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B
Bailly-Bechet M, Braunstein A, Pagnani A, Weigt M, Zecchina R. Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. BMC bioinformatics. 2010;11:355. Abstract
Bradde S, Braunstein A, Mahmoudi H, Tria F, Weigt M, Zecchina R. Aligning graphs and finding substructures by a cavity approach. EPL (Europhysics Letters). 2010;89:37009. Abstract
Braunstein A, Pagnani A, Weigt M, Zecchina R. Gene-network inference by message passing. In: Journal of Physics: Conference Series. Vol 95. IOP Publishing; 2008. 012016.
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
Braunstein A, Mulet R, Pagnani A, Weigt M, Zecchina R. Polynomial iterative algorithms for coloring and analyzing random graphs. Physical Review E. 2003;68:36702.
C
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.
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.
K
Krząkała F, Pagnani A, Weigt M. Threshold values, stability analysis, and high-q asymptotics for the coloring problem on random graphs. Physical Review E. 2004;70:46705.
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Lage-Castellanos A, Pagnani A, Weigt M. The importance of dilution in the inference of biological networks. In: Communication, Control, and Computing, 2009. Allerton 2009. 47th Annual Allerton Conference on. IEEE; 2010. p. 531-8.
Lage-Castellanos A, Pagnani A, Weigt M. Statistical mechanics of sparse generalization and graphical model selection. Journal of Statistical Mechanics: Theory and Experiment. 2009;2009:P10009.
Lunt B, Szurmant H, Procaccini A, Hoch JA, Hwa T, Weigt M. Inference of direct residue contacts in two-component signaling. Methods Enzymol. 2010; 471: 17-41 .
M
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.
Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences. 2011;108:E1293-E1301. Abstract
Mulet R, Pagnani A, Weigt M, Zecchina R. Coloring Random Graphs. Physical Review Letters. 2002;89:268701.
P
Pagnani A, Tria F, Weigt M. Classification and sparse-signature extraction from gene-expression data. Journal of Statistical Mechanics: Theory and Experiment. 2009;2009:P05001.