Publications

2010

T. Schneider, J. Gibson and J. Burke "Snakes and ladders: localized solutions of plane Couette flow", Phys. Rev. Lett. (2010) preprint
Kohanski MA, DePristo MA and Collins JJ. "Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis", Mol Cell. 2010 Feb 13.
Neilans, E.G., Welch, T.E., Maddox, R.K., Shinn-Cunningham, B.G., and Dent, M.L. "Are all syllables perceived equally? A comparative analysis of songsyllable perception in zebra finches (Taeniopygia guttata) and budgerigars (Melopsittacus undulatus)", (2010) preprint
Ed Reznik and Daniel Segrè "On the stability of metabolic cycles", Journal of Theoretical Biology (2010) , preprint
William Riehl, Paul Krapivsky, Sidney Redner and Daniel Segrè "Arithmetic simplicity beneath metabolic network architecture", PLoS Computational Biology , revision in progress. (2010) , preprint
N. Kopell, C. Borgers, D. Pervouchine, P. Malerba, and A. B.L.Tort. "Gamma and theta rhythms in biophysical models of hippocampal circuits", Hippocampal Microcircuits: A Computational Modeller's Resource Book. Eds. V. Cutsuridis, B.P. Graham, S. Cobb, I. Vida. Springer 2010. Ch. 15. Code for figures: Fig. 1, Fig. 2, Figs. 3 and 4.
T. Gloveli, N. Kopell and T. Dugladze. "Neuronal Activity Patterns during Hippocampal Network Oscillations in Vitro", Hippocampal Microcircuits: A Computational Modeller's Resource Book. Eds. V. Cutsuridis, B.P. Graham, S. Cobb, I. Vida. Springer 2010. Ch. 8.
Yang, S. and Kolaczyk, E.D. "Target detection via network filtering", IEEE Transactions on Information Theory (2010) preprint

2009

Kramer, M.A., Eden, U.T., Cash, S.S., and Kolaczyk, E.D. "Network inference — with confidence — from multivariate time series", Physical Review E, 79 , 061916. (2009)
Lee S., Sen K., Kopell N. "Cortical gamma rhythms modulate NMDAR-mediated spike timing dependent plasticity in a biophysical model.", PLoS Computational Biology, 5 (12), e1000602. (2009)
M. Molla, A. Delcher, S. Sunyaev, C. Cantor and S. Kasif "Triplet Repeat Length Bias and Variation in the Human Transcriptome.", Proceedings of the National Academy of Sciences 106 (40): 17095-17100. October 6, 2009
Dwyer DJ, Kohanski MA J and Collins JJ. "Role of reactive oxygen species in antibiotic action and resistance.", Current Opinions in Microbiology. 12 (5): 482-489. July 30, 2009.
Hoffman A and Kennedy B "Existence and uniqueness of traveling waves in unidirectional lattice differential equations", DCDS-A (2009)
Niels Klitgord and Daniel Segrè: "The importance of compartmentalization in metabolic flux models: yeast as an ecosystem of organelles", Genome Informatics 22 : 41-55. (2009)
Huang Y, Brandon MP, Griffin AL, Hasselmo ME, Eden UT, "Decoding movement trajectories through a T-maze using point process filters applied to place field data from rat Hippocampal region CA1", Neural Computation, 21 (12):3305-3334 (2009)
G Kidd Jr., TM Streeter, A Ihlefeld, RK Maddox, CR Mason, "The intelligibility of pointillistic speech", Journal of the Acoustical Society of America, 126 (6), EL196-201. (2009)
Prerau MJ, Smith A, Eden UT, Kubota Y, Yanike M, Suzuki W, Graybiel A, Brown EN, "Characterizing learning by simultaneous analysis of continuous and binary measures of performance", J. Neurophys. 102 :3060-3072 (2009)
Prerau MP, Eden UT. "Characterizing the Time Course of Neural Activity Using a Cross-Validated Kernel Smoother", Under Revision (2009) preprint
J. Burke, S. M. Houghton, and E. Knobloch, "Swift-Hohenberg equation with broken reflection symmetry", Phys. Rev. E 80 -036202. (2009)
J. Burke and E. Knobloch, "Multipulse states in the Swift-Hohenberg equation", Discrete and Continuous Dyn. Syst. Suppl. 109 (2009)
Davies BW, Kohanski MA, Simmons L A, Winkler JA, Collins JJ and Walker GC. "Hydroxyurea induces hydroxyl radical-mediated cell death in Escherichia coli", Mol Cell. 36 (5): 845-860. Dec 11, 2009
L. Kay, J. Beshel, J. Brea, C. Martin. D. Rojas-Liban and N. Kopell, "Olfactory oscillations: the what, how and what for", Trends in the Neurosci. 32 (4):207-14. 2009 Apr; Epub 2009 Feb 23.
