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Publications

2012
Caraglio M, Pelizzola A. Effects of confinement on thermal stability and folding kinetics in a simple Ising-like model. Physical Biology. 2012;9:016006. Abstract
Cirillo EN, Gonnella G, Pelizzola A. Folding transitions in three-dimensional space with defects. Nuclear Physics B. 2012;862:821-34. Abstract
Rajendran V, Purohit R, Sethumadhavan R. In silico investigation of molecular mechanism of laminopathy caused by a point mutation (R482W) in lamin A/C protein. Amino Acids. 2012;43:603-15.
Kumar A, Rajendran V, Sethumadhavan R, Purohit R. In silico prediction of a disease-associated STIL mutant and its affect on the recruitment of centromere protein J (CENPJ). FEBS Open Bio. 2012;2:285-93.
kamraj B, Purohit R. In-silico analysis of Betaine Aldehyde Dehydrogenase2 of Oryza sativa and significant mutations responsible for fragrance. Journal of Plant Interactions. 2012.
Alemi-Neissi A, Baldassi C, Braunstein A, Pagnani A, Zecchina R, Zoccolan D. Information theoretic and machine learning approaches to quantify non-linear visual feature interaction underlying visual object recognition. BMC Neuroscience. 2012;13:1-2.
Kumar A, Rajendran V, Sethumadhavan R, Purohit R. Insight into Nek2A activity regulation and its pharmacological prospects. Egyptian Journal of Medical Human Genetics. 2012:-.
Zamparo M, Stramaglia S, Banavar JR, Maritan A. Inverse problem for multivariate time series using dynamical latent variables. Physica A: Statistical Mechanics and its Applications. 2012;391:3159-69.
Zhang P, Ramezanpour A, Zdeborova L, Zecchina R. Message passing for quantified Boolean formulas. J. Stat. Mech. 2012.
Ramezanpour A, Zecchina R. Sign problem in the Bethe approximation. Phys. Rev. B . 2012;86.
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).
Gulati G, Gaonkar KS, kamraj B, Kumar A, Purohit R. Structure based energy calculation to determine the regulation of G protein signalling by RGS and RGS-G protein interaction specificity. Interdisciplinary Sciences: Computational Life Sciences. 2012;4:173-82.
2011
Braunstein A, Kayhan F, Zecchina R. Efficient data compression from statistical physics of codes over finite fields. Phys. Rev. E. 2011;84:051111.
Braunstein A, Ramezanpour A, Zecchina R, Zhang P. Inference and learning in sparse systems with multiple states. Phys. Rev. E. 2011;83:056114.
Altarelli F, Braunstein A, Ramezanpour A, Zecchina R. Stochastic Matching Problem. Phys. Rev. Lett.. 2011;106:190601.
Caraglio M, Imparato A, Pelizzola A. Direction-dependent mechanical unfolding and green fluorescent protein as a force sensor. Phys. Rev. E. 2011;84:021918.
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
ElBaroudi M, Corà D, Bosia C, Osella M, Caselle M. A Curated Database of miRNA Mediated Feed-Forward Loops Involving MYC as Master Regulator. PLoS ONE. 2011;6:e14742. Abstract
Osella M, Bosia C, Corá D, Caselle M. The Role of Incoherent MicroRNA-Mediated Feedforward Loops in Noise Buffering. PLoS Comput Biol. 2011;7:e1001101. Abstract
Bayati M, Borgs C, Chayes J, Zecchina R. Belief Propagation for Weighted -Matchings on Arbitrary Graphs and its Relation to Linear Programs with Integer Solutions. SIAM Journal on Discrete Mathematics. 2011;25:989-1011.
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
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.
Dall'Asta L, Pin P, Ramezanpour A. Optimal equilibria of the best shot game. Journal of Public Economic Theory. 2011;13(6).
Pelizzola A, Pretti M, van Mourik J. Palette-colouring: a belief propagation approach. Journal of Statistical Mechanics: Theory and Experiment. 2011;2011:P05010. Abstract
Purohit R, Rajendran V, Sethumadhavan R. Relationship between mutation of serine residue at 315th position in M. tuberculosis catalase-peroxidase enzyme and Isoniazid susceptibility: An in silico analysis. Journal of Molecular Modeling. 2011;17:869-77.