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Pathogenicity
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.
Photon counting
De Martini F, Mataloni P, Di Giuseppe G, Altarelli F. Stochastic quantum interferometry with Fock states. J. Opt. Soc. Am. B. 2002;19:1009-18.
Photon statistics
De Martini F, Mataloni P, Di Giuseppe G, Altarelli F. Stochastic quantum interferometry with Fock states. J. Opt. Soc. Am. B. 2002;19:1009-18.
Prize-collecting Steiner forest
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).
probability
Ramezanpour A, Realpe J, Zecchina R. Statistical physics approach to graphical games: local and global interactions. Eur. Phys. J. B. 2011;81(3).
Altarelli F, Braunstein A, Ramezanpour A, Zecchina R. Stochastic optimization by message passing. JOURNAL OF STATISTICAL MECHANICS: THEORY AND EXPERIMENT. 2011;2011. Abstract
Pagnani A, Parisi G. Multisurface coding simulations of the restricted solid-on-solid model in four dimensions. Physical Review E. 2013;87(1).
Pelizzola A, Pretti M, van Mourik J. Palette-colouring: a belief propagation approach. Journal of Statistical Mechanics: Theory and Experiment. 2011;2011:P05010. Abstract
protein flexibility
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.
protein-ligand interaction
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.
proteins
Zamparo M, Pelizzola A. Nearly symmetrical proteins: Folding pathways and transition states. The Journal of Chemical Physics. 2009;131:035101. Abstract
Imparato A, Pelizzola A, Zamparo M. Protein mechanical unfolding: A model with binary variables. The Journal of Chemical Physics. 2007;127:145105.
Bruscolini P, Pelizzola A, Zamparo M. Downhill versus two-state protein folding in a statistical mechanical model. The Journal of Chemical Physics. 2007;126:215103.
Protein–protein docking
Sudandiradoss C, Doss GP, Rajasekaran R, Ramanathan K, Purohit R, Sethumadhavan R. Investigations on the interactions of scorpion neurotoxins with the predicted structure of D1 dopamine receptor by protein–protein docking method. A bioinformatics approach. Comptes Rendus Biologies. 2008;331:489-99.