M Shamir, O. Ghitza, S. Epstein, N. Kopell, "Representations of time-varying stimuli by a network exhibiting oscillations on a faster time scale", PLoS Comput. Biol. 5 (5):e1000370. 2009 May; Epub 2009 May 1.
D. Vierling-Claassen and N. Kopell, "The dynamics of a periodically forced cortical microcircuit, with an application to schizophrenia", SIAM J. Applied Dynamical systems 8 (2): 710-733 (2009)
P. Wulff, A.A Ponomarenko, M. Bartos, T. M. Korotkova, E.C. Fuchs, F. Bдhner, M. Both, A.B. L. Tort, N. Kopell, W. Wisden, and H. Monyer, "Hippocampal theta rhythm and its coupling with gamma oscillations require fast inhibition onto parvalbumin-positive interneurons", Proc Natl Acad Sci 106 (9):3561-6. Mar 3, 2009; Epub Feb 9, 2009.
G Van Baalen, D Kreimer, D Uminsky, and K Yeats, "The QED beta-function from global solutions to Dyson-Schwinger equations", Annals of Physics 324 (1):205-219. January 2009.
R Nagem, G Sandri, D Uminsky, and CE Wayne "Generalized Helmholtz/Kirchoff Model for Two-Dimensional Distributed Vortex Motion", SIAM Journal on Applied Dynamical Systems 8 (1): 160-179. (2009)
T Ellis, X Wang, and JJ Collins "Diversity-based, Model-guided Construction of Synthetic Gene Networks with Predicted Functions", Nature Biotechnology, doi:10.1038/nbt.1536 (*equally contributed). (2009)
F Schembri, S Sridhar, C Perdomo, AM Gustafson, X Zhang, A Ergun, J Lu, G Liu, X Zhang, J Bowers, C Vaziri, K Ott, K Sensinger, JJ Collins, JS Brody, R Getts, ME Lenburg, and A Spira "MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium", Proceedings of the National Academy of Sciences 106 : 2319-2324. (2009)
TK Lu and JJ Collins "Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy", PNAS doi: 10.1073. February, 2009.
