Boolean models of genetic networks

S. Bornholdt, Modeling Genetic Networks and Their Evolution: A Complex Dynamical Systems Perspective, Biological Chemistry 382 (2001) 1289-1299. [PDF]

S. Bornholdt, Less is more in modeling large genetic networks, Science 310 (2005) 449. [Summary] [Full text]

S. Bornholdt, Boolean network models of cellular regulation: prospects and limitations, J. Roy. Soc. Interface 5 (2008) S85-S94. [PDF]

Bornholdt, S., and Kopperschmidt, G., Gene regulation: Experiments with the LECTRON experimental kit (2015) ISBN 978-3-00-051441-8. [PDF]

Bornholdt, S., and Kopperschmidt, G., Genregulation: Versuche mit dem  LECTRON Experimentierkasten (2015) ISBN 978-3-00-051404-3. [PDF]

S. Bornholdt and S.A. Kauffman, Ensembles, Dynamics, and Cell Types: Revisiting the Statistical Mechanics Perspective on Cellular Regulation, J. Theor. Biol. 467 (2019) 15-22. [PDF]

Neural networks: Development, learning, criticality

K. Klemm, S. Bornholdt, and H.G. Schuster, Beyond Hebb: Exclusive-OR and biological learning, Phys. Rev. Lett. 84 (2000) 3013-3016. [PDF]

S. Bornholdt and T. Roehl, Self-organized critical neural networks, Phys. Rev. E 67 (2003) 066118. [PDF]

M. Rybarsch and S. Bornholdt, Avalanches in self-organized critical neural networks: a minimal model for the neural SOC universality class, PloS ONE 9 (2014) e93090. [PDF]

M. Rybarsch and S. Bornholdt, Self-organized criticality in neural network models. In: Criticality in Neural Systems, D. Plenz and E. Niebur (eds.), Wiley-VCH Verlag, Weinheim, 2014. [PDF]

JP Neto, MAM de Aguiar, JA Brum, and S Bornholdt, Inhibition as a determinant of activity and criticality in dynamical networks, arXiv:1712.08816 (2017). [PDF]

S Landmann, L Baumgarten, S Bornholdt, Self-organized criticality in neural networks from activity-based rewiring, Phys. Rev. E 103 (2021) 032304. [PDF]

The interdependent network  of genome and metabolism

D.F. Klosik, A. Grimbs, S. Bornholdt, and M.T. Hütt, The interdependent network of gene regulation and metabolism is robust where it needs to be, Nature communications 8 (2017) 534. [PDF]

A. Grimbs, D.F. Klosik, S. Bornholdt, and M.T. Hütt, A system-wide network reconstruction of gene regulation and metabolism in Escherichia coli, arXiv:1803.05429 (2018). [PDF]

Socio- and Econophysics

S. Bornholdt, M.H. Jensen, and K. Sneppen, Emergence and Decline of Scientific Paradigms, Phys. Rev. Lett. 106 (2011) 058701 [PDF]

S. Bornholdt and K. Sneppen, Do Bitcoins make the world go round? On the dynamics of competing crypto-currencies, arXiv preprint arXiv:1403.6378 (2014). [PDF]

S.M. Krause, S. Börries, and S. Bornholdt, Econophysics of adaptive power markets: When a market does not dampen fluctuations but amplifies them, Phys. Rev. E 92 (2015) 012815. [PDF]

G.G. Jensen and S. Bornholdt, Social evolution of structural discrimination,  Scientific Reports 9 (2019) 3776.  [PDF]

K. Sneppen and S. Bornholdt, Globalization in a nutshell, Phys. Rev. E 98 (2018) 042314.  [PDF

Complex networks: Internet and society

S. Bornholdt and H. Ebel, World Wide Web Scaling Exponent from Simon’s 1955 Model, Phys. Rev. E 64 (2001) 035104(R). [PDF]

J. Davidsen, H. Ebel, and S. Bornholdt, Emergence of a small world from local interaction: Modeling acquaintance networks, Phys. Rev. Lett. 88 (2002) 128701. [PDF]

H. Ebel, L.-I. Mielsch, and S. Bornholdt, Scale-free topology of e-mail networks, Phys. Rev. E 66 (2002) 035103(R) [PDF] [Data]

