Papers in Regular Journals & Preprints

A. E. Akil, R. Rosenbaum, and K. Josić. “Synaptic Plasticity in Correlated Balanced Networks.” Submitted (2020).

R. N. Alnahhas, M. Sadeghpour, Y. Chen, A. A. Frey, W. Ott, K. Josić, and M. R. Bennett. “Majority sensing in synthetic microbial consortia.” Submitted (2020).

B. Karamched, S. Stolarczyk, Z. Kilpatrick, and K. Josić. “Optimal evidence accumulation on social networks.” Submitted (2019).

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 (2019).

Y. Wang, Z. Kilpatrick, and K. Josić. “A hierarchical model of perceptual multistability involving interocular grouping”. Submitted (2019).

A. E. Radillo, A.VelizCuba, K. Josić, Z. Kilpatrick. “Performance of normative and approximate evidence accumulation on the dynamic clicks task.” Neurons, Behavior, Data Analysis, and Theory(2019).

N. Barendregt, K. Josić, Z. Kilpatrick. “Analyzing dynamic decisionmaking models using ChapmanKolmogorov equations.” Accepted in Journal of Computational Neuroscience (2019).

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).

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..” Accepted in BioInformatics (2019).

Z. Kilpatrick, W. Holmes, T. Eissa, and K. Josić. “Optimal models of decisionmaking in dynamic environments.” Current Opinions in Neurobiology 58 pp. 5460 (2019).

J. K. Kim, Y. Chen, A. J. Hirning, R. Alnahhas, K. Josić, M. R. Bennett. “Temporal coordination of gene expression in spatially extended synthetic microbial consortia popu: yes.” Nature Chemical Biology 15, p.1102 (2019).

B. R. Karamched, W. Ott, I. Timofeyev, R. Alnahhas, M.R. Bennett, and K. Josić. “Boundarydriven emergent spatiotemporal order in growing microbial colonies.” Physica D 395 p.1 (2019).

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

D. Zong, S. Cinar, D.L. Shis, K. Josić, W. Ott, M.R. Bennett. “Predicting transcriptional output of synthetic multiinput promoters.” ACS Synthetic Biology 7:8, p. 1834 (2018).

Y. Cheng, C. Gupta, J. Long, D. S. Wagner, W. Ott, K. Josić, M. Bennett. “Tuning the dynamic range of bacterial promoters regulated by ligandinducible transcription factors.” Nature Communications 9:64 (2018).

G. Ocker, Y. Hu, B. Doiron, R. Rosenbaum, K. Josić, M. Buice, E. SheaBrown. “From the statistics of connectivity to the statistics of spike times in neuronal networks.” Current Opinion in Neurobilogy 46 p.109 (2017).

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).

J. Winkle, O. Igoshin, M. Bennett, K. Josić, W. Ott. “Modeling mechanical interactions in growing populations of rodshaped bacteria.” Physical Biology 14:5, 055001 (2017).

S. Stolarczyk, M. Bhardwaj, K.E. Basler, W. J. Ma, K. Josić. “Loss of information in feedforward social networks.” To appear in Journal of Complex Networks (2017).

G. Ocker, K. Josić, E. SheaBrown, M. A. Buice. “Linking structure and activity in nonlinear spiking networks.” PLoS Computational Biol 13(6): e1005583 (2017).

M. Sadeghpour, A. VelizCuba, G. Orosz, K. Josić, M. Bennett. “Bistability and oscillations in corepressive synthetic microbial consortia.” Quantitative Biology 5:1, p. 55 (2017).

A. Radillo, A. VelizCuba, K. Josić, Z. Kilpatrick. “Evidence accumulation and change rate inference in dynamic environments.” To appear in Neural Computation (2017).

A. JacotGuillarmod, 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).

A. VelizCuba, C. Gupta, M. R. Bennett, K. Josić, W. Ott. “Effects of cell cycle noise on excitable gene circuits.” Physical Biology 13:6 (2017).

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

M. Bhardwaj, R. van den Berg, W.J. Ma, K. Josić. “Do humans take stimulus correlations into account in visual search?.” PLoS One 11(3): e0149402 (2016).

A. VelizCuba, Z. Kilpatrick, and K. Josić. “Visual Decisions in the Presence of Measurement and Stimulus Correlations.” SIAM Review 58(2), p. 264 (2016).

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

A. VelizCuba, A. J. Hirning, A. A. Atanas, F. Hussain, F. Vancia, K. Josić, M. R. Bennett. “Measuring intrinsic and extrinsic noise in a synthetic gene oscillator.” PLoS Computational Biology 11:12, e1004674 (2015).

A. VelizCuba, 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).

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).