D Camacho and JJ Collins "Systems biology strikes gold", Cell 137 : 24-26. (2009)
GD Graña, CP Billimoria, and K Sen "Analyzing Variability in Neural Respons to Complex Natural Sounds in the Awake Songbird", J Neurophysiol doi:10.1152/jn.90917.2008. (April 8, 2009)
ED Larson, CP Billimoria, and K Sen "A Biologically Plausible Computational Model for Auditory Object Recognition", J Neurophysiol 101 :323-331. (2009)
CP Billimoria, BJ Kraus, R Narayan, RK Maddox, and K Sen "Invariance and sensitivity to intensity in neural discrimination of natural sounds", J Neurosci 28 (25):6304-8. (2009)
DE O'Gorman, J White, and CA Shera, "Dynamical Instability Determines the Effect of Ongoing Noise on Neural Firing", JARO 10 : 251–267 (2009). Supplementary material
A Zagaris, CW Gear, TJ Kaper, and Y Kevrekidis, "Analysis of the accuracy and convergence of equation-free projection to a slow manifold", Modelisation Mathematique et Analyse Numerique 43 (2009)
JA White, FR Fernandez, MN Economo, and TJ Kispersky, "Using ‘Hard’ Real-Time Dynamic Clamp to Study Cellular and Network Mechanisms of Synchronization in the Hippocampal Formation", Dynamic-Clamp: From Principles to Applications. Springer Series in Computational Neuroscience, Vol. 1 Destexhe, Alain; Bal, Thierry (Eds.) (2009)
A Doelman, P van Heijster, and TJ Kaper, "Pulse dynamics in a three-component system: existence analysis", Journal of Dynamics and Differential Equations, 21 (1): 73—115 (2009)

2008

A Bergeon, J Burke, E Knobloch, and I Mercader, "Eckhaus instability and homoclinic snaking", Phys. Rev. E 78 046201. (2008)
EJ Berns, TI Netoff, JA White, and SR Eisenberg "Understanding interferential therapy: Neuronal thresholds and responses to sinusoidal, amplitude-modulated, and interferential current stimulation", IEEE Transactions on Neural Systems and Rehabilitation under review. (2008) preprint
JC Bettencourt, KP Lillis, L Stupin, and JA White "Effects of imperfect dynamic clamp: computational and experimental results", Journal of Neuroscience Methods 169 : 282-289. (2008)
H Chiu and D Segrè, "Comparative determination of biomass composition in differentially active metabolic states", Genome Informatics, 20 , 171-182. (2008)
EJ Cosgrove, Y Zhou, TS Gardner, and ED Kolaczyk, "Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia", Bioinformatics, 24 (21), 2482-2490. (2008)
RE Deville, A Harkin, M Holzer, K Josic, and T Kaper, "Analysis of a renormalization group method and normal form theory for perturbed ordinary differential equations", Physica D. 237 (2008)
DJ Dwyer, MA Kohanski, and JJ Collins, "Networking opportunities for bacteria", Cell 135 (7): 1153-1156. Dec 26, 2008
FR Fernandez and JA White "Artificial synaptic conductances reduce subthreshold oscillations and periodic firing in stellate cells of the entorhinal cortex", Journal of Neuroscience 28 : 3790-3803. (2008)
TS Heng, MW Painter, K Elpek, V Lukacs-Kornek, N Mauermann, SJ Turley, D Koller, FS Kim, AJ Wagers, N Asinovski, S Davis, M Fassett, M Feuerer, DH Gray, S Haxhinasto, JA Hill, G Hyatt, C Laplace, K Leatherbee, D Mathis, C Benoist, R Jianu, DH Laidlaw, JA Best, J Knell, AW Goldrath, J Jarjoura, JC Sun, Y Zhu, LL Lanier, A Ergun, Z Li, JJ Collins, SA Shinton, RR Hardy, R Friedline, K Sylvia, and J Kang, "The Immunological Genome Project: networks of gene expression in immune cells", Nature Immunolology 9 : 1091-1094. (2008)
A Hoffman and CE Wayne, "Counter-propagating two-soliton solutions in the Fermi-Pasta-Ulam lattice", Nonlinearity 21 , 2911—2947. (2008)
