Johannes Berg

List of Publications

Adaptive gene regulatory networks,
F. Stauffer and J. Berg, EPL 88, 48004 (2009).
Dynamics of gene expression under feedback,
O. Pulkkinen and J. Berg, http://arxiv.org/abs/0807.3521
Out-of-equilibrium dynamics of gene expression and the Jarzynski equality,
J. Berg, Phys. Rev. Lett. 100, 188101 (2008).
(PRL Editors' Suggestion, featured in HFSP Journal)
Dynamics of gene expression and the regulatory inference problem,
J. Berg, Europhys. Lett. 82, 28010 (2008).
(featured in HFSP Journal)
From protein interactions to functional annotation: Graph alignment in Herpes,
M. Kolář, M. Lässig, and J. Berg, BMC Systems Biology, 2:90 (2008).
Statistical modelling and analysis of biological networks
J. Berg, in Complex Systems, Les Houches lecture notes, J.-P. Bouchaud, M. Mézard, and J. Dalibard (Eds.), (Elsevier, Amsterdam, 2007).
Gene expression profiling identifies new biological markers of neoplastic germ cell,
K. Biermann et al. (14 authors), Anticancer Res. 27(5A), 3091-3100 (2007).
Genome-wide Expression Profiling Reveals New Insights into Pathogenesis and Progression of Testicular Germ Cell Tumors,
K. Biermann et al. (12 authors), Cancer Genomics Proteomics 4(5), 359-368 (2007).
Bayesian analysis of biological networks: clusters, motifs, cross-species correlations,
J. Berg and M. Lässig, to appear in Statistical and Evolutionary Analysis of Biological Network Data, M. Stumpf and C. Wiuf (Eds.).
Cross-species analysis of biological networks by Bayesian alignment,
J. Berg and M. Lässig, PNAS 103(29), 10967-10972 (2006).
Competition and cooperation:aspects of dynamics in sandpiles,
A. Mehta, J.-M. Luck, J. Berg, and G. Barker, J. Phys. A17, 1-31 (2005).
The asymptotic expected number of Nash equilibria of two player normal form games,
A. McLennan and J. Berg, Games and Economic Behavior 51(2), 264-295 (2005).
Local graph alignment and motif search in biological networks,
J. Berg and M. Lässig, PNAS 101(41), 14689-14694 (2004).
Adaptive evolution of transcription factor binding sites,
J. Berg, S. Willmann, and M. Lässig, BMC Evolutionary Biology 4(1):42 (2004).
Structure and Evolution of Protein Interaction Networks: A Statistical Model for Link Dynamics and Gene Duplications,
J. Berg, M. Lässig, and A. Wagner, BMC Evolutionary Biology 4:51 (2004).
Stochastic evolution of transcription factor binding sites,
J. Berg and M. Lässig, Biophysics 48(1), 36-44 (2003).
Correlated random networks,
J. Berg and M. Lässig, Phys. Rev. Lett. 89(22), 228701 (2002).
Are financial markets efficient? Phase transition in the aggregation of information,
J. Berg, M. Marsili, A. Rustichini, and R. Zecchina, Complexity 8(2), 20-23 (2002).
Testing the Edwards hypothesis in spin systems under tapping dynamics,
J. Berg, S. Franz, and M. Sellitto, Eur. Phys. J. B 26, 349-356 (2002).
Metastable configurations of spin models on random graphs,
J. Berg and M. Sellitto, Phys. Rev. E 65, 016115 (2002).
Glassy dynamics in granular compaction: sand on random graphs,
J. Berg and A. Mehta, Phys. Rev. E 65, 031305 (2002).
Spin-models of granular compaction: From one-dimensional models to random graphs,
J. Berg and A. Mehta, contribution to "Challenges in Granular Media", ICTP Trieste; Advances in Complex Systems 4(4), 309-320 (2001).
On random graphs and the statistical mechanics of granular matter,
J. Berg and A. Mehta, Europhys. Lett. 56 (6), 784-790 (2001).
Statistical mechanics of asset markets with private information,
J. Berg, M. Marsili, A. Rustichini, and R. Zecchina, J. Quant. Finance 1(2), 203-211 (2001).
Statistical mechanics of random two-player games,
J. Berg, Phys. Rev. E 61(3), 2327-2339 (2000).
Entropy and typical properties of Nash equilibria in two-player Games,
J. Berg and M. Weigt, Europhys. Lett. 48(2), 129-135 (1999).
Matrix games, mixed strategies, and statistical mechanics,
J. Berg and A. Engel, Phys. Rev. Lett. 81, 4999-5002 (1998).
A multifractal phase-space analysis of perceptrons with biased patterns,
J. Berg and A. Engel, J. Phys. A 31, 2509-2517 (1998).
Nonlinear dynamics of intermittent-contact mode atomic force microscopy,
J. Berg and G.A.D. Briggs, Phys. Rev. B 55(22), 14899-14908 (1997).

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