Adaptive gene regulatory networks (2009)
Stauffer, Franck, Berg, Johannes
Regulatory interactions between genes show a large amount of cross-species variability, even when the underlying functions are conserved: There are many ways to achieve the same function. Here we...
From protein interactions to functional annotation: graph alignment in Herpes (2008)
Kolář, Michal, Lässig, Michael, Berg, Johannes
Abstract Background Sequence alignment is a prolific basis of functional annotation, but remains a challenging problem in the 'twilight zone' of high sequence divergence or short gene length. Here we...
Dynamics of gene expression under feedback (2008)
Pulkkinen, Otto, Berg, Johannes
Gene expression is a stochastic process governed by the presence of specific transcription factors. Here we study the dynamics of gene expression in the presence of feedback, where a gene regulates...
Roukens, Anna H, Berg, Johannes, Barbey, Alex, Visser, Leo G
Abstract Background Falciparum malaria remains a major occupational illness that accounts for several deaths per year and numerous lost working days among the expatriate population, working or living...
Universal intermittent properties of particle trajectories in highly turbulent flows (2008)
Arneodo, Alain, Benzi, Roberto, Berg, Johannes, Biferale, Luca, Bodenschatz, Eberhard, Busse, A., ...
Dynamics of gene expression and the regulatory inference problem (2007)
From the response to external stimuli to cell division and death, the dynamics of living cells is based on the expression of specific genes at specific times. The decision when to express a gene is...
Non-equilibrium dynamics of gene expression and the Jarzynski equality (2007)
In order to express specific genes at the right time, the transcription of genes is regulated by the presence and absence of transcription factor molecules. With transcription factor concentrations...
From Protein Interactions to Functional Annotation: Graph Alignment in Herpes (2007)
Kolář, Michal, Lässig, Michael, Berg, Johannes
Sequence alignment forms the basis of many methods for functional annotation by phylogenetic comparison, but becomes unreliable in the `twilight' regions of high sequence divergence and short gene...
Bayesian analysis of biological networks: clusters, motifs, cross-species correlations (2006)
Berg, Johannes, Lässig, Michael
An important part of the analysis of bio-molecular networks is to detect different functional units. Different functions are reflected in a different evolutionary dynamics, and hence in different...
Cross-species analysis of biological networks by Bayesian alignment (2006)
Berg, Johannes, Lässig, Michael
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction...
Berg, Johannes, Lässig, Michael, Wagner, Andreas
Abstract Background The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure...
Adaptive evolution of transcription factor binding sites (2004)
Berg, Johannes, Willmann, Stana, Lässig, Michael
Abstract Background The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and...
Local graph alignment and motif search in biological networks (2003)
Berg, Johannes, Lässig, Michael
Interaction networks are of central importance in post-genomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks...
Adaptive evolution of transcription factor binding sites (2003)
Berg, Johannes, Willmann, Stana, Lässig, Michael
The regulation of a gene depends on the binding of transcription factors to specific sites located in the regulatory region of the gene. The generation of these binding sites and of cooperativity...
Andrew Mclennan, Johannes Berg
* We are indebted to Robin Pemantle for suggestions that led to the development of Theorem 2,
Andrew Mclennan, Johannes Berg
* We are indebted to Robin Pemantle for suggestions that led to the development of Theorem 2,
Berg, Johannes, Lässig, Michael, Wagner, Andreas
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred...
Correlated random networks (2002)
Berg, Johannes, Lässig, Michael
We develop a statistical theory of networks. A network is a set of vertices and links given by its adjacency matrix $\c$, and the relevant statistical ensembles are defined in terms of a partition...
The Asymptotic Expected Number of Nash Equilibria of Two Player Normal Form Games (2002)
Johannes Berg, Andrew McLennan, Andrew Mclennan
The formula given by McLennan (2002) for the mean number of Nash equilibria of a normal form game, for a particular support, is applied to investigate the expected number of Nash equilibria of two...
Testing the Edwards hypothesis in spin systems under tapping dynamics (2001)
Berg, Johannes, Franz, Silvio, Sellitto, Mauro
The Edwards hypothesis of ergodicity of blocked configurations for gently tapped granular materials is tested for abstract models of spin systems on random graphs and spin chains with kinetic...
Spin-models of granular compaction: From one-dimensional models to random graphs (2001)
We discuss two athermal types of dynamics suitable for spin-models designed to model repeated tapping of a granular assembly. These dynamics are applied to a range of models characterised by a 3-spin...
Metastable configurations of spin models on random graphs (2001)
Berg, Johannes, Sellitto, Mauro
One-flip stable configurations of an Ising-model on a random graph with fluctuating connectivity are examined. In order to perform the quenched average of the number of stable configurations we...
Glassy dynamics in granular compaction: sand on random graphs (2001)
We discuss the use of a ferromagnetic spin model on a random graph to model granular compaction. A multi-spin interaction is used to capture the competition between local and global satisfaction of...
Statistical mechanics of asset markets with private information (2001)
Berg, Johannes, Marsili, Matteo, Rustichini, Aldo, Zecchina, Riccardo
Traders in a market typically have widely different, private information on the return of an asset. The equilibrium price of the asset may reflect this information more accurately if the number of...
On random graphs and the statistical mechanics of granular matter (2000)
The dynamics of spins on a random graph with ferromagnetic three-spin interactions is used to model the compaction of granular matter under a series of taps. Taps are modelled as the random flipping...
Statistical mechanics of random two-player games (1999)
Using methods from the statistical mechanics of disordered systems we analyze the properties of bimatrix games with random payoffs in the limit where the number of pure strategies of each player...
Entropy and typical properties of Nash equilibria in two-player games (1999)
We use techniques from the statistical mechanics of disordered systems to analyse the properties of Nash equilibria of bimatrix games with large random payoff matrices. By means of an annealed bound,...
Föderative Kooperation im öffentlichen Schienenpersonennahverkehr / (1993)
Zugl.: Kiel, Univ., Diss., 1993.
Ausz.
Local graph alignment and motif search in biological networks
Berg, Johannes, Lässig, Michael
Interaction networks are of central importance in postgenomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks...
Local graph alignment and motif search in biological networks
Berg, Johannes, Lässig, Michael
Interaction networks are of central importance in postgenomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks...
Cross-species analysis of biological networks by Bayesian alignment
Berg, Johannes, Lässig, Michael
Complex interactions between genes or proteins contribute a substantial part to phenotypic evolution. Here we develop an evolutionarily grounded method for the cross-species analysis of interaction...
SPIN-MODELS OF GRANULAR COMPACTION: FROM ONE-DIMENSIONAL MODELS TO RANDOM GRAPHS
We discuss two athermal types of dynamics suitable for spin-models designed to model repeated tapping of a granular assembly. These dynamics are applied to a range of models characterized by a 3-spin...
Statistical mechanics of asset markets with private information
Johannes Berg, Matteo Marsili, Aldo Rustichini, Riccardo Zecchina
Traders in a market typically have widely different, private information on the return of an asset. The equilibrium price of the asset may reflect this information more accurately if the number of...