X Jiang, N Nariai, M Steffen, S Kasif, and ED Kolaczyk, "Integration of relational and hierarchical network information for protein function prediction", BMC Bioinformatics, 9 :350. (2008)
X Jiang, N Nariai, M Steffen, S Kasif, D Gold, and ED Kolaczyk, "Combining Hierarchical Inference in Ontologies with Heterogeneous Data Sources Improves Gene Function Prediction", Proceedings of the 2008 International IEEE Conference on Bioinformatics and Biomedicine. (2008)
T Keck, KP Lillis, YD Zhou, and JA White, "Frequency-dependent glycinergic inhibition modulates plasticity in hippocampus", Journal of Neuroscience, 28 : 7359-69. (2008)
TJ Kispersky and JA White "Stochastic models of ion channel gating", Scholarpedia 3 : 1327. (2008)
MA Kohanski, DJ Dwyer, J Wierzbowski, G Cottarel, and JJ Collins, "Mistranslation of membrane proteins and two-component system activation trigger antibiotic-mediated cell death", Cell, 135 (4): 679-690. Nov 14, 2008
MA Kohanski and JJ Collins, "Rewiring bacteria, two components at a time", Cell, 133 (6): 947-948. Jun 13, 2008
MA Kramer, A Tort, N Kopell, "Sharp edge artifacts and spurious coupling in EEG frequency comodulation measures", J Neurosci Methods 70 (2):352-7, Feb 2, 2008
MA Kramer, AK Roopun, LM Carracedo, RD Traub, MA Whittington, and N Kopell, "Rhythm Generation through Period Concatenation in Rat Somatosensory Cortex", PLoS Computational Biology, 4 (9): e1000169 doi:10.1371/journal.pcbi.1000169. (2008)
MA Kramer, RD Traub, and N Kopell, "New dynamics in cerebellar Purkinje cells: torus canards", Physical Review Letters, 101 , 068103. (2008)
M Krupa, N Popovic, N Kopell, H Rotstein. "Mixed-Mode Oscillations in a Three Time-Scale Model of Oscillations in the Dopaminergic Neuron", Chaos, 18 , 015106 (2008)
A Leray, K Lillis, and J Mertz, "Enhanced background rejection in thick tissue with differential-aberration two-photon microscopy", Biophysical Journal, 94 , 1449-58. (2008)
KP Lillis, A Eng, JA White, and J Mertz, "Two-photon imaging of spatially extended neuronal network dynamics with high temporal resolution", Journal of Neuroscience Methods. (2008)
MM McCarthy, EN Brown, and N Kopell, "Potential network mechanisms mediating electroencephalographic beta rhythm changes during propofol-induced paradoxical excitation", J Neurosci 28 (50):13488-13504. (2008)
WJ Riehl and D Segrè, "Optimal metabolic regulation using a constraint-based model", Genome Informatics, 20 , 159-170. (2008)
AK Roopun, MA Kramer, LM Carracedo, M Kaiser, CH Davies, RD Traub, NJ Kopell, and MA Whittington "Temporal interactions between cortical rhythms", Frontiers in Neuroscience 2 (2):145-154 (2008)
ES Snitkin and D Segrè "Optimality criteria for the prediction of metabolic fluxes in yeast mutants", Genome Informatics 20 :123-134 (2008)
ABL Tort, M. A. Kramer, C Thorn, DJ Gibson, Y Kubota, AM Graybiel, and N Kopell "Dynamic cross-frequency couplings of local field potential oscillations in rat striatum and hippocampus during performance of a T-maze task", Proc Nat Acad Sci 105 (51): 20517-20522 (2008)
P van Heijster, A Doelman, and TJ Kaper "Pulse dynamics in a three-component system: stability and bifurcations", PhysicaD 237 : 3335-3368 (2008)
D Vierling-Claassen, P Seikmeyer, S Stufflebeam, and N Kopell, "Modeling GABA alterations in schizophrenia: a link between impaired inhibition and altered gamma and beta range inhibitory entrainment", J. Neurophysiol 99 (5): 2656-71 (2008)

