Afrikanova, T., Serruys, A.S., Buenafe, O.E., Clinckers, R., Smolders, I., de Witte, P.A., Crawford, A.D., Esguerra, C.V. (2013) Validation of the zebrafish pentylenetetrazol seizure model: locomotor versus electrographic responses to antiepileptic drugs. PLoS One 8, e54166.

Aguirre, J., & Manrubia, S. (2015). Tipping points and early warning signals in the genomic composition of populations induced by environmental changes. Scientific reports, 5.

Akerboom, J., et al. (2012) Optimization of a GCaMP calcium indicator for neural activity imaging. J. Neuroscience 32, 2601-12.

Allen, F., & Gale, D. (2000). Financial contagion. Journal of political economy, 108(1), 1-33.

Bu, X., Wang, X., Xiang, Y., Shen, L., Wang, Q., Liu, Y., Jiao, S., Wang, Y., Cao, H., Yi, X., Liu, C., Deng, B., Yao, X., Xu, Z., Zhou, H., & Wang, Y. (2015). The association between infectious burden and Parkinson's disease: A case-control study. Parkinsonism Relat Disord 21(8), 877-81.

Chen, L., Liu, R., Liu, Z.-P., Li, M. & Aihara, K. (2012). Detecting early-warning signals for sudden deterioration of complex diseases by dynamical network biomarkers. Sci. Rep. 2, 18–20.

Claessens, S., & Forbes, K. (Eds.). (2013). International financial contagion. Springer Science & Business Media.

CXO Advisory Group, (2005). When Stock Market Models Crash. Online at

Dent, H., (2009). The great depression ahead: how to prosper in the crash following the greatest boom in history. Free Press.

Dhabhar, F.S. (2008). Enhancing versus Suppressive Effects of Stress on Immune Function: Implications for Immunoprotection versus Immunopathology. Allergy Asthma Clin Immunol 4, 2-11.

D’Souza, K., Epureanu, B. I., & Pascual, M. (2015). Forecasting Bifurcations from Large Perturbation Recoveries in Feedback Ecosystems. PloS one, 10(9), e0137779.

Elowitz, M.B., Levine, A.J., Siggia E.D., & Swain, P.S. (2002). Stochastic Gene Expression in a Single Cell Science 297, 1183-1186.

Enders, W. (2008). Applied econometric time series. John Wiley & Sons.

Feigenbaum, J., & Freund, P. (1998). Discrete Scale Invariance and the ‘Second Black Monday’. Modern Physics Letters B, 12, 57-60.

Föllmer, H., & Schied, A. (2011). Stochastic finance: an introduction in discrete time. Walter de Gruyter.

Forbes, K. J., & Rigobon, R. (2002). No contagion, only interdependence: measuring stock market comovements. The journal of finance, 57(5), 2223-2261.

Forró, Z., Woodard, R., & Sornette, D. (2015). Using trading strategies to detect phase transitions in financial markets. Physical Review E, 91(4), 042803.

Fuster, V., Rydén, L. E., Cannom, D. S., Crijns, H. J., Curtis, A. B., Ellenbogen, K. A., ... & Wann, S. (2006). Guidelines for the management of patients with atrial fibrillation. Executive summary. Revista española de cardiología, 59(12), 1329.

Ge, H. & Qian H. (2011). Non-equilibrium phase transition in mesoscopic biochemical systems: from stochastic to nonlinear dynamics and beyond. J. R. Soc. Interface 8, 107.

Glazier, J. A., & Graner, F. (1993). Simulation of the differential adhesion driven rearrangement of biological cells. Physical Review E, 47(3), 2128.

Gorban, A. N., Smirnova, E. V., & Tyukina, T. A. (2010). Correlations, risk and crisis: From physiology to finance. Physica A: Statistical Mechanics and its Applications, 389(16), 3193-3217.

Grünewald, A., Lax, N., Rocha, M., Reeve, A., Hepplewhite, P., Rygiel, K., Taylor, R., & Turnbulla, D. (2014). Quantitative quadruple-label immunofluorescence of mitochondrial and cytoplasmic proteins in single neurons from human midbrain tissue. J Neurosci Methods, 232(100), 143–149.

Gu, H., Zhao, Z., Jia, B., & Chen, S. (2015). Dynamics of On-Off Neural Firing Patterns and Stochastic Effects near a Sub-Critical Hopf Bifurcation. PloS one, 10(4).

Guan J, Gupta R, Filipp F V (2015). Cancer systems biology of TCGA SKCM: Efficient detection of genomic drivers in melanoma. Sci Rep 5, 7857.

He, F., & Balling, R. (2013). The role of regulatory T cells in neurodegenerative diseases. Wiley Interdiscip Rev Syst Biol Med 5, 153-180.

He, F., Balling, R., & Zeng, A.-P. (2009). Reverse engineering and verification of gene networks: Principles, assumptions, and limitations of present methods and future perspectives. Journal of Biotechnology 144, 190-203.

He, F., Chen, H., Probst-Kepper, M., Geffers, R., Eifes, S., Del Sol, A., Schughart, K., Zeng, A.-P., & Balling R. (2012). PLAU inferred from a correlation network is critical for suppressor function of regulatory T cells. Mol Syst Biol 8, 624-642.

