Papers in Regular Journals & Preprints
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H. Kim, M. Subedi, and K. Josić. “Emergence of multiple foraging strategies under competition.” Submitted (2024).
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S. Linn, S. D. Lawley, B. R. Karamched, Z. P. Kilpatrick, and K. Josić. “Fast decisions reflect biases, slow decisions do not.” To appear in Physical Review E (2024).
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B. de Freitas Magalhaes, G. Fan, E. Sontag, K. Josić, and M. R. Bennett.
“Pattern formation and bistability in a synthetic intercellular genetic toggle.” Submitted (2023). -
H. Hong, M. J. Cortez, H. J. Kim, B. Choi, K. Josić, and J. K. Kim. “Inferring delays in partially observed gene regulatory networks.” Bioinformatics 39:1 (2023)
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A. B. Kunin, J. Guo, K. Bassler, X. Pitkow, and K. Josić. “Hierarchical Modular Structure of the Drosophila Connectome.” Journal of Neuroscience 43:37, pp. 6384-6400 (2023).
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A. R. Andrei, A. E. Akil, N. Kharas, S. Pojoga, R. Rosenbaum, R. Janz, K. Josić, and V. Dragoi. “Rapid compensatory plasticity revealed by dynamic correlated activity in vivo.” Nature Neuroscience 26, pp. 1960-1969 (2023).
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W. Zhang, S. Wu, K. Josić, and B. Doiron. “Sampling-based Bayesian inference in recurrent circuits of stochastic spiking neurons.” Nature Communications 14, Article number: 7074 (2023).
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M. Stickler, W. Ott, Z. P. Kilpatrick, K. Josić, and B. Karamched. “Impact of correlated information on pioneering decisions.” Physical Review Research 5, 033020 (2023).
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D. M. Zong, M. Sadeghpour, R. N. Alnahhas, A. J. Hirning, S. Molinari, W. Ott, K. Josić, and M. R. Bennett. “Predictable tuning of gene circuit dynamics in a synthetic microbial consortium.” To appear in ACS Synthetic Biology (2024).
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N.W. Barendregt, K. Josić, J.I. Gold, and Z.P. Kilpatrick. “Normative Decision Rules in Changing Environments.” eLife (2022).
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M. J. Cortez, A. E. Akil, , K. Josić, A.J. Stewart. “Incorporating computational challenges into a multidisciplinary course on stochastic processes.” Submitted (2021).
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K. Schapiro, K. Josić, Z. Kilpatrick, J. Gold. “Strategy-dependent effects of working-memory limitations on human perceptual decision-making.” eLife (2022).
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T.L. Eissa, J.I. Gold, K. Josić, and Z.P. Kilpatrick. “Suboptimal human inference inverts the bias-variance trade-off for decisions with asymmetric evidence..” PLoS Computational Biology 18(7) (2022).
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S. Sarmadi, J.J. Winkle, R.N. Alnahhas, M.R. Bennett, K. Josić, A. Mang, and R. Azencott. “Stochastic neural networks for automatic cell tracking in microscopy image sequences of bacterial colonies.” Mathematical and Computational Applications 27(2) (2022).
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J.J. Winkle, B.R. Karamched, M.R. Bennett, W. Ott, and K. Josić. “Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia.” PLoS Computational Biology 17(9)(2021).
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M. J. Cortez, H. Hong, B. Choi, J. K. Kim, and K. Josić. “Hierarchical Bayesian models for inference in biochemical reactions with delays.” Bioinformatics 38(1) (2021).
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A. E. Akil, R. Rosenbaum, and K. Josić. “Balanced networks under spike-time dependent plasticity.” PLoS Comput Biol 17(5) e1008958 (2020).
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B. Karamched, M, Stickler, W. Ott, B. Lindner, Z. P. Kilpatrick, and K. Josić. “Heterogeneity improves speed and accuracy in social networks.” Physical Review Letters 125:21, 218302 (2020).
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B. Karamched, S. Stolarczyk, Z. Kilpatrick, and K. Josić. “Bayesian evidence accumulation on social networks.” SIAM Journal on Applied Dynamical Systems 19:3, p.1884 (2020).
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R. N. Alnahhas, M. Sadeghpour, Y. Chen, A. A. Frey, W. Ott, K. Josić, and M. R. Bennett. “Majority sensing in synthetic microbial consortia.” Nature Communications 11, 3659 (2020).