2007

Acker CD and White JA "Roles of IA and morphology in action potential propagation in CA1 pyramidal cell dendrites", Journal of Computational Neuroscience 23 : 201-216 (2007)
Dasika VK, White JA, Colburn HS "Simple models show the general advantages of dendrites in coincidence detection ", Neurophysiol 97 (5):3449-3459 (2007)
Dumortier F., Popovic N., Kaper T.J. "The critical wave speed for the FKPP equation with cutoff ", Nonlinearity 20 :855-877 (2007)
Dumortier F., Popovic N., Kaper, T.J. "The asymptotic critical wave speed in a family of scalar reaction-diffusion equations ", Journal of Mathematical Analysis and Applications 326 (2):1007-1023 (2007)
Krigman, S. and Wayne, C.E. "Boundary controllability of Maxwell's equations with nonzero conductivity inside a cube, I: Spectralcontrollability ", Journal of Mathematical Analysis and Applications 329 (2):1375-1396 (2007)

2006

Beck M.A., Doelman A., Kaper T.J. "A geometric analysis of traveling waves in a bioremediation model ", Journal of Nonlinear Science 16 (4):329-349 (2006)
Beck M.A., Doelman, A., Kaper T.J. "Stability of traveling waves in a bioremediation model ", (2006) preprint
http://wolff.bu.edu/publ/local/CunninghamMODPervouchineCRaccaNKopellCHDaviesRSGJonesRDTraubandMAWhittington_Neuronalmetabolismgovernscorticalnetworkresponserate_ProcNatAcadSci_103_5597601.pdf "Neuronal metabolism governs cortical network response rate ", Proc. Nat. Acad. Sci. 103 :5597-601 (2006)
Dorval AD and White JA "Synaptic input statistics tune the variability and reproducibility of neuronal responses ", Chaos 16 (026105):1-16 (2006)
Driscoll, M.E., Gardner T.S. "Identification and control of gene networks in living organisms via supervised and unsupervised learning ", Journal of Process Control 16 :303-311 (2006)
Faith, J.J., B. Hayete, J.T. Thaden, I. Mogno, J. Wierzbowski, G. Cottarel, S. Kasif, J.J. Collins, and T.S. Gardner "Shotgun mapping of Escherichia coli transcriptional regulation from a compendium of expression profiles ", (2006) preprint
Gear C.W., Kevrekidis I.G., Kaper T.J., Zagaris A. "Analysis of the accuracy and convergence of equation-free projection to a slow manifold ", 2006 , preprint
Guido NJ , Wang X, Adalsteinsson D, McMillen D, Hasty J, Cantor CR, Elston TC and Collins, JJ "A bottom-up approach to gene regulation ", Nature 439 :856-860 (2006)
Haas JS, Dorval AD, and White JA "Contributions of Ih to feature selectivity in layer II stellate cells of the entorhinal cortex ", Journal of Computational Neuroscience in press 22 (2):161-171 (2006)
Kloetzer, M. and C. Belta "A fully automated framework for control of linear systems from LTL specifications ", Lecture Notes in Computer Science 3927 :333-347 (2006)
Kuznetsov, A., C. Wilson and N. Kopell "Reachability analysis of multi-affine systems ", Lecture Notes in Computer Science 3927 :348-362 (2006)
Kuznetsov, A., C. Wilson and N. Kopell "Transient high frequency firing in a coupled_oscillator model of the mesencephalic dopaminergic neuron ", J Neurophysiol 95 (2):932-47 (2006)
Nahum LA, Reynolds MT, Wang ZO, Faith JJ, Jonna R, Jiang ZO, Meyer TJ, Pollock DD "EGenBio: A Data Management System for Evolutionary Genomics and Biodiversity. ", submitted (2006) preprint
Narayan R, Grana G & Sen K "Dual Time-Scales in Cortical Discrimination of Complex Sounds ", Journal of Neurophysiology in press (2006) preprint
Patel, H. B. and Gardner, T. S. "Genomic Normalization for Affymetrix E. coli Microarrays. ", Nucleic Acids Research. In preparation. (2006) preprint
