Andrea Pagnani

Publication Activity (10 Years)

Years Active: 2002-2024
Publications (10 Years): 9

Top Topics

Sharing Information

Expectation Propagation

Bayesian Classifier

Biological Sequences

Top Venues

PLoS Comput. Biol.

Publications

Luca Sesta, Andrea Pagnani, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni
Inference of annealed protein fitness landscapes with AnnealDCA. PLoS Comput. Biol. 20 (2) (2024)
Matteo De Leonardis, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni, Andrea Pagnani
Unsupervised modeling of mutational landscapes of adeno-associated viruses viability. BMC Bioinform. 25 (1) (2024)
Anna Paola Muntoni, Andrea Pagnani
DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors. Bioinform. 39 (9) (2023)
Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al Nasr
LPTD: a novel linear programming-based topology determination method for cryo-EM maps. Bioinform. 38 (10) (2022)
Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi
adabmDCA: adaptive Boltzmann machine learning for biological sequences. BMC Bioinform. 22 (3) (2021)
Alfredo Braunstein, Thomas Gueudré, Andrea Pagnani, Mirko Pieropan
Expectation propagation for the diluted Bayesian classifier. CoRR (2020)
Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani, Mirko Pieropan
Compressed sensing reconstruction using Expectation Propagation. CoRR (2019)
Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
The intrinsic dimension of protein sequence evolution. PLoS Comput. Biol. 15 (4) (2019)
Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, Andrea Pagnani
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity. PLoS Comput. Biol. 12 (4) (2016)
Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell
Improving Contact Prediction along Three Dimensions. PLoS Comput. Biol. 10 (10) (2014)
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer T. Chayes, Riccardo Zecchina, Ernest Fraenkel
Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases. Pacific Symposium on Biocomputing (2014)
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
Perturbation Biology: Inferring Signaling Networks in Cellular Systems. PLoS Comput. Biol. 9 (12) (2013)
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. J. Comput. Biol. 20 (2) (2013)
Andrea Pagnani
Exploiting Co-evolution across Protein Families for Predicting Native Contacts and Protein-Protein Interaction Surfaces. CiE (2013)
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem. RECOMB (2012)
Debora S. Marks, Lucy J. Colwell, Robert P. Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander
3D Protein Structure Predicted from Sequence CoRR (2011)
Marc Bailly-Bechet, Alfredo Braunstein, Andrea Pagnani, Martin Weigt, Riccardo Zecchina
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach. BMC Bioinform. 11 (2010)
Alejandro Lage-Castellanos, Andrea Pagnani, Martin Weigt
The importance of dilution in the inference of biological networks. Allerton (2009)
Alfredo Braunstein, Roberto Mulet, Andrea Pagnani
Estimating the size of the solution space of metabolic networks. BMC Bioinform. 9 (2008)
Michele Leone, Andrea Pagnani
Predicting protein functions with message passing algorithms. Bioinform. 21 (2) (2005)
Florent Krzakala, Andrea Pagnani, Martin Weigt
Threshold values, stability analysis and high-q asymptotics for the coloring problem on random graphs CoRR (2004)
Roberto Mulet, Andrea Pagnani, Martin Weigt, Riccardo Zecchina
Coloring random graphs CoRR (2002)