Johannes Berg

Publications

Phylodynamic inference on single-cell data,
T. Dieselhorst and J. Berg, https://www.biorxiv.org/content/10.1101/2024.12.05.627005v1
Branch length statistics in phylogenetic trees under constant-rate birth-death dynamics,
T. Dieselhorst and J. Berg, https://arxiv.org/submit/5740094
High-density sampling reveals volume growth in human tumours,
A.Angaji, M. Owusu, C. Velling, N. Dick, D. Weghorn, J. Berg, eLife13:RP95338 (2024)
Characterizing Evolutionary Dynamics Reveals Strategies to Exhaust the Spectrum of Subclonal Resistance in EGFR-Mutant Lung Cancer,
N. Müller, C. Lorenz, J. Ostendorp, P. Heisel, U. P. Friese, M. Cartolano, D. Plenker, H. Tumbrink, A. Heimseoeth, P. Baedeker, J. Weiss,
S. Ortiz-Cuaran, R. Büttner, M. Peifer, R. K. Thomas, M. L. Sos, J. Berg, and J. Brägelmann, Cancer Research 83 (15): 2471-2479 (2023)
Inferring stochastic regulatory networks from perturbations of the non-equilibrium steady state,
N. Bonacker and J. Berg, https://arxiv.org/abs/2212.13168
Switching off: the phenotypic transition to the uninduced state of the lactose uptake pathway,
P. M. Bhogale, R. A. Sorg, J.-W. Veening, and J. Berg, Biophysical Journal 121(2), 183-192 (2022)
Stochastic clonal dynamics and genetic turnover in exponentially growing populations,
A. Angaji, C. Velling, and J. Berg, J. Stat. Mech. 103502 (2021).
Inferring the parameters of a Markov process from snapshots of the steady state,
S.L. Dettmer and J. Berg, J. Stat. Mech., 023403 (2018)
Inverse statistical problems: from the inverse Ising problem to data science,
H.C. Nguyen, R. Zecchina and J. Berg, Advances in Physics, 66 (3), 197-261 (2017)
Statistical mechanics of the inverse Ising problem and the optimal objective function,
J. Berg, JSTAT, 083402 (2017)
Pervasive adaptation of gene expression in Drosophila,
A. Nourmohammad, J. Rambeau, T. Held, V. Kovacova, J. Berg, and M. Lässig, Cell Reports 20 (6) 1385-1395 (2017)
Network inference in the non-equilibrium steady state,
S. Dettmer, H.C. Nguyen, and J. Berg, Phys. Rev. E 94 (5), 052116 (2016)
Heterogeneous mechanisms of primary and acquired resistance to third-generation EGFR inhibitors,
S. Ortiz-Cuaran et al. (>30 authors), Clincal Cancer Research 1915.2015 (2016)
Multiple-Line Inference of Selection on Quantitative Traits,
N. Riedel, B. S. Khatri, M. Lässig, and J. Berg, Genetics 201 (1), 305-322 (2015)
Dynamic BMP signaling polarized by Toll patterns the dorsoventral axis in a hemimetabolous insect,
L. Sachs, Y.-T. Chen, A. Drechsler, J. A. Lynch, K. A. Panfilio, M. Lässig, J. Berg, and S. Roth, eLIFE 4:e05502 (2015)
What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems,
P. Bhogale, R. Sorg, J.-W. Veening, J. Berg, Nucleic Acids Research 42 (18),11321-11328 (2014)
A genomics-based classification of human lung tumors,
D. Seidel et al. (>100 authors), Science Translational Medicine 5:209ra153 (2013)
Can we always sweep the details of RNA-processing under the carpet?,
F. Klironomos, J. de Meaux, and J. Berg, Phys. Biol. 10, 056007 (2013)
How epigenetic mutations can affect genetic evolution: Model and mechanism,
F. Klironomos, J. Berg, and S. Collins, Bioessays, 35 (6), 571-578 (2013) (editorial highlight)
A statistical mechanics approach to the sample deconvolution problem,
N. Riedel and J. Berg, Phys. Rev. E 87, 042715 (2013) (synopsis writeup on physics.aps.org)
Quantitative analysis of competition in post-transcriptional regulation reveals a novel signature in target expression variation,
F. Klironomos and J. Berg, Biophysical Journal, 104 (4), 951-958 (2013)
Mean-field theory for the inverse Ising problem at low temperatures,
H.C. Nguyen and J. Berg, Phys. Rev. Lett. 109, 050602 (2012).
Bethe-Peierls approximation and the inverse Ising problem,
H.C. Nguyen and J. Berg, J. Stat. Mech., P03004 (2012).
GraphAlignment: Bayesian pairwise alignment of biological networks,
M. Kolář, J. Meier, V. Mustonen, M. Lässig and J. Berg, BMC Systems Biology 2012 6:144 (2012).
Nonlinear fitness landscape of a molecular pathway,
L. Perfeito, S. Ghozzi, J. Berg, K. Schnetz, and M. Lässig, PLoS Genetics 7(7): e1002160, (2011).
Significance analysis and statistical mechanics: an application to clustering,
M. Łuksza, M. Lässig and J. Berg, Phys. Rev. Lett. 105, 220601 (2010).
Adaptive gene regulatory networks,
F. Stauffer and J. Berg, EPL 88, 48004 (2009).
Out-of-equilibrium dynamics of gene expression and the Jarzynski equality,
J. Berg, Phys. Rev. Lett. 100, 188101 (2008).
(PRL Editors' Suggestion and 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, in Statistical and Evolutionary Analysis of Biological Network Data, M. Stumpf and C. Wiuf (Eds.), Imperial College Press (2010).
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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