Patel, H. B. and Gardner, T. S. "Transcriptional Profile of the Stringent Response in E. coli. ", Journal of Bacteriology. (2006) preprint
Pervouchine DD, TI Netoff, HG Rotstein, JA White, MO Cunningham, MA Whittington, and N Kopell "Low-Dimensional Maps Encoding Dynamics in Entorhinal Cortex and Hippocampus ", Neural Computation 18 (11 ):2617-2650 (2006)
Popovic N, Kaper T.J. "Rigorous asymptotic expansions for critical wave speeds in a family of reaction-diffusion equations ", Journal of Dynamics and Differential Equations 18 :1003-139 (2006)
Rotstein H., Oppermann T., White J. and Kopell N. "A reduced model for medial entorhinal cortex stellate cell: subthreshold oscillations, spiking and synchronization ", submitted (2006) , preprint
Rotstein H.G., Oppermann T., White J.A., and Kopell N. "The dynamic structure underlying subthreshold oscillatory activity and the onset of spikes in a model of medial entorhinal cortex stellate cells ", J Comp. Neurosci. 21 (3):271-292 (2006)
Shamir, M. "The scaling of 'Winner takes all' accuracy with the population size. ", Neural Computation (2006) preprint
Shamir, M., & H. Sompolinsky "Implications of Neuronal Diversity on Population Coding. ", Neural Computation (2006) preprint
Soto G, Kopell N, Sen K "Network Architecture, Receptive Fields and Neuromodulation: Computational and Functional Implications of Cholinergic Modulation in Primary Auditory Cortex ", (2006) preprint
Volfson D., Marciniak J., Blake WJ, Ostroff N., Tsimring LS, Hasty J. "Origins of extrinsic variability in eukaryotic gene expression. ", Nature 439 (7078):861-4 (2006)

2005

Blake WJ, and Collins JJ. "And the noise played on: stochastic gene expression and HIV-1 ", Cell 122 :147-149 (2005)
C. Borgers and N. Kopell "Effects of noisy drive on rhythms in networks of excitatory and inhibitory neurons ", Neural Computation 17 (3):557-608 (2005)
Christoph Borgers and Steven Epstein and Nancy J. Kopell "Background gamma rhythmicity and attention in cortical local circuits: A computational study ", PNAS 102 (19):7002-7007 (2005)
Clewley R., Rotstein H.G., Kopell N. "A computational tool for the reduction of nonlinear ODE systems possessing multiple scales ", Multiscale Modeling and Simulation (2005) , preprint
Dasika V., White J.A., Carney L.H., and Colburn H.S. "Effects of inhibitory feedback in a network model of avian brainstem ", Journal of Neurophysiology 94 :400-414 (2005)
Davis M.J., Zagaris A., Kaper T.J. "Reductions in elementary PDEs, parts I and II ", Journal of Chemical Physics (2005) preprint
Deville L. "Reduced equations for models of laminated materials in thin domains, II ", Asymptotic Analysis (2005) preprint
Deville L., Wayne C.E. "Reduced equations for models of laminated materials in thin domains, I ", Asymptotic Analysis 42 :263--309 (2005)
Dorval A.D. and White JA "Channel noise is essential for perithreshold oscillations in entorhinal stellate neurons ", Journal of Neuroscience 25 :10025-10028 (2005)
Driscoll M.E., Gardner T.S. "Identification and Control of Gene Networks in Living Organisms via Supervised and Unsupervised Learning ", Journal of Process Control (2005) preprint
Gardner T.S., Faith, J.J. "Reverse-engineering transcription control networks ", Physics of Life Reviews 2 :65-88 (2005)
Gear C.W., Kaper T.J., Kevrekidis I., Zagaris A. "Projecting to a slow manifold: Part 2. The validity of the zero-derivative principle ", SIAM Journal on Applied Dynamical Systems 4 :711--731 (2005)