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Y. Wang, Z. Kilpatrick, and K. Josić. “A hierarchical model of perceptual multistability involving interocular grouping”. Journal of Computational Neuroscience 48, p.177 (2020).
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A. E. Radillo, A.Veliz-Cuba, K. Josić, Z. Kilpatrick*. “Performance of normative and approximate evidence accumulation on the dynamic clicks task.” Neurons, Behavior, Data Analysis, and Theory(2019).
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N. Barendregt, K. Josić, Z. Kilpatrick. “Analyzing dynamic decision-making models using Chapman-Kolmogorov equations.” Journal of Computational Neuroscience 47, pages 205–222 (2019).
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R. N. Alnahhas, J. J. Winkle, A. J. Hirning, B. Karamched, W. Ott, K. Josić, M. R. Bennett. “Spatiotemporal dynamics of synthetic microbial consortia in microfluidic devices” ACS Synthetic Biology 8:9, p.2051(2019).
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B. Choi, Y. Cheng, S. Cinar, W. Ott, M. R. Bennett, K. Josić, and J.K. Kim. “Bayesian inference of distributed time delay in transcriptional and translational regulation..” Bioinformatics, Volume 36, Issue 2, pages 586–593 (2019).
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Z. Kilpatrick, W. Holmes, T. Eissa, and K. Josić. “Optimal models of decision-making in dynamic environments.” Current Opinions in Neurobiology 58 pages 54-60 (2019).
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J. K. Kim, Y. Chen, A. J. Hirning, R. Alnahhas, K. Josić, M. R. Bennett. “Long-range temporal coordination of gene expression in spatially extended synthetic microbial consortia popu: yes.” Nature Chemical Biology 15, p.1102 (2019).
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B. R. Karamched, W. Ott, I. Timofeyev, R. Alnahhas, M.R. Bennett, and K. Josić. “Boundary-driven emergent spatiotemporal order in growing microbial colonies.” Physica D 395 p.1 (2019).
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K. Nguyen, K. Josić, and Z. Kilpatrick. “Optimizing sequential decisions in the drift-diffusion model.” Journal of Mathematical Psychology 88 p.32 (2019).
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D. Zong, S. Cinar, D.L. Shis, K. Josić, W. Ott, M.R. Bennett. “Predicting transcriptional output of synthetic multi-input promoters.” ACS Synthetic Biology 7:8, p.1834 (2018).
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Y. Cheng, J. Ho, D.L. Shis, C. Gupta, J. Long, D. S. Wagner, W. Ott, K. Josić, M. Bennett. “Tuning the dynamic range of bacterial promoters regulated by ligand-inducible transcription factors.” Nature Communications 9:64 (2018).
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S. Stolarczyk, M. Bhardwaj, K.E. Basler, W. J. Ma, K. Josić. “Loss of information in feedforward social networks.” Journal of Complex Networks 6:3 pages 448–469 (2018).
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G. Ocker, Y. Hu, B. Doiron, R. Rosenbaum, K. Josić, M. Buice, E. Shea-Brown. “From the statistics of connectivity to the statistics of spike times in neuronal networks.” Current Opinion in Neurobilogy 46 p.109 (2017).
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Y. Cheng, A. Hirning, K. Josić, M. Bennett. “The timing of transcriptional regulation in synthetic gene circuits.” ACS Synthetic Biology DOI: 10.1021/acssynbio.7b00118 (2017).
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J. Winkle, O. Igoshin, M. Bennett, K. Josić, W. Ott. “Modeling mechanical interactions in growing populations of rod-shaped bacteria.” Physical Biology 14:5, 055001 (2017).
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G. Ocker, K. Josić, E. Shea-Brown, M. A. Buice. “Linking structure and activity in nonlinear spiking networks.” PLoS Computational Biol 13(6): e1005583 (2017).
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M. Sadeghpour, A. Veliz-Cuba, G. Orosz, K. Josić, M. Bennett. “Bistability and oscillations in co-repressive synthetic microbial consortia.” Quantitative Biology* 5:1, p. 55 (2017).
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A. Radillo, A. Veliz-Cuba, K. Josić, Z. Kilpatrick. “Evidence accumulation and change rate inference in dynamic environments.” Neural Computation 29:6 pages 1561–1610 (2017).
