Home

Publications

2009
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.
Piscitelli A, Corberi F, Gonella G, Pelizzola A. Fluctuation relations in non-equilibrium stationary states of Ising models. Journal of Statistical Mechanics-Theory and Experiment. 2009. Abstract
Zamparo M, Pelizzola A. Nearly symmetrical proteins: Folding pathways and transition states. The Journal of Chemical Physics. 2009;131:035101. Abstract
Gonella G, Pelizzola A, Rondoni L, Saracco GP. Nonequilibrium work fluctuations in a driven Ising model. Physica a-Statistical Mechanics and Its Applications. 2009;388:2815-20. 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.
Altarelli F, Monasson R, Semerjian G, Zamponi F. A review of the Statistical Mechanics approach to Random Optimization Problems. In: Biere A, Heule M, van Maaren H, Walsh T, editors. Handbook of Satisfiability.; 2009. p. 569-611.
Zhang P, Zeng Y, Zhou H. Stability analysis on the finite-temperature replica-symmetric and first-step replica-symmetry-broken cavity solutions of the random vertex cover problem. Phys. Rev. E. 2009;80:021122.
Altarelli F, Braunstein A, Realpe-Gomez J, Zecchina R. Statistical mechanics of budget-constrained auctions. Journal of Statistical Mechanics: Theory and Experiment. 2009;2009:P07002 (27pp). Abstract
Dall'Asta L, Pin P, Ramezanpour A. Statistical Mechanics of Maximal Independent Sets. Phys. Rev. E . 2009;80.
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.
Purohit R, Sethumadhavan R. Structural basis for the resilience of Darunavir (TMC114) resistance major flap mutations of HIV-1 protease. Interdisciplinary Sciences: Computational Life Sciences. 2009;1:320-8.
Biazzo I, Caltagirone F, Parisi G, Zamponi F. Theory of Amorphous Packings of Binary Mixtures of Hard Spheres. Phys. Rev. Lett.. 2009;102(19).
Baldassi C. Generalization Learning in a Perceptron with Binary Synapses. Journal of Statistical Physics. 2009;136(5). Abstract  Download: Baldassi09.pdf (562.66 KB)
Bailly-Bechet M, Bradde S, Braunstein A, Flaxman A, Foini L, Zecchina R. Clustering with shallow trees. JSTAT. 2009:17pp. Abstract
Braunstein A, Kayhan F, Zecchina R. Efficient LDPC Codes over GF(q) for Lossy Data Compression. In: IEEE International Symposium on Information Theory, 2009. ISIT 2009. Seul, Korea; 2009. Abstract  Download: ISIT2009.pdf (814.41 KB)
Imparato A, Pelizzola A, Zamparo M. Equilibrium Properties and Force-Driven Unfolding Pathways of RNA Molecules. Phys. Rev. Lett.. 2009;103:188102.
2010
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
Purohit R, Sethumadhavan R. Effect of flap mutation I54L/M in inhibition of human immunodeficiency virus type 1 protease: relationship to drug resistance. Journal of Computer Science and System Biology. 2010;3:80-5.
Bailly-Bechet M, Borgs C, Braunstein A, Chayes J, Dagkessamanskaia A, François JM, et al. Finding undetected protein associations in cell signaling by belief propagation. Proceedings of the National Academy of Sciences. 2010;108(2):882-7. Abstract  Download: PNAS-2011-Bailly-Bechet-882-7.pdf (324.11 KB)
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.
Tria F, Caglioti E, Loreto V, Pagnani A. A Stochastic Local Search algorithm for distance-based phylogeny reconstruction. Molecular Biology and Evolution. 2010.
Tria F, Caglioti E, Loreto V, Pagnani A. A stochastic local search approach to language tree reconstruction. Diachronica. 2010;27:341-58.
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
Pagnani A, Pretti M. A discrete model of water with two distinct glassy phases. Europhysics Letters . 2010;92.
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 .