Papers in Regular Journals & Preprints

  1. 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 (2022).

  2. N.W. Barendregt, K. Josić, J.I. Gold, and Z.P. Kilpatrick. “Normative Decision Rules in Changing Environments.” eLife (2022).

  3. M. J. Cortez, A. E. Akil, , K. Josić, A.J. Stewart. “Incorporating computational challenges into a multidisciplinary course on stochastic processes.” Submitted (2021).

  4. K. Schapiro, K. Josić, Z. Kilpatrick, J. Gold. “Strategy-dependent effects of working-memory limitations on human perceptual decision-making.” eLife (2022).

  5. 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).

  6. W. Zhang, S. Wu, K. Josić, and B Doiron. “Recurrent circuit based neural population codes for stimulus representation and inference.” Submitted (2022).

  7. 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).

  8. 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).

  9. 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).

  10. 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.” Submitted (2021).

  11. A. E. Akil, R. Rosenbaum, and K. Josić. “Balanced networks under spike-time dependent plasticity.” PLoS Comput Biol 17(5) e1008958 (2020).

  12. 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).

  13. 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).

  14. 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).

  15. Y. Wang, Z. Kilpatrick, and K. Josić. “A hierarchical model of perceptual multistability involving interocular grouping”. Journal of Computational Neuroscience 48, p.177 (2020).

  16. 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).

  17. N. Barendregt, K. Josić, Z. Kilpatrick. “Analyzing dynamic decision-making models using Chapman-Kolmogorov equations.” Journal of Computational Neuroscience 47, pages 205–222 (2019).

  18. 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).

  19. 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).

  20. 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).

  21. 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).

  22. 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).

  23. K. Nguyen, K. Josić, and Z. Kilpatrick. “Optimizing sequential decisions in the drift-diffusion model.” Journal of Mathematical Psychology 88 p.32 (2019).

  24. 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).

  25. 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).

  26. 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).

  27. 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).

  28. 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).

  29. 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).

  30. 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).

  31. 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).

  32. 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).

  33. 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).

  34. 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).

  35. B. Doiron, A. Litwin-Kumar, R. Rosenbaum, G. Ocker, K. Josić. “The mechanics of state dependent neural correlations.” Nature Neuroscience 19, p. 383 (2016).

  36. 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).

  37. A. Veliz-Cuba, Z. Kilpatrick, and K. Josić. “Stochastic eodels of evidence accumulation in changing environments.” SIAM Review 58(2), p. 264 (2016).

  38. J.K. Kim, K. Josić, M. R. Bennett. “The relationship between stochastic and deterministic quasi-steady state approximations.” BMC Systems Biology 9:87 (2015).

  39. 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).

  40. 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).

  41. 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).

  42. 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).

  43. 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).

  44. 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).

  45. 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).

  46. 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).

  47. 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).

  48. 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).

  49. 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).

  50. 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).

  51. 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).

  52. S. Carroll, K. Josić, and Z. Kilpatrick. “Encoding certainty in bump attractors.” To appear in the Journal of Computational Neuroscience 37:29–48 (2013).

  53. C. Gupta, M Lopez, W. Ott, K. Josić, and M. Bennett. “Transcriptional delay stabilizes bistable systems.” Physical Review Letters, vol. 111, 058104 (2013).

  54. 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).

  55. Y. Hu, J. Trousdale, K. Josić, and E. Shea-Brown. “Motif Statistics and Spike Correlations in Neuronal Networks.” Journal of Statistical Mechanics P03012 (2013).

  56. 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).

  57. 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).

  58. 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).

  59. R. van den Berg, M. Vogel, K. Josić, and W. Ma. “” Proceedings of the National Academy of Sciences, 109:8, 3178- 3183 (2012).

  60. R. Rosenbaum and K. Josić. “Membrane potential and spike train statistics depend distinctly on input statistics.” Physical Review E, 84:5, article 051902 (2011).

  61. 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).

  62. 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).

  63. 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).

  64. A. Kumar and K. Josić. “Reduced models of networks of coupled enzymatic reactions.” Journal of Theoretical Biology 278:1, 87-106 (2011).

  65. R. Rosenbaum, J. Trousdale and K. Josić. “The effects of pooling on spike train correlations.” Frontiers in Neuroscience 5:58 (2011).

  66. R. Rosenbaum and K. Josić. “Mechanisms that modulate transfer of spiking correlations.” Neural Computation 23:5, 1261-1305 (2011) (2011).

  67. 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).

  68. 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).

  69. 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).

  70. 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).

  71. 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).

  72. 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).

  73. 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).

  74. 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).

  75. 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).

  76. 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).

  77. R. Rosenbaum and K. Josić. “Unstable Solutions of Non-autonomous Linear Differential Equations.” SIAM Review vol. 50, 570–584 (2008).

  78. 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).

  79. 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).

  80. 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).

  81. 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).

  82. 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).

  83. 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).

  84. 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).

  85. 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).

  86. 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).

  87. 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).

  88. 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).

  89. K. Josić and A. Török. “Network architecture and spatio-temporally symmetric dynamics.” Physica D 224(1-2), 52-68 (2006).

  90. K. Parwani and K. Josić. “Rotation sets for networks of circle maps.” Chaos. 16(1), 015115 (2006).

  91. 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).

  92. 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).

  93. 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).

  94. K. Josić and S. Peleš. “Synchronization in networks of general weakly non-linear oscillators.” Journal of Physics A, vol. 39, p. 11801-11817 (2004).

  95. M.S. Baptista, S. Boccaletti, K. Josić, and I. Leyva. “Irrational Phase Synchronization.” Physical Review E, vol. 69, number 056228 (2004).

  96. K. Josić and E. Sander. “The structure of synchronization sets for noninvertible systems.” Chaos, vol. 14:2, pp. 249-262 (2004).

  97. 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).

  98. 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)

  99. E. Barreto, K. Josić, C. Morales, E. Sander, and P. So. “The geometry of chaos synchronization.” Chaos, vol 13:1 pp. 151-164 (2003).

  100. K. Josić and M. Beck. “A geometric theory of chaotic phase synchronization.” Chaos, vol 13:1 pp. 247-258 (2003).

  101. 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

  102. 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

  103. 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

  104. K. Josić. “Phase Synchronization of Chaotic Systems.” unpublished (2001).

  105. K. Josić and R.W. Hall. “The Mathematics of Musical Instruments.” American Mathematical Monthly, 108:4, p. 347-357 (2001).

  106. K. Josić and R.W. Hall. “Planetary motion and the duality of force laws.” SIAM Review, 42:1, p. 114-125 (2000).

  107. 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.

  108. K. Josić. “Synchronization of chaotic systems and invariant manifolds.” Nonlinearity, 13:4, pp. 1321-1336 (2000).

  109. K. Josić. “Invariant manifolds and synchronization of coupled dynamical systems.” Physical Review Letters, 80:14, pp. 3053-3056 (1998). Also: PS Format

  110. 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

My Complete Thesis

Book chapters and encyclopedia entries

Refereed entries are marked with a star (*).

  1. 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).

  2. (*) K. Josić, E. Shea-Brown, and J. Moehlis. “Scholarpedia entry on isochrons.”

  3. (*) J. Moehlis, K. Josić, and E. Shea-Brown. “Scholarpedia entry on periodic orbits.”

  4. 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).

  5. Golubitsky, K. Josić, and T.J. Kaper. “An Unfolding Theory Approach to Bursting in Fast-Slow Systems.” chapter in Global Analysis of Dynamical Systems.