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A. Jacot-Guillarmod, Y. Wang, C. Pedroza, H. Ogmen, Z. Kilpatrick, K. Josić. “Extending Levelt’s Propositions to perceptual multistability involving interocular grouping.” Vision Research 133, p. 37 (2017).
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A. Veliz-Cuba, C. Gupta, M. R. Bennett, K. Josić, W. Ott. “Effects of cell cycle noise on excitable gene circuits.” Physical Biology 13:6 (2017).
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B. Doiron, A. Litwin-Kumar, R. Rosenbaum, G. Ocker, K. Josić. “The mechanics of state dependent neural correlations.” Nature Neuroscience 19, p. 383 (2016).
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M. Bhardwaj, R. van den Berg, W.J. Ma, K. Josić. “Do people take stimulus correlations into account in visual search?.” PLoS One 11(3): e0149402 (2016).
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A. Veliz-Cuba, Z. Kilpatrick, and K. Josić. “Stochastic eodels of evidence accumulation in changing environments.” SIAM Review 58(2), p. 264 (2016).
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J.K. Kim, K. Josić, M. R. Bennett. “The relationship between stochastic and deterministic quasi-steady state approximations.” BMC Systems Biology 9:87 (2015).
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A. Veliz-Cuba, A. J. Hirning, A. A. Atanas, F. Hussain, F. Vancia, K. Josić, M. R. Bennett. “Sources of variability in a synthetic gene oscillator.” PLoS Computational Biology 11:12, e1004674 (2015).
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A. Veliz-Cuba, H. Shouval, K. Josić, and Z. Kilpatrick. “Networks that learn the precise timing of event sequences.” Journal of Computational Neuroscience 39:3, p. 235 (2015).
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Y. Chen, J. K. Kim, A. J. Hirning, K. Josić, M. R. Bennett. “Emergent genetic oscillations in a synthetic microbial consortium.” Science 349(6251): 986 (2015).
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T. D. Nguyen-Huu, C. Gupta, B. Ma, W. Ott, K. Josić, M. R. Bennett. “Timing and variability of galactose metabolic gene activation depend on the rate of environmental change.” PLoS Computational Biology 11:7, e1004399 (2015).
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M.Bhardwaj, S.Carroll, W.J. Ma, K. Josić. “Visual decisions in the presence of measurement and stimulus correlations.” Neural Computation 27(11): 2318–2353 (2015).
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D. Yatsenko, K. Josić, A. Ecker, E. Froudarakis, R. J. Cotton, A. Tolias. “Improved estimation and interpretation of correlations in neural circuits.” PLoS Computational Biology 11:3, e1004083 (2015).
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A. Veliz-Cuba, A. Kumar, and K. Josić. “Piecewise Linear and Boolean Models of Chemical Reaction Networks.” Bulletin of Mathematical Biology 76:12 pages 2945-2984 (2014).
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J. Trousdale, S. Carroll, F. Gabbiani, and K. Josić, “Near-optimal decoding of transient stimuli from coupled neuronal subpopulations in the fly.” Journal of Neuroscience 34(36):12206 (2014).
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J.K. Kim, K. Josić, and M. Bennett. “The validity of quasi steady-state approximations in discrete stochastic simulations.” Biophysical Journal 107:3, p. 783 (2014).
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C. Gupta, M. Lopez, R. Azencott, M. Bennett, K. Josić, and W. Ott. “Modeling delay in genetic networks: From delay birth-death processes to delay stochastic differential equations.” Journal of Chemical Physics 140:204108 (2014).
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J.K. Kim, Z. Kilpatrick, M. Bennett, and K. Josić. “Molecular mechanisms that regulate the coupled period of the mammalian circadian clock.” Biophysical Journal, 106: 9, p. 2071 (2014).
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Y. Hu, J. Trousdale, K. Josić, and E. Shea-Brown. “Local paths to global coherence: Cutting networks down to size.” Physical Review E 89:032802 (2014).
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F. Hussain, C. Gupta, A. J. Hirning, W. Ott, K. Matthews, K. Josić, and M. Bennet. “Engineered temperature compensation in a synthetic genetic clock.” Proceedings of the National Academy of Sciences 111:3, p. 972 (2014).
