Computational Neuroscience



Frank LM, Brown EN, Wilson MA. Trajectory encoding in the hippocampus and entorhinal cortex. Neuron 2000;27:169-178.

Frank LM, Brown EN, Wilson MA. A comparison of the firing properties of putative excitatory and inhibitory neurons from CA1 and the entorhinal cortex of the awake behaving rat. Journal of Neurophysiology 2001; Oct;86(4):2029-40.


Barbieri R, Quirk MC, Frank LM, Wilson MA, Brown EN. Construction and analysis of non-Poisson stimulus response models of neural spike train activity. Journal of Neuroscience Methods 2001;105:25-37.

Brown EN, Nguyen DP, Frank LM, Wilson MA, Solo V. An analysis of neural receptive field plasticity by point process adaptive filtering. Proceedings of the National Academy of Sciences 2001; 98:12261-66.


Brown EN, Barbieri R, Ventura V, Kass RE, Frank LM. The time-rescaling theorem and its application to neural spike train data analysis. Neural Computation 2002;14(2):325-46.

Frank LM, Eden UT, Solo V, Wilson MA, Brown EN. Contrasting patterns of receptive field plasticity in the hippocampus and the entorhinal cortex: an adaptive filtering approach. Journal of Neuroscience 2002; 22:3817-30.


Nguyen D, Frank LM, Brown EN. An application of reversible-jump MCMC to spike classification of multiunit extracellular recordings. Network: Computation in Neural Systems 2003;14:61-82.

Smith AC, Brown EN. Estimating a state-space model from point process observations. Neural Computation 2003;15:965-991.

Wirth S, Yanike M. Frank LM, Smith AC, Brown EN, Suzuki WA. Single neurons in the monkey hippocampus and learning of new associations. Science 2003; 300:1578-1581.

Brown EN, Barbieri R, Eden UT, Frank LM. Likelihood methods for neural data analysis. In: Feng J, ed. Computational Neuroscience: A Comprehensive Approach. London: CRC, 2003; Chapter 9, pp 253-286.


Barbieri R, Frank LM, Nguyen DP, Quirk MC, Solo V, Wilson MA, Brown EN. Dynamic analyses of information encoding by neural ensembles. Neural Computation 2004; 16(2):277-308.

Smith AC, Frank LM, Wirth S, Yanike M, Hu D, Kubota Y, Graybiel AM, Suzuki W, Brown EN. Dynamic analysis of learning in behavioral experiments. Journal of Neuroscience 2004; 24(2):447-461.

Eden UT, Frank LM, Barbieri R, Solo V, Brown EN. Dynamic analyses of neural encoding by point process adaptive filtering. Neural Computation 2004; 16(5), 971-998.

Brown EN, Kass RE, Mitra PP. Multiple neural spike train data analysis: state-of-the-art and future challenges. Nature Neuroscience 2004; 7(5):456-61.

Frank LM, Stanley GB, Brown EN. Hippocampal plasticity across multiple days of exposure to novel environments. Journal of Neuroscience 2004; 24(35):7681-89.

Truccolo W, Eden U, Fellow M, Donoghue JD, Brown EN. A point process framework for relating neural spiking activity to spiking history, neural ensemble and covariate effects. Journal of Neurophysiology, (published online Sept 8, 2004), 2005, 93:1074-1089.

Barbieri R, Matten EC, Alabi A, Brown EN. A point process model of human heart beat intervals: new definitions of heart rate and heart rate variability, American Journal of Physiology: Heart and Circulatory Physiology (published on line Sept. 16, 2004), 2005, 288: H424-H435.

Smith AC, Stefani MR, Moghaddam B, Brown EN. Analysis and design of behavioral experiments to characterize population learning. Journal of Neurophysiology (published on line Sept 29, 2004), 2005, 93: 1776-1792.

Law JR, Flanery MA, Wirth S, Yanike M, Suzuki WA, Smith AC, Frank LM, Brown EN, Stark CEL. fMRI activity during the gradual acquisition and expression of paired-associate memory. Journal of Neuroscience 2005, 25(24): 5720-5729.

