Andrea Pagnani

According to our database, Andrea Pagnani authored at least 21 papers between 2002 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Inference of annealed protein fitness landscapes with AnnealDCA.

Luca Sesta, Andrea Pagnani, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni

PLoS Comput. Biol., February, 2024

2023

DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors.

Anna Paola Muntoni, Andrea Pagnani

Bioinform., September, 2023

2022

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

2021

adabmDCA: adaptive Boltzmann machine learning for biological sequences.

Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi

BMC Bioinform., 2021

2020

Predicting Interacting Protein Pairs by Coevolutionary Paralog Matching.

Thomas Gueudré, Carlo Baldassi, Andrea Pagnani, Martin Weigt

Proceedings of the Protein-Protein Interaction Networks, Methods and Protocols., 2020

Expectation propagation for the diluted Bayesian classifier.

Alfredo Braunstein, Thomas Gueudré, Andrea Pagnani, Mirko Pieropan

CoRR, 2020

2019

The intrinsic dimension of protein sequence evolution.

Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio

PLoS Comput. Biol., 2019

Compressed sensing reconstruction using Expectation Propagation.

Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani, Mirko Pieropan

CoRR, 2019

2016

Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.

Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, Andrea Pagnani

PLoS Comput. Biol., 2016

2014

Improving Contact Prediction along Three Dimensions.

Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell

PLoS Comput. Biol., 2014

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

Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

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 Mills, David B. Solit, Christine A. Pratilas, Martin Weigt, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander

PLoS Comput. Biol., 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

Exploiting Co-evolution across Protein Families for Predicting Native Contacts and Protein-Protein Interaction Surfaces.

Andrea Pagnani

Proceedings of the Nature of Computation. Logic, Algorithms, Applications, 2013

2011

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

2010

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

2009

The importance of dilution in the inference of biological networks.

Alejandro Lage-Castellanos, Andrea Pagnani, Martin Weigt

Proceedings of the 47th Annual Allerton Conference on Communication, 2009

2008

Estimating the size of the solution space of metabolic networks.

Alfredo Braunstein, Roberto Mulet, Andrea Pagnani

BMC Bioinform., 2008

2005

Predicting protein functions with message passing algorithms.

Michele Leone, Andrea Pagnani

Bioinform., 2005

2004

Threshold values, stability analysis and high-q asymptotics for the coloring problem on random graphs

Florent Krzakala, Andrea Pagnani, Martin Weigt

CoRR, 2004

2002

Coloring random graphs

Roberto Mulet, Andrea Pagnani, Martin Weigt, Riccardo Zecchina

CoRR, 2002