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S. Carroll, K. Josić, and Z. Kilpatrick. “Encoding certainty in bump attractors.” To appear in the Journal of Computational Neuroscience 37:29–48 (2013).
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C. Gupta, M Lopez, W. Ott, K. Josić, and M. Bennett. “Transcriptional delay stabilizes bistable systems.” Physical Review Letters, vol. 111, 058104 (2013).
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J. Trousdale, Y. Hu, E. Shea-Brown, and K. Josić. “A generative spike train model with time-structured higher order correlations.” Frontiers in Computational Neuroscience 7:84 (2013).
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Y. Hu, J. Trousdale, K. Josić, and E. Shea-Brown. “Motif Statistics and Spike Correlations in Neuronal Networks.” Journal of Statistical Mechanics P03012 (2013).
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E. A. Pnevmatikakis, K. Kelleher, R. Chen, P. Saggau, K. Josić, and L. Paninski. “Fast spatiotemporal smoothing of calcium measurements in dendritic trees.” PLoS Computational Biology, 8:3, e1002408 (2012).
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A. Hazra, R. Rosenbaum, B. Bodmann, S. Kao, K. Josić, and J. Žiburkus. “β-Adrenergic modulation of spontaneous spatiotemporal activity patterns and synchrony in hyperexcitable hippocampal circuits”. Journal of Neurophysiology, 108:2, pp. 658-671 (2012).
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J. Trousdale, Y. Hu, E. Shea-Brown, and K. Josić. “Impact of network structure and cellular response on spike time correlations.” PLoS Computational Biology 8(3): e1002408. (2012).
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R. van den Berg, M. Vogel, K. Josić, and W. Ma. “pnas.org/content/109/8/3178.” Proceedings of the National Academy of Sciences, 109:8, 3178- 3183 (2012).
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R. Rosenbaum and K. Josić. “Membrane potential and spike train statistics depend distinctly on input statistics.” Physical Review E, 84:5, article 051902 (2011).
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K. Josić, W. Ott, J. M. Lopez, L.-J. Shiau and M. Bennett. “Stochastic delay accelerates signaling in gene networks.” PLoS Computational Biology, 7(11): e1002264 (2011).
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Y. Wang, B. Iliescu, J. Ma, K. Josić and V. Dragoi. “Adaptive changes in neuronal synchronization in macaque V4.” Journal of Neuroscience 31:37, 13204-13213 (2011).
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R. Rosenbaum, F. Marpeau, J. Ma, A. Barua and K. Josić. “Finite volume and asymptotic methods for stochastic neuron models with correlated inputs.” Journal of Mathematical Biology 65, pages 1–34 (2011).
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A. Kumar and K. Josić. “Reduced models of networks of coupled enzymatic reactions.” Journal of Theoretical Biology 278:1, 87-106 (2011).
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R. Rosenbaum, J. Trousdale and K. Josić. “The effects of pooling on spike train correlations.” Frontiers in Neuroscience 5:58 (2011).
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R. Rosenbaum and K. Josić. “Mechanisms that modulate transfer of spiking correlations.” Neural Computation 23:5, 1261-1305 (2011) (2011).
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E. Elhaik, D. Graur, K. Josić and G. Landan. “Identifying compositionally homogeneous and nonhomogeneous domains within the human genome using a novel segmentation algorithm.” Nucleic Acids Research 38 (15): e158 (2010).
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R. Rosenbaum, J. Trousdale and K. Josić. “Pooling and correlated neural activity.” Frontiers in Computational Neuroscience 4:9, doi:10.3389/fncom.2010.00009 (2010).
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D. Gutnisky and K. Josić. “Generation of spatio-temporally correlated spike-trains and local- field potentials using a multivariate autoregressive process.” Journal of Neurophysiology 103:5, 2912-2030 (2010).
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E. Elhaik, D. Graur and K. Josić. “Genome order index should not be used for defining compositional constraints in nucleotide sequences - a case study of the Z-curve.” Biology Direct 5:10 (online) (2010).
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E. Elhaik, D. Graur and K. Josić. “Comparative testing of DNA segmentation algorithms using benchmark simulations.” Molecular Biology and Evolution, 27:5, 1015-1024 (2010).
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Y. Sun, B. Danila, K. Josić and K. E. Bassler. “Improved community structure detection using a modified fine tuning strategy Europhysics Letters 86, 28004 (2009).
