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networks
Bayati M, Borgs C, Braunstein A, Chayes J, Ramezanpour A, Zecchina R. Statistical Mechanics of Steiner Trees. Physical Review Letters. 2008;101:37208. Abstract  Download: prl-steiner.pdf (210.2 KB)
Ramezanpour A. Biology helps to construct weighted scale-free networks. Europhysics Letters. 2004;68:316-22.
Altarelli F, Braunstein A, Dall’Asta L, Zecchina R. Optimizing spread dynamics on graphs by message passing. Journal of Statistical Mechanics: Theory and Experiment. 2013;2013(09):P09011.
Lanza V, Ambrosi D, Preziosi L. Exogenous control of vascular network formation in vitro: a mathematical model. NETWORKS AND HETEROGENEOUS MEDIA. 2006;1:621.
Braunstein A, Mulet R, Pagnani A. Estimating the size of the solution space of metabolic networks. BMC Bioinformatics. 2008;9:240. Abstract
Bailly-Bechet M, Braunstein A, Zecchina R. A Prize-Collecting Steiner Tree Approach for Transduction Network Inference. In: Proceedings of the 7th International Conference on Computational Methods in Systems Biology. Springer; 2009. 95.
Mahmoudi H, Pagnani A, Weigt M, Zecchina R. Propagation of external regulation and asynchronous dynamics in random Boolean networks. Chaos: An Interdisciplinary Journal of Nonlinear Science. 2007;17:026109.
Mashaghi AR, Ramezanpour A, Karimipour V. Investigation of a protein complex network. The European Physical Journal B-Condensed Matter and Complex Systems. 2004;41:113-21.
Altarelli F, Braunstein A, Dall'Asta L, Zecchina R. Large deviations of cascade processes on graphs. Phys. Rev. E. 2013;87:062115.
Ramezanpour A, Vaez Allaei SM. Elastic properties of small-world spring networks. Physical Review E. 2005;72:66115.
Braunstein A, Zecchina R. Learning by message-passing in networks of discrete synapses. Phys. Rev. Lett.. 2006;96:030201. Download: prl-synapses.pdf (233.04 KB)
Karimipour V, Ramezanpour A. Correlation effects in a simple model of small-world network. Journal reference: Phys. Rev. E. 2002;65:036122.
Bayati M, Braunstein A, Zecchina R. A rigorous analysis of the cavity equations for the minimum spanning tree. Journal of Mathematical Physics. 2008;49:125206. Download: BaBrZe2008.pdf: Copyright (2008) American Institute of Physics. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics. (270.23 KB)
Ramezanpour A, Karimipour V. Simple models of small-world networks with directed links. Physical Review E. 2002;66:36128.
Dall'Asta L, Marsili M, Pin P. Collaboration in social networks. Proceedings of the National Academy of Sciences. 2012;109:4395-400. Abstract
Ramezanpour A. Intermittent exploration on a scale-free network. EPL. 2007;77:60004.
Correale L, Leone M, Pagnani A, Weigt M, Zecchina R. The computational core and fixed point organization in Boolean networks. Journal of Statistical Mechanics: Theory and Experiment. 2006;3:P03002.
Ramezanpour A, Karimipour V, Mashaghi A. Generating correlated networks from uncorrelated ones. Physical Review E. 2003;67:46107.
Lanza V, Corinto F, Gilli M. On the study of cellular nonlinear networks via amplitude and phase dynamics. Neural Networks. 2008;21:122-9.
Baldassi C, Braunstein A, Brunel N, Zecchina R. Efficient supervised learning in networks with binary synapses. Proceedings of the National Academy of Sciences. 2007;104:11079-84.
Ramezanpour A, Realpe J, Zecchina R. Statistical physics approach to graphical games: local and global interactions. Eur. Phys. J. B. 2011;81(3).
Braunstein A, Pagnani A, Weigt M, Zecchina R. Inference algorithms for gene networks: a statistical mechanics analysis. Journal of Statistical Mechanics: Theory and Experiment. 2008;2008:P12001 (29pp). Abstract
Correale L, Leone M, Pagnani A, Weigt M, Zecchina R. Core Percolation and Onset of Complexity in Boolean Networks. Physical Review Letters. 2006;96:18101.
Ramezanpour A. Ising model on the edge-dual of random networks. Physical Review E. 2004;69:66114.
Molinelli EJ, Korkut A, Wang W, Miller ML, Gauthier NP, Jing X, et al. Perturbation Biology: Inferring Signaling Networks in Cellular Systems. PLoS Computational Biology. 2013;9(12):e1003290.