T. D. NguyenHuu, 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).

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).

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).

A. VelizCuba, A. Kumar, and K. Josić. “Piecewise Linear and Boolean Models of Chemical Reaction Networks.” Bulletin of Mathematical Biology 76:29452984 (2014).

J. Trousdale, S. Carroll, F. Gabbiani, and K. Josić, “Nearoptimal decoding of transient stimuli from coupled neuronal subpopulations.” Journal of Neuroscience 34(36):12206 (2014).

J.K. Kim, K. Josić, and M. Bennett. “The validity of quasi steadystate approximations in discrete stochastic simulations.” Biophysical Journal 107:3, p. 783 (2014).

C. Gupta, M. Lopez, R. Azencott, M. Bennett, K. Josić, and W. Ott. “Modeling delay in genetic networks: From delay birthdeath processes to delay stochastic differential equations.” Journal of Chemical Physics 140:204108 (2014).

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).

Y. Hu, J. Trousdale, K. Josić, and E. SheaBrown. “Local paths to global coherence: Cutting networks down to size.” Physical Review E 89:032802 (2014).

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).

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

C. Gupta, M Lopez, W. Ott, K. Josić, and M. Bennett. “Delay Stabilizes Bistable Systems.” Physical Review Letters, vol. 111, 058104 (2013).

J. Trousdale, Y. Hu, E. SheaBrown, and K. Josić. “A generative spike train model with timestructured higher order correlations.” Frontiers in Computational Neuroscience 7:84 (2013).

Y. Hu, J. Trousdale, K. Josić, and E. SheaBrown. “Motif Statistics and Spike Correlations in Neuronal Networks.” Journal of Statistical Physics P03012 (2013).

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).

A. Hazra, R. Rosenbaum, B. Bodmann, S. Kao, K. Josić, and J. Žiburkus. “βAdrenergic modulation of spontaneous spatiotemporal activity patterns and synchrony in hyperexcitable hippocampal circuits”. Journal of Neurophysiology, 108:2, pp. 658671 (2012).

J. Trousdale, Y. Hu, E. SheaBrown, and K. Josić. “Impact of network structure and cellular response on spike time correlations.” PLoS Computational Biology 8(3): e1002408. (2012).

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

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

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. doi:10.1371/journal.pcbi.1002264 (2011).

Y. Wang, B. Iliescu, J. Ma, K. Josić and V. Dragoi. “Adaptive changes in neuronal synchronization in macaque V4”. Journal of Neuroscience 31:37, 1320413213 (2011).

R. Rosenbaum, F. Marpeau, J. Ma, A. Barua and K. Josić. “Finite volume and asymptotic methods for stochastic neuron models with correlated inputs.” To appear in the Journal of Mathematical Biology (2011).

A. Kumar and K. Josić. Reduced models of networks of coupled enzymatic reactions. Journal of Theoretical Biology 278:1, 87106 (2011).

R. Rosenbaum, J. Trousdale and K. Josić. The effects of pooling on spike train correlations, Frontiers in Neuroscience 5:58. doi: 10.3389/fnins.2011.00058 (2011) (2011).

R. Rosenbaum and K. Josić Mechanisms that modulate transfer of spiking correlations, Neural Computation 23:5, 12611305 (2011) (2011).

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).

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).

D. Gutnisky and K. Josić Generation of spatiotemporally correlated spiketrains and local field potentials using a multivariate autoregressive process Journal of Neurophysiology 103:5, 29122030 (2010).

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 Zcurve. Biology Direct 5:10 (online) (2010).

E. Elhaik, D. Graur and K. Josić Comparative testing of DNA segmentation algorithms using benchmark simulations Molecular Biology and Evolution, 27:5, 10151024 (2010)  Contact for reprint.

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).

K. Josić, E. SheaBrown, B. Doiron, and J. de la Rocha StimulusDependent Correlations and Population Codes Neural Computation 21:10, 2774–2804 (2009).

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. 51235128 (2009).

D. Dingli, C. Offord, R. Myers, K–W. Peng, T. W. Carr, K. Josić, S. J. Russell and ´ Z Bajzer Dynamics of Multiple Myeloma Tumor Therapy with a Recombinant Measles Virus. Cancer Gene Therapy 16, 873–882 (2009).

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).

R. Rosenbaum and K. Josić Unstable Solutions of Nonautonomous Linear Differential Equations SIAM Review vol. 50, 570–584 (2008).

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).

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).

E. SheaBrown, K. Josić, B. Doiron, and J. de la Rocha Universal properties of correlation transfer in integrateandfire neurons. Physical Review Letters vol. 100, 108102 (2008).