He, F., Wang, W., Zheng, P., Sudhakar, P., Sun, J., & Zeng A.-P. (2014). Essential O2-responsive genes of Pseudomonas aeruginosa and their network revealed by integrating dynamic data from inverted conditions. Integr Biol (Camb) 6, 215-223.

Jiruska, P., de Curtis, M., Jefferys, J.G., Schevon, C.A., Schiff, S.J., Schindler, K. (2013). Synchronization and desynchronization in epilepsy: controversies and hypotheses. J. Physiol. 591, 787-97.

Johansen, A., (2003). Comment on Recent Claims by Sornette and Zhou. Social Science Electronic Publishing. Online at

Kaminsky, G. L., & Reinhart, C. M. (2000). On crises, contagion, and confusion. Journal of international Economics, 51(1), 145-168.

Keller, P.J., Ahrens, M.B. (2015) Visualizing whole-brain activity and development at the single-cell level using light-sheet microscopy. Neuron 85, 462-83.

Khalil, H. K., & Grizzle, J. W. (1996). Nonlinear systems (Vol. 3). New Jersey: Prentice Hall.

Kirchhof, P., Bax, J., Blomstrom-Lundquist, C., Calkins, H., Camm, A. J., Cappato, R., ... & Breithardt, G. (2009). Early and comprehensive management of atrial fibrillation: executive summary of the proceedings from the 2nd AFNET-EHRA consensus conference ‘research perspectives in AF’. European heart journal, 30(24), 2969-2980.

Kirchhof, P., Breithardt, G., Aliot, E., Al Khatib, S., Apostolakis, S., Auricchio, A., ... & Pieske, B. (2013). Personalized management of atrial fibrillation: Proceedings from the fourth Atrial Fibrillation competence NETwork/European Heart Rhythm Association consensus conference. Europace, 15(11), 1540-1556.

Kuehn, C., Zschaler, G., & Gross, T. (2015). Early warning signs for saddle-escape transitions in complex networks. Scientific Reports, 5, 13190.

Laczny, C. C., Pinel, N., Vlassis, N., & Wilmes, P. (2014). Alignment-free visualization of metagenomic data by nonlinear dimension reduction. Scientific Reports, 4.

Lahti, L., Salojärvi, J., Salonen, A., Scheffer, M., & Willem M. (2014). Tipping elements in the human intestinal ecosystem. Nature Communications, 5.

Lovecchio, E., Allegrini, P., Geneston, E., West, B. J., & Grigolini, P. (2012). From self-organized to extended criticality. Frontiers in Physiology, 3.

Marttila, R. J., Kalimo, K. O. K., Ziola, B., Halonen, P., and Rinne, U.K. (1978). Herpes simplex virus subunit antibodies in patients with Parkinson's disease. Arch Neurol, 35(10), 668–671.

McHugh, R., (2013). The coming economic ice age; five steps to survive and prosper. Thomas Noble Books.

Moignard V. et al. (2013). Characterization of transcriptional networks in blood stem and progenitor cells using high-throughput single-cell gene expression analysis. Nature Cell Biol. 15, 363–372.

Montell, D. J. (2008). Morphogenetic cell movements: diversity from modular mechanical properties. Science, 322(5907), 1502-1505.

Morales, I. O., Landa, E., Angeles, C. C., Toledo, J. C., Rivera, A. L., Temis, J. M., & Frank, A. (2015). Behavior of Early Warnings near the Critical Temperature in the Two-Dimensional Ising Model. Plos One, 10(6), e0130751.

Muller, E. E., Glaab, E., May, P., Vlassis, N., & Wilmes, P. (2013). Condensing the omics fog of microbial communities. Trends in microbiology, 21(7), 325-333.

Muller, E. E., Pinel, N., Laczny, C. C., Hoopmann, M. R., Narayanasamy, S., Lebrun, L. A., ... & Wilmes, P. (2014). Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage. Nature communications, 5.

Murray, J. D. (2001). Mathematical Biology. II Spatial Models and Biomedical Applications Interdisciplinary Applied Mathematics Vol. 18. Springer-Verlag New York Incorporated.

Murray, J. D. (2002). Mathematical Biology I: An Introduction, Interdisciplinary Applied Mathematics Vol. 17. Springer-Verlag New York Incorporated.

Nazarov, P.V., Reinsbach, S.E., Muller, A., Nicot, N., Philippidou, D., Vallar, L., Kreis, S. (2013) Interplay of microRNAs, transcription factors and target genes: Linking dynamic expression changes to function. Nucleic Acids Res, 41:2817–2831.

Rieu, J. P., Upadhyaya, A., Glazier, J. A., Ouchi, N. B., & Sawada, Y. (2000). Diffusion and deformations of single hydra cells in cellular aggregates. Biophysical Journal, 79(4), 1903-1914.

Risken, H. (1989). The Fokker-Planck Equation: Methods of Solution and Applications. 2nd edition, Springer.