H. Ebel and S. Bornholdt, Coevolutionary games on networks, Phys. Rev. E 66 (2002) 056118. [PDF]

H. Ebel and S. Bornholdt, Evolutionary games and the emergence of complex networks, (2002) cond-mat/0211666.  [PDF]

H. Ebel, J. Davidsen, and S. Bornholdt, Dynamics of social networks, Complexity 8(2) (2003) 24-27. [PDF]

T. P. Peixoto and S. Bornholdt Evolution of robust network topologies: Emergence of central backbones, Phys. Rev. Lett. 109 (2012) 118703. [PDF]

S.M. Krause, T.P. Peixoto, and S. Bornholdt, Spontaneous centralization of control in a network of company ownerships, PloS ONE 8 (2013) e80303. [PDF]

D.F. Klosik, S. Bornholdt, and M.T. Hütt, Motif-based success scores in coauthorship networks are highly sensitive to author name disambiguation, Phys. Rev. E 90 (2014) 032811. [PDF]

D.F. Klosik and S. Bornholdt, The citation wake of publications detects Nobel laureates’ papers, PloS ONE 9 (2014) e113184. [PDF]

Applying statistical physics to economy and finance

S. Bornholdt, Expectation bubbles in a spin model of markets: Intermittency from frustration across scales, Int. J. Mod. Phys. C, Vol. 12, No. 5 (2001) 667-674. [PDF] [JAVA applet]

T. Kaizoji, S. Bornholdt, and Y. Fujiwara, Dynamics of price and trading volume in a spin model of stock markets with heterogeneous agents, Physica A 316 (2002) 441-452. [PDF]

S. Bornholdt and F. Wagner, Stability of money: Phase transitions in an Ising economy, Physica A 316 (2002) 453-468. [PDF]

I. Simonsen, L. Buzna, K. Peters, S. Bornholdt, D. Helbing, Transient dynamics increasing network vulnerability to cascading failures, Phys. Rev. Lett. 100 (2008) 218701. [PDF]

S. M. Krause, P. Böttcher, and S. Bornholdt Mean-field-like behavior of the generalized voter-model-class kinetic Ising model, Phys. Rev. E 85 (2012) 031126. [PDF]

T. P. Peixoto and S. Bornholdt, No need for conspiracy: Self-organized cartel formation in a modified trust game, Phys. Rev. Lett. 108 (2012) 218702. [PDF]

S. M. Krause and S. Bornholdt, Opinion formation model for markets with a social temperature and fear, Phys. Rev. E 86 (2012) 056106. [PDF]

S.M. Krause and S. Bornholdt, Spin models as microfoundation of macroscopic market models, Physica A: Statistical Mechanics and its Applications 392 (2013) 4048-4054. [PDF]

Statistical physics of complex networks I: Boolean networks

Bornholdt and T. Rohlf Topological evolution of dynamical networks: Global criticality from local dynamics, Phys. Rev. Lett. 84 (2000) 6114-6117. [PDF]

T. Rohlf and S. Bornholdt, Criticality in Random Threshold Networks: Annealed Approximation and Beyond, Physica A 310 (2002) 245-259. [PDF]

K. Klemm and S. Bornholdt, Stable and unstable attractors in Boolean networks, Phys. Rev. E 72 (2005) 055101(R). [PDF]

M. Rybarsch and S. Bornholdt Binary threshold networks as a natural null model for biological networks, Phys. Rev. E 86, 026114 (2012) [PDF]

Dynamics and evolution of diseases

K. Sneppen, A. Trusina, M.H. Jensen, and S. Bornholdt, A Minimal Model for Multiple Epidemics and Immunity Spreading PLoS ONE 5 (2010) e13326 [PDF] [JAVA applet]

Stochastic Boolean networks and reliability of molecular networks

K. Klemm and S. Bornholdt, Robust gene regulation: Deterministic dynamics from asynchronous networks with delay, (2003) q-bio/0309013. [PDF]

K. Klemm and S. Bornholdt, Topology of biological networks and reliability of information processing, Proc. Natl. Acad. Sci. USA 102 (2005) 18414. [PDF]

S. Braunewell and S. Bornholdt, Reliability of genetic networks is evolvable, Phys. Rev. E 77 (2008) 060902. [PDF]

S. Braunewell and S. Bornholdt, Reliability of regulatory networks and its evolution, J. Theor. Biol. 258 (2009) 502-512. [PDF]

Biological networks and morphogenesis

T. Rohlf and S. Bornholdt, Self-organized pattern formation and noise-induced control from particle computation, JSTAT (2005) L12001. [PDF] [JAVA applet]

