Alejandro Lage-Castellanos, Andrea Pagnani, and  Gretel Quintero Angulo, Stability of the replica symmetric solution in diluted perceptron learning, Accepted for publication in JSTAT (2013).

Andrea Pagnani, and Giorgio Parisi,  Multisurface coding simulations of the restricted solid-on-solid model in four dimensions, Physical Review E (Vol.87, No.1) , 2013.

Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, and Ernest Fraenkel,  Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem, JOURNAL OF COMPUTATIONAL BIOLOGY Volume 20, Number 2, 2012. (In proofs).

Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer Chayes, Christian Borgs, Riccardo Zecchina, and Ernest Fraenkel,  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).

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.

Marks DS, Colwell LJ, Sheridan R, Hopf TA, Pagnani A, Zecchina R, Sander C. (2011) Protein 3D Structure Computed from Evolutionary Sequence Variation. PLoS ONE 6(12): e28766. doi:10.1371/journal.pone.0028766

Faruck Morcos, Andrea Pagnani, Bryan Lunt, Arianna Bertolino,Debora S. Marks, Chris Sander, Riccardo Zecchina, Josť N. Onuchic, Terence Hwa, and Martin Weigt Direct-coupling analysis of residue coevolution captures native contacts across many protein families, PNAS 2011

Andrea Pagnani, Marco Pretti, A discrete model of water with two distinct glassy phases, EPL (Europhysics Letters) 92 46008, 2010.

M. Bailly-Bechet, A. Braunstein, A. Pagnani,  M. Weigt, R. Zecchina, Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach, BMC Bioinformatics, 2010, 11:355.

Francesca Tria, Emanuele Caglioti, Vittorio Loreto, Andrea Pagnani, A stochastic local search algorithm for distance-based phylogeny  reconstruction,  Mol. Biol. Evol., Advance Access published on June 18, 2010; doi: doi:10.1093/molbev/msq15

Francesca Tria, Emanuele Caglioti, Vittorio Loreto, Andrea Pagnani A stochastic local search    approach to language tree reconstruction, Diachronica, XVII:2 (2010)

Alejandro Lage-Castellanos, Andrea Pagnani, Martin Weigt,  The importance of dilution in the inference of biological  networks , 47th Annual Allerton Conference on Communication, Control, and
Communication ``Statistical mechanics of sparse generalization and model selection'', IEEE express, 10.1109/ALLERTON.2009.5394907

Alejandro Lage-Castellanos, Andrea Pagnani, Martin Weigt Statistical mechanics of sparse generalization and model selection,  J. Stat. Mech. (2009)  P10009
         
Andrea Pagnani, Francesca Tria, Martin Weigt,  Classification and sparse-signature extraction from gene-expression data, J. Stat. Mech. (2009) P05001         

A. Braunstein, A. Pagnani, M. Weigt, R. Zecchina, Inference algorithms for gene networks: a statistical mechanics analysis,  J. Stat. Mech. (2008) P12001

Pena-Castillo L., Pagnani A., Leone M. et al., A critical assessment of Mus musculus gene function prediction using integrated genomic evidence, Genome Biology 2008, 9(Suppl 1):S2 (2008)

A. Braunstein, A. Pagnani, M. Weigt, R. Zecchina, Gene-network inference by message passing, Journal of Physics: Conference Series 95 (2008) 012016

Alfredo Braunstein, Roberto Mulet, Andrea Pagnani, The space of feasible solutions in metabolic networksJ. Phys.: Conf. Ser. 95 012016 (2008)

Alfredo Braunstein, Roberto Mulet, Andrea Pagnani, Estimating the size of the solution space of metabolic networks, BMC Bioinformatics 2008, 9:249 (27 May 2008)
          
Hamed Mahmoudi, Andrea Pagnani, Martin Weigt, Riccardo Zecchina, Propagation of external regulation and asynchronous dynamics in random Boolean networks, Chaos 17, 026109 (2007)

Michele Leone, Andrea Pagnani, Giorgio Parisi, Osvaldo Zagordi, Finite size corrections to random Boolean networks J. Stat. Mech. (2006) P12012    
   
L. Correale, M. Leone, A. Pagnani, M. Weigt, R. Zecchina,  Computational core and fixed-point organisation in Boolean networks, J. Stat. Mech. (2006) P03002

L. Correale, M. Leone, A. Pagnani, M. Weigt, R. Zecchina,  Core percolation and onset of complexity in Boolean networks,  Phys. Rev. Lett.   96, 018101 (2006).
M. Leone, A. Pagnani, Predicting protein functions with message passing algorithms Bioinformatics 21: 239-247 (2005).
F. Krzakala, A. Pagnani, M. Weigt, Threshold values, stability analysis and high-q asymptotics for the coloring problem on random graphs, Phys. Rev. E 70, 046705 (2004).

A. Pagnani, G. Parisi, M. Ratieville, Near optimal configurations in mean field disordered systems, Phys. Rev. E 68, 046706 (2003).

C. Amoruso, E. Marinari, O.C. Martin, A. Pagnani, Scalings of domain wall energies in two dimensional Ising spin glasses, Phys. Rev. Lett. 91, 087201 (2003).

A. Braunstein, R. Mulet, A. Pagnani, M. Weigt, R. Zecchina, Polynomial iterative algorithms for coloring and analyzing random graphs, Phys. Rev. E 68, 036702 (2003).
E. Marinari, A. Pagnani,  F. Ricci-Tersenghi, Zero Temperature Properties of RNA Secondary Structures, Phys. Rev. E 65, 041919 (2002).

A. Pagnani, G. Parisi, M. Ratieville, Metastable configurations on the Bethe lattice, Phys. Rev. E 67, 026116 (2003).

R. Mulet, A. Pagnani, M. Weigt, R. Zecchina,  Coloring random graphs Phys. Rev. Lett. 89, 268701 (2002).

E. Marinari, A. Pagnani, F. Ricci-Tersenghi, Zero Temperature Properties of RNA Secondary Structures, Phys. Rev. E 65, 041919 (2002).

E.. Marinari, A. Pagnani, G. Parisi, Critical Exponents of the KPZ Equation via Multi-Surface Coding Numerical Simulations, J. Phys. A: Math. Gen. 33 8181 (2000).

E. Marinari, A. Pagnani, G. Parisi, Z. Racz,  Width Distributions and the Upper Critical Dimension of KPZ InterfacePhys. Rev. E 65, 026136 (2002).

R. Mulet, A. Pagnani, G. Parisi,  Against temperature chaos in naive Thouless-Anderson-Palmer equations, Phys. Rev. B 63, 184438 (2001).
A. Pagnani, G. Parisi, F. Ricci-Tersenghi, Reply to the Comment on Glassy Transition in a Disordered Model for the RNA Secondary StructurePhys. Rev. Lett. 86, 1383 (2001).

E. Marinari, A. Pagnani, G. Parisi, Critical Exponents of the KPZ Equation via Multi-Surface Coding Numerical Simulations, J. Phys. A: Math. Gen. 33, 8181 (2000).

E. Marinari, V. Martin-Mayor, A. Pagnani, Spin Glass Ordering in Diluted Magnetic Semiconductors: a Monte Carlo Study, Phys. Rev. B, 62 4999 (2000).

A. Pagnani, G. Parisi, F. Ricci-Tersenghi, Glassy transition in a disordered model for the RNA secondary structure, Phys. Rev. Lett. 84,  2026 (2000).
A. Pagnani, Testing a Variational Approach to Random Directed Polymers, cond-mat/9902338.