Gloveli T., Dugladze T., Rotstein H., Traub R., Heinemann U., Monyer H., Whittington M. and Kopell N. "N., Orthogonal arrangement of rhythm generating microcircuits in the hippocampus ", PNAS 102 :13295-300 (2005)
Gorchetchnikov, A. and Hasselmo, M.E. "A biophysical implementation of a bidirectional graph search algorithm to solve multiple goal navigation tasks. ", Connection Science 17 :145-164 (2005)
Gorchetchnikov, A., Versace, M. and Hasselmo, M.E. "A model of STDP based on spatially and temporally local information: Derivation and combination with gated decay. ", Neural Networks 18 (5-6):458-66 (2005)
HG Rotstein, DD Pervouchine, CD Acker, MJ Gillies, JA White, EH Buhl, MA Whittington, and N Kopell "Slow and fast inhibition and an h-current interact to create a theta rhythm in a model of CA1 interneuron network ", J Neurophysiol 94 :1509-1518 (2005)
Harry J.D., Niemi J.B., Priplata A.A. and Collins J.J. "Balancing act ", IEEE Spectrum 1 :36-41 (2005)
Hasselmo, M. and Zilli, E. "Hebbian synaptic modification in cortical circuits and memory-guided behavior in ", Proceedings of International Joint Conference on Neural Networks 0 :0 (2005)
Hayete, B., J. Bienkowska. "GOTrees: Predicting GO Associations from Protein Domain Composition Using Decision Trees ", Pacific Symposium on Biocomputing 10 :127-138 (2005)
Hyman, J.M., Zilli, E.A., Paley, A.M., Hasselmo, M.E. "Medial prefrontal cortex cells show dynamic modulation with the hippocampal theta rhythm dependent on behavior ", Soc. Neurosci. Abstr. 31 :0 (2005)
Isaacs F.J., Blake W.J., and Collins J.J. "Signal processing in single cells ", Science 307 :1886-1888 (2005)
Isaacs F.J., and Collins J.J. "Plug-and-play with RNA ", Nature Biotechnology 23 :306-307 (2005)
Jones, S.R. and N. Kopell "Local network parameters can affect inter-network phase lags ", J. Math. Biol. 52 :115-140 (2005)
Kaern M, Elston TC, Blake WJ and Collins JJ. "Stochasticity in gene expression: from theories to phenotypes ", Nature Reveiws Genetics 6 :451-464 (2005)
Koene, R. A. and Hasselmo, M.E. "An integrate and fire model of prefrontal cortex provides a biological implementation of action selection in reinforcement learning theory that reuses known ... ", Proc. IJCNN 0 :0 (2005)
Koene, R.A. and Hasselmo, M.E. "An integrate and fire model of prefrontal cortex neuronal activity during performance of goal-directed decision making ", Cerebral Cortex 15 (12):1964-81 (2005)
Kuznetsov A., Wilson C. and Kopell N. "High frequency transitional processes in a model of the dopamine neuron ", revised and submitted J. Neurophysiol. (2005) preprint
Lecomte, C., McDaniel, J.G., and Barbone, P.E. "Error bounds for dynamic condensation methods ", (2005) preprint
Leiderman, R., Barbone P.E. and Braga, A.M.B. "Scattering of ultrasonic waves by defective adhesion interfaces in submerged laminated plates ", J. Acoust. Soc. Am. (2005) preprint
McGaughy, J., Koene, R. A., Eichenbaum, H. & Hasselmo, M. E. "Cholinergic deafferentation of the entorhinal cortex in rats impairs encoding of novel but not familiar stimuli in a delayed non-match to sample task (DNMS). ", J. Neurosci. 25 (44):10273-81 (2005)
Merriam, E.B., Netoff, T.I., Banks, M.I. "Bistable network behavior of layer I interneurons in auditory cortex ", Journal of Neuroscience 25 (26 ):6175-6186 (2005)
N. Kopell "Does it Have to be This Complicated? Focus on Single-Column Thalamocortical Network Model Exhibiting Gamma Oscillations, Spindles, and Epileptogenic Bursts ", J Neurophysiol 93 :1829-1830 (2005)