Barbieri R, Wilson MA, Frank LM, Brown EN. An analysis of hippocampal spatio-temporal representations using a Bayesian algorithm for neural spike train decoding. IEEE Transactions on Neural Systems & Rehabilitation Engineering 2005, 13(2): 131-136.

Kass RE, Ventura V, Brown EN. Statistical issues in the analysis of neuronal data. Journal of Neurophysiology 2005, 94: 8-25.

Okatan M, Wilson MA, Brown EN. Analyzing functional connectivity using a network likelihood model of ensemble neural spiking activity. Neural Computation 2005, 17(9): 1927-1961.

Brown EN. Theory of Point Processes for Neural Systems. In: Chow CC, Gutkin B, Hansel D, Meunier C, Dalibard J, eds. Methods and Models in Neurophysics. Paris, Elsevier; 2005, Chapter 14, pp. 691-726.

Brown EN and Barbieri R. Dynamic Analyses of Neural Representations Using the State-Space Modeling Paradigm. In: Madras B, Von Zastrow M, Colvis C, Rutter J, Shurtleff D, Pollock J. The Cell Biology of Addiction, New York, Cold Spring Harbor Laboratory Press, 2005, p. 415-432.

Suzuki WA, Brown EN. Behavioral and neurophysiological analysis of dynamic learning processes. Behavioral and Cognitive Neuroscience Reviews, 2005, 4(2): 67-95.


Lee WCA, Huang H, Feng G, Sanes JR, Brown EN, So PT, Nedivi E. Dynamic remodeling of dendritic arbors in GABAergic interneurons of adult visual cortex. Public Library of Science – Biology, 2006, Feb 4(2): e29.

Barbieri R, Brown EN. Analysis of heart beat dynamics by point process adaptive filtering. IEEE Transactions on Biomedical Engineering 2006, 53(1): 4-12.

Haslinger R, Ulbert I, Moore C, Brown EN, Devor A. Laminar analysis of the effect of ongoing cortical activity on the stimulus evoked response in rat somatosensory cortex. Journal of Neurophysiology, 2006, 96(3):1658-63.

Srinivasan L, Eden UT, Willsky AS, Brown EN. A state-space analysis for reconstruction of goal-directed movements using neural signals. Neural Computation, 2006, 18(10): 2465-2494.

Frank LM, Brown EN, Stanley GB. Hippocampal and cortical place cell plasticity: Implications for episodic memory. Hippocampus, 2006, 16(9): 775-784.

Karameh FN, Dahleh MA, Brown EN, Massaquoi SG. Modeling the contribution of lamina 5 neuronal and network dynamics to low frequency EEG phenomena. Biological Cybernetics, 2006, 95(4): 289-310.

Ergun A, Barbieri R, Eden UT, Wilson MA, Brown EN. Construction of point process adaptive filter algorithms for neural systems using sequential Monte Carlo methods. IEEE Transactions on Biomedical Engineering, 2007, 54(3): 419-428.

Srinivasan L, Brown EN. A state-space framework for movement control to dynamic goals through brain-driven interfaces. IEEE Transactions on Biomedical Engineering, 2007, 54(3): 526-535.

Smith AC, Wirth A, Suzuki WA, Brown EN. Bayesian analysis of interleaved learning and response bias in behavioral experiments. Journal of Neurophysiology, 2007, 97(3): 2516-2524.

Diniz Behn C, Brown EN, Scammell TE, Kopell NJ. A mathematical model of network dynamics governing mouse sleep-wake behavior. Journal of Neurophysiology, 2007, 97(6): 3828-3840.

Srinivasan L, Eden UT, Mitter SK, Brown EN. General purpose filter design for neural prosthetic devices. Journal of Neurophysiology, 2007, 98(4):2456-75.

Diniz Behn CG, Kopell N, Brown EN, Mochizuki T, Scammell TE. Delayed orexin signaling consolidates wakefulness and sleep: physiology and modeling. Journal of Neurophysiology, 2008, 99(6):3090-103.

