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D

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

E

Bailly-Bechet M, Benecke A, Hardt WD, Lanza V, Sturm A, Zecchina R. An externally modulated, noise-driven switch for the regulation of SPI1 in Salmonella enterica serovar Typhimurium. Journal of Mathematical Biology. 2011;63:637-62.

P

Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, et al. Protein 3D Structure Computed from Evolutionary Sequence Variation. PLoS ONE. 2011;6:e28766. Abstract

R

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.

S

Tuncbag N, Braunstein A, Pagnani A, Huang S-, Chayes J, Borgs C, et al. Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. In: Chor B, editor. Research in Computational Molecular Biology. Vol 7262. Springer Berlin Heidelberg; 2012. p. 287-301. (Lecture Notes in Computer Science; vol 7262).

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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 .