Ž. Bajzer, T. Carr, K. Josi ˇ c, S.J. Russell, and D. Dingli Modeling of cancer virotherapy with recombinant measles viruses Journal of Theoretical Biology 252:1, 109–122 (2008).

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).

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).

J. de la Rocha, B. Doiron, E. SheaBrown, K. Josić, and A. Reyes. Correlation between neural spike trains increases with firing rate Nature 448, 802–806 (2007)  Contact for reprint.

N. Barlas, K. Josić, S. Lapin and I. Timofeyev. Nonuniform decay of predictability and return of skill in stochastic oscillatory models Physica D vol. 232(2), 116–127(2007).

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 sumovertrips approach. Biological Cybernetics vol. 93, 91–108 (2007).

J. Rubin and K. Josić. Neuronal firing in the presence of stochastic trains of strong synaptic inputs Neural Computation 19, 12511294 (2007).

S. Coombes, B. Doiron, K. Josić, and E. SheaBrown. Toward blueprints for network architecture, biophysical dynamics, and signal transduction Proceedings of the Royal Society A 364, 33013318 (2006).

K. Josić and A. Török. Network structure and spatiotemporally symmetric dynamics Physica D 224(12), 5268 (2006).

M. Golubitsky, K. Josić, and E. SheaBrown, Rotation Sets for Networks of Circle Maps Chaos, vol. 16, issue 1, p. 015115 (2006).

D. Dingli, M.D. Cascino, K. Josić, S.J. Russell, and ´ Z. Bajzer, A mathematical model of cancer radiovirotherapy Mathematical Biosciences, vol. 199, issue 1, pp. 5578 (2006) (Epublished Dec 22, 2005)  Contact for reprint.

M. Golubitsky, K. Josić, E. SheaBrownWinding Numbers and Average Frequencies in Phase Oscillator Networks Journal of Nonlinear Science, vol. 16, issue 4, pp. 201231, (2006).

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. 5377, (2005).

Applications of Asymptotic Normal Form Theory and its Connections with the Renormalization Group Method preprint (2004).

K. Josić and S. Peleš. Synchronization in Networks of General Weakly NonLinear Oscillators Journal of Physics A, vol. 39, p. 1180111817 (2004).

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

K. Josić and E. Sander The Structure of Synchronization Sets for Noninvertible Systems Chaos, vol. 14:2, pp. 249262 (2004).

R.L. Devaney, K. Josić, and Y. Shapiro Singular perturbations of quadratic maps International Journal of Bifurcations and Chaos, vol. 14:1, pp. 161171 (2004).

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. 704709, October, 2004. Also: PS Format

E. Barreto, K. Josić, C. Morales, E. Sander, and P. So The geometry of chaos synchronization Chaos, vol 13:1 pp. 151164 (2003).

K. Josić and M. Beck. A geometric theory of chaotic phase synchronization Chaos, vol 13:1 pp. 247258 (2003). Also: PS format. Example that illustrates the discussion is Section 7 of the paper.

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

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

R. Bhattacharjee, R. L. Devaney, R. E. L. Deville, K. Josić, and M. MorenoRocha Accessible Points of Julia Sets of Stable Exponentials Discrete and Continuous Dynamical Systems B, 1:3, p. 299318 (2001). Also: PS Format

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

K. Josić and R.W. Hall The Mathematics of Musical Instruments American Mathematical Monthly, 108:4, p. 347357 (2001).

K. Josić and R.W. Hall, Planetary Motion and the Duality of Force Laws SIAM Review, 42:1, p. 114125 (2000).

K. Josić and C.E. Wayne, Dynamics of a Diffusively Coupled Ring of Lorenz Oscillators Journal of Statistical Physics, 98:1, p. 130 (2000). Also: PS Format. The interval arithemtic code used for some estimates in the paper is available.

K. Josić Synchronization of Chaotic Systems and Invariant Manifolds Nonlinearity, 13:4, pp. 13211336 (2000).

K. Josić Invariant Manifolds and Synchronization of Coupled Dynamical Systems Physical Review Letters, 80:14, pp. 30533056 (1998). Also: PS Format
 K. Josić Local Bifurcations in the Symmetric Model of Selection with Fertility Differences Journal of Theoretical Biology, 189, pp. 291295 (1997). Also: PS Format
Book chapters and encyclopedia entries
Refereed entries are marked with a star (*).

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).

(*) K. Josić, E. SheaBrown, and J. Moehlis. Scholarpedia entry on isochrons

(*) J. Moehlis, K. Josić, and E. SheaBrown. Scholarpedia entry on periodic orbits

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 FastSlow Systems chapter in Global Analysis of Dynamical Systems.