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K. Josić, E. Shea-Brown, B. Doiron, and J. de la Rocha. “Stimulus-Dependent Correlations and Population Codes.” Neural Computation 21:10, 2774–2804 (2009).
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D. Nevozhay, R. Adams, K. Murphy, K. Josić and G. Balazsi. “Negative autoregulation linearizes the dose response and suppresses the heterogeneity of gene expression.” Proceedings of the National Academy of Science, vol. 106, p. 5123-5128 (2009).
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D. Dingli, C. Offord, R. Myers, K–W. Peng, T. W. Carr, K. Josić, S. J. Russell and Ž Bajzer. “Dynamics of Multiple Myeloma Tumor Therapy with a Recombinant Measles Virus.” Cancer Gene Therapy 16, 873–882 (2009).
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F. Marpeau, A. Barua and K. Josić. “A finite volume method for stochastic integrate–and–fire models.” Journal of Computational Neuroscience, vol 26, p. 445 - 457 (2009).
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R. Rosenbaum and K. Josić. “Unstable Solutions of Non-autonomous Linear Differential Equations.” SIAM Review vol. 50, 570–584 (2008).
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K. Kelleher, V. Hajdik, K. Josić and C. Colbert. “Learning by structural remodeling in a class of single cell models.” Journal of Computational Neuroscience vol. 25:2, 282–295 (2008).
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Y. Timofeeva, S.J. Cox, S. Coombes and K. Josić. “Democratization in a passive dendritic tree: an analytical investigation.” Journal of Computational Neuroscience, vol. 25:2, 228–244 (2008).
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E. Shea-Brown, K. Josić, B. Doiron, and J. de la Rocha. “Universal properties of correlation transfer in integrate-and-fire neurons.” Physical Review Letters vol. 100, 108102 (2008).
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Ž. Bajzer, T. Carr, K. Josić, S.J. Russell, and D. Dingli. “Modeling of cancer virotherapy with recombinant measles viruses.” Journal of Theoretical Biology 252:1, 109–122 (2008).
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R.E.L. DeVille, A. Harkin, M. Holzer, K. Josić, and T. Kaper. “Analysis of a Renormalization Group Method for Solving Perturbed Ordinary Differential Equations.” Physica D 237: 8, 1029– 1052 (2008).
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E. Elhaik, D. Graur, and K. Josić. “‘Genome order index’ should not be used for defining compositional constraints in nucleotide sequences,” Computational Biology and Chemistry, 32, 147 (2008).
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J. de la Rocha, B. Doiron, E. Shea-Brown, K. Josić, and A. Reyes. “Correlation between neural spike trains increases with firing rate.” Nature 448, 802–806 (2007).
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N. Barlas, K. Josić, S. Lapin and I. Timofeyev. “Non-uniform decay of predictability and return of skill in stochastic oscillatory models.” Physica D vol. 232(2), 116–127(2007).
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S. Coombes, Y. Timofeeva, C.-M. Svensson, G.J. Lord, K. Josić, S.J. Cox and C.M. Colbert. “Branching Dendrites with Resonant Membrane: A sum-over-trips approach.” Biological Cybernetics vol. 93, 91–108 (2007).
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J. Rubin and K. Josić. “The firing of an excitable neuron in the presence of stochastic trains of strong synaptic inputs.” Neural Computation 19, 1251-1294 (2007).
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S. Coombes, B. Doiron, K. Josić, and E. Shea-Brown. “Toward blueprints for network architecture, biophysical dynamics, and signal transduction Proceedings of the Royal Society A 364, 3301-3318 (2006).
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K. Josić and A. Török. “Network architecture and spatio-temporally symmetric dynamics.” Physica D 224(1-2), 52-68 (2006).
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K. Parwani and K. Josić. “Rotation sets for networks of circle maps.” Chaos. 16(1), 015115 (2006).
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D. Dingli, M.D. Cascino, K. Josić, S.J. Russell, and Ž. Bajzer. “A mathematical model of cancer radiovirotherapy.” Mathematical Biosciences, vol. 199, issue 1, pp. 55-78 (2006).
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M. Golubitsky, K. Josić, E. Shea-Brown. “Winding numbers and average frequencies in phase oscillator networks.” Journal of Nonlinear Science, vol. 16, issue 3, pp. 201-231, (2006).