Nancy Kopell "Biased Random Walk: A Brief Mathematical Biography ", in Complexities: Women in Mathematics 1 :349-354 (2005)
Narayan R., Ergun A., Sen K. "Discrimination of Natural Sounds and Cortical Receptive Field Structure. ", J. Neurophys. 94 :2970-2975 (2005)
Netoff T.I., Acker CD, Bettencourt JC, White J.A. "Beyond two-cell networks: experimental measurement of neuronal responses to multiple synaptic inputs ", J Comput Neurosci. 18 (3):287-95 (2005)
O. Jensen and P. Goel and N. Kopell and M. Pohja and R. Hari and B. Ermentrout "On the human sensorimotor-cortex beta rhythm: sources and modeling ", Neuroimage 26 (2):347-55 (2005)
Pinto D., Jackson R. and Wayne C.E. "Existence and stability of traveling pulses in a continuous neuronal network ", SIAM Journal on Applied Dynamical Systems 4 :954-984 (2005)
Popovic N., and Kaper T.J. "Rigorous asymptotic expansions for critical wave speeds in a family of scalar reaction-diffusion equations ", Journal of Dynamics and Differential Equations (2005) preprint
Raina SZ, Faith JJ, Seligmann H, Disotell T, Stewart C-B, and Pollock DD. "Evolution of base substitution gradients in primate mitochondrial genomes. ", Genome Research. 0 :0 (2005)
Rotstein H.G., Gillies M.J., Acker C.D., White J.A., Buhl E.H., Whittington M.A., and Kopell N. "Slow and fast inhibition and an h-current interact to create a theta rhythm in a model CA1 interneuron network ", Journal of Neurophysiology 94 :1508-1517 (2005)
S.R Jones and N. Kopell "Local network parameters can affect inter-network phase lags in central pattern generators ", J. Math. Biol. (2005) preprint
Schon, K., Atri, A., Hasselmo, M.E., Tricarico, M.D., LoPresti, M.L., Stern, C.E. "Scopolamine reduces persistent activity related to long-term encoding in the parahippocampal gyrus during delayed matching in humans. ", J. Neurosci. 40 :9112-23 (2005)
Sivan E. and Kopell N. "Slow patterning in the olfactory system of the locust antennal lobe ", J. Comput. Neurosci. (2005) , preprint
Steve Kunec and Michael E. Hasselmo and Nancy Kopell "Encoding and Retrieval in the CA3 Region of the Hippocampus: A Model of Theta-Phase Separation ", J Neurophysiol 94 :70-82 (2005)
Theoden I. Netoff, Matthew I. Banks, Alan D. Dorval, Corey D. Acker, Julie S. Haas, Nancy Kopell, and John A. White "Synchronization in Hybrid Neuronal Networks of the Hippocampal Formation ", J Neurophysiol. 93 (3):1197-208 (2005)
Thompson M.J., Driscoll M.E., Gardner T.S., Collins J. J. "Reverse engineering gene regulatory networks. ", Wiley Encyclopedia of Genetics (2005) preprint
Zagaris A., Kaper H., Kaper T.J. "Two perspectives on reduction in ordinary differential equations ", Mathematische Nachrichten 278 :1629-1642 (2005)
Zagaris A., Kaper H.G., Kaper T.J. "Two perspectives on reduction of ordinary differential equations ", Mathematische Nachrichten (2005) preprint
Zhou Y.-D., Acker C.D., Netoff T.I., Sen K, and White JA "Increasing calcium transients by broadening postsynaptic action potentials enhances timing-dependent synaptic depression. ", Proceedings of the National Academy of Sciences 102 :19121-19125 (2005)
di Bernardo D., Thompson M.J ., Gardner T.S., Chobot S.E., Eastwood E.L., Wojtovich A.P., Elliot S.J., Schaus S.E. and Collins J.J. "Blockade of central cholinergic receptors impairs new learning and increases proactive interference in a word paired-associate memory task ", Behavioral Neurosci 118 (1):223-36 (2005)