Czanner G, Eden UT, Wirth S, Yanike M, Suzuki WA, Brown EN. Analysis of between-trial and within-trial neural spiking dynamics. Journal of Neurophysiology, 2008, 99(5): 2672-2693. PMID 18216233

Napadow V, Dhond R, Conti G, Makris N, Brown EN, Barbieri R. Brain correlates of autonomic modulation: combining heart rate variability with fMRI. NeuroImage, 2008, 42(1): 169-177. PMID 18524629

Prerau MJ, Smith AC, Eden UT, Yanike M, Suzuki WA, Brown EN. A mixed filter algorithm for state estimation from simultaneously recorded continuous-valued and binary observation. Biological Cybernetics, 2008, 99(1): 1-14. PMID 18438683

Eden UT, Brown EN. Continuous-time filters for state estimation from point process models of neural data. Statistica Sinica, 2008, 18(4): 1293-1310.

Molins A, Stufflebeam SM, Brown EN, Hamalainen MS. Quantification of the benefit from integrating MEG and EEG data in minimum L2-norm estimation. NeuroImage, 2008, 42(3): 1069-1077. PMID: 18602485

Yanike M, Wirth S, Smith AC, Brown EN, Suzuki WA. Comparison of associative learning-related signals in the macaque perhihinal cortex and hippocampus. Cerebral Cortex, 2008, October 20. PMID: 19074022

McCarthy MM, Brown EN, Kopell NK. Potential network mechanisms mediating electroencephalographic beta rhythm changes during propofol-induced paradoxical excitation. Journal of Neuroscience, 2008, Dec 10; 28(50): 13488-13504. PMID 19074022.

Temereanca S, Brown EN, Simons DJ. Rapid changes in thalamic firing synchrony during repetitive whisker stimulation. Journal of Neuroscience, 2008, 28(44): 11153-11164. PMID: 18971458

Chen Z, Vijayan S, Wilson MA, Barbieri R, Brown EN. Discrete- and continuous-time probabilistic models and algorithms for inferring neuronal UP/DOWN states. Neural Computation, 2009, March 26 Epub. PMID: 19323637

Scholz J, Triantafyllou C, Whitfield-Gabrieli S, Brown EN, Saxe R. Distinct regions of right temporo-parietal junction are selective for theory of mind and exogenous attention. PLoS One, 2009, 4(3): e4869 Epub March 17. PMID: 19290043

Koyama S, Eden UT, Brown EN, Kass RE. Bayesian decoding of neural spike trains. Annals of the Institute of Statistical Mathematics, 2009, In Press.

Chen Z, Brown EN, Barbieri R. Assessment of autonomic control and respiratory sinus arrhythmia using point process models of human heart beat dynamics. IEEE Transactions on Biomedical Engineering, 2009, In Press.

Wirth S, Avsar E, Chiu CC, Varun S, Smith AC,  Brown EN, Suzuki WA. Trial outcome and associative learning signals in the monkey hippocampus. Neuron, 2009, 61(6): 930-940. PMID: 19324001

Purdon PL, Pierce ET, Bonmassar G, Walsh JL, Harrell PG, Kwo J, Deschler D, Barlow M, Merhar RC, Lamus C, Mullaly CM, Sullivan M, Maginnis S, Skoniecki D, Higgins H, Brown EN. Simultaneous electroencephalography and functional magnetic resonance imaging of general anesthesia. Annals of the New York Academy of Science, 2009,1157: 61-70. PMID: 19351356

Functional Neural Imaging

Solo V, Purdon P, Weisskoff R, Brown EN. A signal estimation approach to functional MRI. IEEE Transactions on Medical Imaging 2001; Vol. 20, No. 1.

Purdon PL, Solo V, Weisskoff RM, Brown EN. Locally regularized spatiotemporal modeling and model comparison for functional MRI. NeuroImage 2001; 14, 912-923.

Bonmassar G, Purdon PL, Jaaskelainen IP, Chiappa K, Solo V, Brown EN, Belliveau JW. Motion and ballistocardiogram artifact removal for interleaved recording of EEG and EPs during MRI. NeuroImage 2002; 16, 1127-1141.