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K. Josić and J. Rubin. “Deriving information about architecture from activity patterns in coupled cell systems.” SIAM Journal of Applied Dynamical Systems, vol. 4, p. 53-77, (2005).
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K. Josić and S. Peleš. “Synchronization in networks of general weakly non-linear oscillators.” Journal of Physics A, vol. 39, p. 11801-11817 (2004).
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M.S. Baptista, S. Boccaletti, K. Josić, and I. Leyva. “Irrational Phase Synchronization.” Physical Review E, vol. 69, number 056228 (2004).
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K. Josić and E. Sander. “The structure of synchronization sets for noninvertible systems.” Chaos, vol. 14:2, pp. 249-262 (2004).
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R.L. Devaney, K. Josić, and Y. Shapiro. “Singular perturbations of quadratic maps.” International Journal of Bifurcations and Chaos, vol. 14:1, pp. 161-171 (2004).
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R. L. Devaney, K. Josić, M. Moreno Rocha, P. Seal, Y. Shapiro, and A. T. Frumosu. “Playing catchup with iterated exponentials.” American Mathematical Monthly, 111:8, pp. 704-709 (2004)
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E. Barreto, K. Josić, C. Morales, E. Sander, and P. So. “The geometry of chaos synchronization.” Chaos, vol 13:1 pp. 151-164 (2003).
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K. Josić and M. Beck. “A geometric theory of chaotic phase synchronization.” Chaos, vol 13:1 pp. 247-258 (2003).
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P. So, E. Barreto, K. Josić, E. Sander, and S. J. Schiff. “Limits to the experimental detection of nonlinear synchrony.” Physical Review E, 65, article 046225 (2002). Also: Figure 1, Figure 2, Figure 3
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K. Josić and D.J. Mar. “Phase Synchronization of Chaotic Systems with Small Phase Diffusion.” Physical Review E, 64, article 056234 (2001). Also: PS Format, Mathematica Notebook
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R. Bhattacharjee, R. L. Devaney, R. E. L. Deville, K. Josić, and M. Moreno-Rocha. “Accessible Points of Julia Sets of Stable Exponentials.” Discrete and Continuous Dynamical Systems B, 1:3, p. 299-318 (2001). Also: PS Format
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K. Josić. “Phase Synchronization of Chaotic Systems.” unpublished (2001).
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K. Josić and R.W. Hall. “The Mathematics of Musical Instruments.” American Mathematical Monthly, 108:4, p. 347-357 (2001).
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K. Josić and R.W. Hall. “Planetary motion and the duality of force laws.” SIAM Review, 42:1, p. 114-125 (2000).
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K. Josić and C.E. Wayne. “Dynamics of a diffusively coupled ring of Lorenz oscillators.” Journal of Statistical Physics, 98:1, p. 1-30 (2000). Also: PS Format. The interval arithemtic code used for some estimates in the paper is available.
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K. Josić. “Synchronization of chaotic systems and invariant manifolds.” Nonlinearity, 13:4, pp. 1321-1336 (2000).
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K. Josić. “Invariant manifolds and synchronization of coupled dynamical systems.” Physical Review Letters, 80:14, pp. 3053-3056 (1998). Also: PS Format
- K. Josić. “Local bifurcations in the symmetric model of selection with fertility differences.” Journal of Theoretical Biology, 189, pp. 291-295 (1997). Also: PS Format
Book chapters and encyclopedia entries
Refereed entries are marked with a star (*).
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Ž. Bajzer, D. Dingli, K. Josić, and T. Carr. “Optimization of tumor virotherapy with recombinant measles viruses.” To appear in Optimization in Medicine and Biology edited by Gino J. Lim and Eva K. Lee (2007).
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(*) K. Josić, E. Shea-Brown, and J. Moehlis. “Scholarpedia entry on isochrons.”
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(*) J. Moehlis, K. Josić, and E. Shea-Brown. “Scholarpedia entry on periodic orbits.”
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M. Golubitsky, K. Josić, and L.J. Shiau. “Bursting in Coupled Systems.” in Bursting: The genesis of rhythm in the nervous system, edited by Stephen Coombes and Paul C. Bressloff (2005).
- Golubitsky, K. Josić, and T.J. Kaper. “An Unfolding Theory Approach to Bursting in Fast-Slow Systems.” chapter in Global Analysis of Dynamical Systems.