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

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]

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]

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. [preprint]

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]

Boolean network models of yeast

S. Braunewell and S. Bornholdt, Superstability of the yeast cell-cycle dynamics: Ensuring causality in the presence of biochemical stochasticity, J. Theor. Biol. 245 (2007) 638-643. [PDF]

Maria I. Davidich and S. Bornholdt, Boolean network model predicts cell cycle sequence of fission yeast, PLoS ONE 3 (2008) e1672. [PDF]

Maria I. Davidich and S. Bornholdt, The transition from differential equations to Boolean networks: A case study in simplifying a regulatory network model, J. Theor. Biol. 255 (2008) 269-277. [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]

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]

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]

Neural networks: Development and learning

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]

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. [preprint]

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. [preprint]

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]

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]

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]

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]