Roume, H., Heintz-Buschart, A., Muller, E. E., May, P., Satagopam, V. P., Laczny, C. C., ... & Wilmes, P. (2015). Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. Nature publishing group journal (npj) Biofilms and Microbiomes, 1.

Roume, H., Muller, E. E., Cordes, T., Renaut, J., Hiller, K., & Wilmes, P. (2013). A biomolecular isolation framework for eco-systems biology. The ISME journal, 7(1), 110-121.

Rygiel, K., Grady, J., Taylor, R., Tuppen, H., & Turnbull, D. (2015). Triplex real-time PCR–an improved method to detect a wide spectrum of mitochondrial DNA deletions in single cells. Scientific Reports, 5(9906).

Sastry, S. (2013). Nonlinear systems: analysis, stability, and control (Vol. 10). Springer Science & Business Media.

Scheffer, M., (2009). Critical Transitions in Nature and Society. Princeton Studies in Complexity, Princeton University Press.

Scheffer, M., Bascompte, J., Brock, W., Brovkin, V., Carpenter, S., Dakos, V., Held, H., van Nes, E., Rietkerk, M., & Sugihara, G., (2009). Early-warning signals for critical transitions. Nature 461, 53-59.

Scheffer, M., (2010). Complex systems: Foreseeing tipping points. Nature 467, 411–412.

Schiff, P., (2012). The real crash: America's coming bankruptcy; how to save yourself and your country. St. Martin's Press.

Schotten, U., Verheule, S., Kirchhof, P., & Goette, A. (2011). Pathophysiological mechanisms of atrial fibrillation: a translational appraisal. Physiological reviews, 91(1), 265-325.

Schubert, J., Siekierska, A., Langlois, M., May, P., Huneau, C., Becker, F., ... & EuroEPINOMICS RES Consortium. (2014). Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes. Nature genetics, 46(12), 1327-1332.

Seifert, U. (2012) Stochastic thermodynamics, fluctuation theorems, and molecular machines. Rep. Prog. Phys. 75, 126001.

Sekulic, A., Haluska, P., Miller, A.J., Genebriera De Lamo, J., Ejadi, S., Pulido, J.S., Salomao, D.R., Thorland, E.C., Vile, R.G., Swanson, D.L., Pockaj, B., Laman, S.D., Pittelkow, M.R., Markovic, S.N. (2008). Malignant melanoma in the 21st century: the emerging molecular landscape.Mayo Clin Proc, 83, 825–46.

Shi et al. (2012). Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells. PNAS 109, 419-424.

Siegel, R., Ma, J., Zou, Z., Jemal, A. (2014). Cancer Statistics 64, 9–29.

Sornette, D., (2004). Why stock markets crash: critical events in complex financial systems. Princeton University Press.

Stewart, S., Hart, C. L., Hole, D. J., & McMurray, J. J. V. (2001). Population prevalence, incidence, and predictors of atrial fibrillation in the Renfrew/Paisley study. Heart, 86(5), 516-521.

Strogatz, S. H. (2014). Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering. Westview press.

Trefois, C., Antony, P., Goncalves, J., Skupin, A., & Balling, R., (2015). Critical transitions in chronic disease: transferring concepts from ecology to systems medicine. Current Opinion in Biotechnology 34, 48–55.

Tsuchiya, M., Giuliani, A., Hashimoto, M., Erenpreisa, J., & Yoshikawa, K. (2015). Emergent Self-Organized Criticality in Gene Expression Dynamics: Temporal Development of Global Phase Transition Revealed in a Cancer Cell Line. PloS one, 10(6), e0128565.

Tsuji, H., Larson M.G., Venditti F.J., Manders E.S., Evans J.C., Feldman C.L., & Levy D., (1996) Impact of reduced heart rate variability on risk for cardiac events. The Framingham Heart Study. Circulation 94, 2850-5.

Upadhyaya, A., Rieu, J. P., Glazier, J. A., & Sawada, Y. (2001). Anomalous diffusion and non-Gaussian velocity distribution of Hydra cells in cellular aggregates. Physica A: Statistical Mechanics and its Applications, 293(3), 549-558.

Van den Broeck, E., & Esposito, M. (2015). Ensemble and trajectory thermodynamics: A brief introduction. Physica A 418, 6.;

West, A., Khoury-Hanold, W., Staron, M., Tal, M., Pineda, C, Lang, S., Bestwick, M., Duguay, B., Raimundo, N., MacDuff, D., Kaech, S., Smiley, J., Means, R., Iwasaki, A., & Shadel, G., (2015). Mitochondrial DNA stress primes the antiviral innate immune response. Nature 520(7548), 553-557.

Yoon, H.S., Price, D.C., Stepanauskas, R., Rajah, V.D., Sieracki, M.E., Wilson, W.H., Yang, E.C., Duffy, S., & Bhattacharya D. (2011). Single-cell genomics reveals organismal interactions in uncultivated marine protists. Science 332,714-4.

Zeighami, Y., Ulla, M., Iturria-Medina, Y., Dadar, M., Zhang, Y., Larcher, K., Fonov, V., Evans, A., Collins, D., & Dagher, A. (2015). Network structure of brain atrophy in de novo Parkinson's disease. eLife, 4, e08440.