T. Rohlf and S. Bornholdt, Morphogenesis by coupled regulatory networks: Reliable control of positional information and proportion regulation, J. Theor. Biol. 261 (2009) 176-193. [PDF] [JAVA applet]

Dynamics of macroevolution

S. Bornholdt and K. Sneppen, Neutral mutations and punctuated equilibrium in evolving genetic networks, Phys. Rev. Lett. 81 (1998) 236-239. [PDF]

S. Bornholdt and K. Sneppen, Robustness as an Evolutionary Principle, Proc. R. Soc. London B 267 (2000) 2281-2286. [PDF]

S. Bornholdt, K. Sneppen, and H. Westphal, Longevity of orders is related to the longevity of their constituent genera rather than genus richness, Theory in Biosciences 128 (2008) 75-83. [PDF] [JAVA applet]

Statistical physics of complex networks II: Community detection

J. Reichardt and S. Bornholdt, Detecting fuzzy communities in complex networks with a Potts model, Phys. Rev. Lett. 93 (2004) 218701. [PDF]

J. Reichardt and S. Bornholdt, Statistical Mechanics of Community Detection, Phys. Rev. E 74 (2006) [PDF]

J. Reichardt and S. Bornholdt, When are networks truly modular? Physica D 224 (2006) 20-26. [PDF]

J. Reichardt and S. Bornholdt, Clustering of sparse data via network communities — a prototype study of a large online market, J. Stat. Mech. (2007) P06016. [PDF]

J. Reichardt and S. Bornholdt, Partitioning and Modularity of Graphs with arbitrary Degree Distribution, Phys. Rev. E 76 (2007) 015102(R). [PDF]

Complex natural systems

E. Moritz, S. Bornholdt, H. Westphal, and M. Meschede, Neural network interpretation of LWD data (ODP Leg 170) confirms complete sediment subduction at the Costa Rica convergent margin, Earth and Planetary Science Letters 174 (2000) 301-312. [PDF]

F. Böhm, H. Westphal, and S. Bornholdt Required but disguised: Environmental signals in limestone-marl alternations. Palaeogeography, Palaeoclimatology, Palaeoecology 2987 (2003) 1-18. [PDF]

H. Westphal, F. Böhm, and S. Bornholdt, Orbital Frequencies in the Sedimentary Record: Distorted by Diagenesis? Facies 50 (2004) 3-11. [PDF]

Applying statistical physics to the immune system

C. Kamp and S. Bornholdt, Co-evolution of quasispecies: B-cell mutation rates maximize viral error catastrophes, Phys. Rev. Lett. 88 (2002) 068104. [PDF]

C. Kamp and S. Bornholdt, From HIV infection to AIDS: A dynamically induced percolation transition?, Proc. R. Soc. London B 269 (2002) 2035-2040. [PDF]

C. Kamp, C.O. Wilke, C. Adami, and S. Bornholdt, Viral evolution under the pressure of an adaptive immune system – optimal mutation rates for viral escape, Complexity 8(2) (2003) 28-33. [PDF] [Nature News and Views feature]

C. Kamp and S. Bornholdt, Critical percolation in self-organized media: A case study on random directed networks, (2002) cond-mat/0210410. [PDF]

Dynamics of evolutionary algorithms

S. Bornholdt, Genetic algorithm dynamics on a rugged fitness landscape, Phys. Rev. E 57 (1998) 3853. [PDF]

S. Bornholdt, Annealing schedule from population dynamics, Phys. Rev. E 59 (1999) 3942. [PDF]



S. Bornholdt and H. G. Schuster (eds.),  “Handbook of Graphs and Networks – From the Genome to the Internet, Wiley-VCH, Berlin (2002) ”  Buy 

S. Bornholdt and K. Klemm (eds.), Dynamical Networks in Complex Systems, Europhysics Conference Abstracts Vol. 25F (2001). Note: We have a few copies of this abstract book left over. For a free copy please send an email to .img@.img..img..img. The corresponding  conference site can be found here: International Conference on Dynamical Networks in Complex Systems 2001.

T. Gramss, S. Bornholdt, M. Gross, M. Mitchell, and T. Pellizari, Non-Standard Computation, VCH Verlag, Weinheim (1998).

S. Bornholdt und P.H. Feindt (eds.), Komplexe adaptive Systeme, Verlag Josef Roell, Dettelbach (1996).