Andrea Pagnani

28 papers B 1C 1Misc 1Journal 23Unranked 1
YearRankTypeTitle / Venue / Authors
2026 J jnl
Controllable protein design via autoregressive direct coupling analysis conditioned on principal components.
PLoS Comput. Biol.
Francesco Caredda, Lisa Gennai, Paolo De Los Rios, Andrea Pagnani
2025 J jnl
Direct coupling analysis and the attention mechanism.
BMC Bioinform.
Francesco Caredda, Andrea Pagnani
2025 J jnl
Mammography classification with multi-view deep learning techniques: Investigating graph and transformer-based architectures.
Medical Image Anal.
Francesco Manigrasso, Rosario Milazzo, Alessandro Sebastian Russo, Fabrizio Lamberti, Fredrik Strand, Andrea Pagnani, Lia Morra
2024 J jnl
Inference and design of antibody specificity: From experiments to models and back.
PLoS Comput. Biol.
Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni, Kévin Ricard, Francesca Anselmi, Clément Nizak, Andrea Pagnani, Olivier Rivoire
2024 J jnl
Inference of annealed protein fitness landscapes with AnnealDCA.
PLoS Comput. Biol.
Luca Sesta, Andrea Pagnani, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni
2024 J jnl
Unsupervised modeling of mutational landscapes of adeno-associated viruses viability.
BMC Bioinform.
Matteo De Leonardis, Jorge Fernandez-de-Cossío-Diaz, Guido Uguzzoni, Andrea Pagnani
2023 J jnl
DCAlign v1.0: aligning biological sequences using co-evolution models and informed priors.
Bioinform.
Anna Paola Muntoni, Andrea Pagnani
2023 J jnl
Generating interacting protein sequences using domain-to-domain translation.
Bioinform.
Barthélémy Meynard-Piganeau, Caterina Fabbri, Martin Weigt, Andrea Pagnani, Christoph Feinauer
2022 J jnl
LPTD: a novel linear programming-based topology determination method for cryo-EM maps.
Bioinform.
Bahareh Behkamal, Mahmoud Naghibzadeh, Andrea Pagnani, Mohammad Reza Saberi, Kamal Al-Nasr
2021 J jnl
adabmDCA: adaptive Boltzmann machine learning for biological sequences.
BMC Bioinform.
Anna Paola Muntoni, Andrea Pagnani, Martin Weigt, Francesco Zamponi
2020 J jnl
Expectation propagation for the diluted Bayesian classifier.
CoRR
Alfredo Braunstein, Thomas Gueudré, Andrea Pagnani, Mirko Pieropan
2020 — ch.
Predicting Interacting Protein Pairs by Coevolutionary Paralog Matching.
Protein-Protein Interaction Networks
Thomas Gueudré, Carlo Baldassi, Andrea Pagnani, Martin Weigt
2019 J jnl
Compressed sensing reconstruction using Expectation Propagation.
CoRR
Alfredo Braunstein, Anna Paola Muntoni, Andrea Pagnani, Mirko Pieropan
2019 J jnl
The intrinsic dimension of protein sequence evolution.
PLoS Comput. Biol.
Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
2016 J jnl
Maximum-Entropy Models of Sequenced Immune Repertoires Predict Antigen-Antibody Affinity.
PLoS Comput. Biol.
Lorenzo Asti, Guido Uguzzoni, Paolo Marcatili, Andrea Pagnani
2014 J jnl
Improving Contact Prediction along Three Dimensions.
PLoS Comput. Biol.
Christoph Feinauer, Marcin J. Skwark, Andrea Pagnani, Erik Aurell
2014 Misc conf
Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases.
Pacific Symposium on Biocomputing
Anthony Gitter, Alfredo Braunstein, Andrea Pagnani, Carlo Baldassi, Christian Borgs, Jennifer T. Chayes, Riccardo Zecchina, Ernest Fraenkel
2013 C conf
Exploiting Co-evolution across Protein Families for Predicting Native Contacts and Protein-Protein Interaction Surfaces.
CiE
Andrea Pagnani
2013 J jnl
Perturbation Biology: Inferring Signaling Networks in Cellular Systems.
PLoS Comput. Biol.
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, Alfredo Braunstein, Andrea Pagnani, Riccardo Zecchina, Chris Sander
2013 J jnl
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem.
J. Comput. Biol.
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
2012 B conf
Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem.
RECOMB
Nurcan Tuncbag, Alfredo Braunstein, Andrea Pagnani, Shao-Shan Carol Huang, Jennifer T. Chayes, Christian Borgs, Riccardo Zecchina, Ernest Fraenkel
2011 J jnl
3D Protein Structure Predicted from Sequence
CoRR
Debora S. Marks, Lucy J. Colwell, Robert P. Sheridan, Thomas A. Hopf, Andrea Pagnani, Riccardo Zecchina, Chris Sander
2010 J jnl
Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach.
BMC Bioinform.
Marc Bailly-Bechet, Alfredo Braunstein, Andrea Pagnani, Martin Weigt, Riccardo Zecchina
2009 — conf
The importance of dilution in the inference of biological networks.
Allerton
Alejandro Lage-Castellanos, Andrea Pagnani, Martin Weigt
2008 J jnl
Estimating the size of the solution space of metabolic networks.
BMC Bioinform.
Alfredo Braunstein, Roberto Mulet, Andrea Pagnani
2005 J jnl
Predicting protein functions with message passing algorithms.
Bioinform.
Michele Leone, Andrea Pagnani
2004 J jnl
Threshold values, stability analysis and high-q asymptotics for the coloring problem on random graphs
CoRR
Florent Krzakala, Andrea Pagnani, Martin Weigt
2002 J jnl
Coloring random graphs
CoRR
Roberto Mulet, Andrea Pagnani, Martin Weigt, Riccardo Zecchina