

by W. E. Bishop, C. A. Chestek, V. Gilja, P. Nuyujukian, S. I. Ryu, K. V. Shenoy, and B. M. Yu.

by B. R. Cowley, M. T. Kaufman, M. M. Churchland, S. I. Ryu, K. V. Shenoy, and B. M. Yu.

**“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.

**“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.

**“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.

**“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.

**“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.

**“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.

*Soc Neurosci Abstr*, no. 818.18, 2007.

**“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.

**“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.

**“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.