Long CL, Brown EN, Manoach D, Solo V. Spatio-temporal wavelet analysis for functional MRI. NeuroImage (published online August 9, 2004), 2004; 23 (2):500-516.

Long CL, Brown EN, Triantafyllou C, Aharon I, Wald L, Solo V. Nonstationary noise estimation in functional MRI. Neuroimage (published online August 29, 2005) 2005; 28(4): 890-903.

Circadian and Neuroendocrine Physiology

Czeisler CA, Kronauer RE, Allan JS, Duffy JF, Jewett ME, Brown EN, Ronda JM. Bright light induction of strong (Type 0) resetting of the human circadian pacemaker. Science 1989;244:1328-33.

Brown EN. A note on the asymptotic distribution of parameter estimates for the harmonic regression model. Biometrika 1990;77:653-56.

Czeisler CA, Johnson MP, Duffy JF, Brown EN, Ronda JM, Kronauer RE. Exposure to bright light and darkness to treat physiologic maladaptation to night work. New England Journal of Medicine 1990;322:1253-59.

Czeisler CA, Dumont M, Duffy JF, Steinberg JD, Richardson GS, Brown EN, Sanchez R, Rios CD, Ronda JM. Association of sleep-wake habits in older people with changes in output of circadian pacemaker. Lancet 1992;340:933-36.

Brown EN, Czeisler CA. The statistical analysis of circadian phase and amplitude in constant routine core-temperature data. Journal Biological Rhythms 1992; 7: 177-202.

Brown EN, McDermott T, Bloch KJ, McCollom AD. Defining the smallest analyte concentration an immunoassay can measure. Clinical Chemistry 1996; 42: 893-903.

Brown EN, Choe Y, Shanahan TL, Czeisler CA. A mathematical model of diurnal variation in plasma melatonin levels. American Journal of Physiology, (Endocrinology and Metabolism 35) 1997; 272: E506-E16.

El-Hajj G, Klerman EB, Brown EN, Choe Y, Brown EM, Czeisler CA. Parathyroid hormone circadian rhythm is truly endogenous. Journal of Clinical Endocrinology and Metabolism 1997;82:281-86.

Czeisler CA, Duffy JF, Shanahan TL, Brown EN, Mitchell JF, Rimmer DW, Ronda JM, Silva E, Allan JS, Emens JS, Dijk DJ, Kronauer RE. Age-independent stability, precision, and near 24-hour period of the human circadian pacemaker. Science 1999;284:2177-81.

Zeitzer JM, Dijk DJ, Kronauer RE, Brown EN, Czeisler CA. Sensitivity of the human circadian pacemaker to nocturnal light: melatonin phase resetting and suppression. Journal of Physiology 2000;526:695-702.

Brown EN, Choe Y, Luithardt H, Czeisler CA. A statistical model of the human core- temperature circadian rhythm. American Journal of Physiology 2000;279:E669-E83.

Brown EN, Meehan PM, Dempster AP. A stochastic differential equation model of diurnal cortisol patterns. American Journal Physiology (Endocrinology and Metababolism) 2001; 280: E450-E461.

Klerman EB, Adler GK, Jin M, Maliszewski AM, Brown EN. A statistical model of diurnal variation in human growth hormone. American Journal of Physiology 2003; E1118-26.

Brown EN, Solo V, Choe Y, Zhang Z. Measuring the period of the human biological clock. In: Brand L, Johnson ML, eds. Methods in Enzymology, Numerical Computer Methods, Vol. 383, Orlando, Academic Press, 2004; 382-405. FIGURE 1, FIGURE 2, FIGURE 3.

Indic P, Forger DB, St. Hilaire MA, Dean DA, Brown EN, Kronauer RE, Klerman EB, Jewett ME. Comparison of amplitude recovery dynamics of two limit cycle oscillator models of the human circadian pacemaker. Chronobiology International, 2005, 22(4): 613-629.

Indic P, Brown EN. Characterizing the amplitude dynamics of the human core-temperature circadian rhythm using a stochastic-dynamical model. Journal of Theoretical Biology, 2006, 239: 499-506.