Coloring random graphs - Roberto Mulet; Andrea Pagnani; Martin Weigt; Riccardo Zecchina (CoRR, 2002)

Threshold values, stability analysis and high-q asymptotics for the coloring problem on random graphs - Florent Krzakala; Andrea Pagnani; Martin Weigt (CoRR, 2004)

Predicting protein functions with message passing algorithms. - Michele Leone; Andrea Pagnani (Bioinform., 2005)

Estimating the size of the solution space of metabolic networks. - Alfredo Braunstein; Roberto Mulet; Andrea Pagnani (BMC Bioinform., 2008)

The importance of dilution in the inference of biological networks. - Alejandro Lage-Castellanos; Andrea Pagnani; Martin Weigt (Allerton, 2009)

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. - Marc Bailly-Bechet; Alfredo Braunstein; Andrea Pagnani; Martin Weigt; Riccardo Zecchina (BMC Bioinform., 2010)

3D Protein Structure Predicted from Sequence - Debora S. Marks; Lucy J. Colwell; Robert P. Sheridan; Thomas A. Hopf; Andrea Pagnani; Riccardo Zecchina; Chris Sander (CoRR, 2011)

Exploiting Co-evolution across Protein Families for Predicting Native Contacts and Protein-Protein Interaction Surfaces. - Andrea Pagnani (CiE, 2013)

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. - Nurcan Tuncbag; Alfredo Braunstein; Andrea Pagnani; Shao-Shan Carol Huang; Jennifer T. Chayes; Christian Borgs; Riccardo Zecchina; Ernest Fraenkel (J. Comput. Biol., 2013)

Perturbation Biology: Inferring Signaling Networks in Cellular Systems. - Evan J. Molinelli; Anil Korkut; Weiqing Wang; Martin L. Miller; Nicholas Paul Gauthier; Xiaohong Jing; Poorvi Kaushik; Qin He; Gordon B. Mills; David B. Solit; Christine A. Pratilas; Martin Weigt; et al. (PLoS Comput. Biol., 2013)

Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases. - Anthony Gitter; Alfredo Braunstein; Andrea Pagnani; Carlo Baldassi; Christian Borgs; Jennifer T. Chayes; Riccardo Zecchina; Ernest Fraenkel (Pacific Symposium on Biocomputing, 2014)

Improving Contact Prediction along Three Dimensions. - Christoph Feinauer; Marcin J. Skwark; Andrea Pagnani; Erik Aurell (PLoS Comput. Biol., 2014)

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. - Lorenzo Asti; Guido Uguzzoni; Paolo Marcatili; Andrea Pagnani (PLoS Comput. Biol., 2016)

Compressed sensing reconstruction using Expectation Propagation. - Alfredo Braunstein; Anna Paola Muntoni; Andrea Pagnani; Mirko Pieropan (CoRR, 2019)

The intrinsic dimension of protein sequence evolution. - Elena Facco; Andrea Pagnani; Elena Tea Russo; Alessandro Laio (PLoS Comput. Biol., 2019)

Expectation propagation for the diluted Bayesian classifier. - Alfredo Braunstein; Thomas Gueudré; Andrea Pagnani; Mirko Pieropan (CoRR, 2020)

Predicting Interacting Protein Pairs by Coevolutionary Paralog Matching. - Thomas Gueudré; Carlo Baldassi; Andrea Pagnani; Martin Weigt (Protein-Protein Interaction Networks, 2020)

adabmDCA: adaptive Boltzmann machine learning for biological sequences. - Anna Paola Muntoni; Andrea Pagnani; Martin Weigt; Francesco Zamponi (BMC Bioinform., 2021)

LPTD: a novel linear programming-based topology determination method for cryo-EM maps. - Bahareh Behkamal; Mahmoud Naghibzadeh; Andrea Pagnani; Mohammad Reza Saberi; Kamal Al Nasr (Bioinform., 2022)

DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors. - Anna Paola Muntoni; Andrea Pagnani (Bioinform., 2023)

Inference and design of antibody specificity: From experiments to models and back. - Jorge Fernandez-de-Cossío-Diaz; Guido Uguzzoni; Kévin Ricard; Francesca Anselmi; Clément Nizak; Andrea Pagnani; Olivier Rivoire (PLoS Comput. Biol., 2024)

Inference of annealed protein fitness landscapes with AnnealDCA. - Luca Sesta; Andrea Pagnani; Jorge Fernandez-de-Cossío-Diaz; Guido Uguzzoni (PLoS Comput. Biol., 2024)

Unsupervised modeling of mutational landscapes of adeno-associated viruses viability. - Matteo De Leonardis; Jorge Fernandez-de-Cossío-Diaz; Guido Uguzzoni; Andrea Pagnani (BMC Bioinform., 2024)

Mammography classification with multi-view deep learning techniques: Investigating graph and transformer-based architectures. - Francesco Manigrasso; Rosario Milazzo; Alessandro Sebastian Russo; Fabrizio Lamberti; Fredrik Strand; Andrea Pagnani; Lia Morra (Medical Image Anal., 2025)

Direct coupling analysis and the attention mechanism. - Francesco Caredda; Andrea Pagnani (BMC Bioinform., 2025)