Andrea Pagnani

发表

The intrinsic dimension of protein sequence evolution

Alessandro Laio, Elena Facco, Andrea Pagnani, 2019, PLoS Comput. Biol..

3D Protein Structure Predicted from Sequence pdf

Robert P. Sheridan, Debora S. Marks, Chris Sander, 2011, ArXiv.

Information theoretic and machine learning approaches to quantify non-linear visual feature interaction underlying visual object recognition

Carlo Baldassi, Riccardo Zecchina, Alfredo Braunstein, 2012, BMC Neuroscience.

Estimating the size of the solution space of metabolic networks

Alfredo Braunstein, Andrea Pagnani, Roberto Mulet, 2007, BMC Bioinformatics.

Unsupervised Inference of Protein Fitness Landscape from Deep Mutational Scan

Andrea Pagnani, Jorge Fernandez-de-Cossio-Diaz, Guido Uguzzoni, 2020, bioRxiv.

Inference of sparse combinatorial-control networks from gene-expression data: a message passing approach

Riccardo Zecchina, Alfredo Braunstein, Andrea Pagnani, 2010, BMC Bioinformatics.

Improved pseudolikelihood regularization and decimation methods on non-linearly interacting systems with continuous variables

Andrea Pagnani, Luca Leuzzi, Alessia Marruzzo, 2017, SciPost Physics.

Expectation propagation for the diluted Bayesian classifier pdf

Andrea Pagnani, Alfredo Braunstein, Thomas Gueudr'e, 2020, ArXiv.

Complex regulatory control in Boolean networks

Riccardo Zecchina, Andrea Pagnani, Michele Leone, 2004 .

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

Florent Krzakala, Andrea Pagnani, Martin Weigt, 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

Compressed sensing reconstruction using expectation propagation pdf

Alfredo Braunstein, Andrea Pagnani, Anna Paola Muntoni, 2019, Journal of Physics A: Mathematical and Theoretical.

Coloring random graphs

Riccardo Zecchina, Andrea Pagnani, Martin Weigt, 2002, Physical review letters.

Simultaneous Reconstruction of Multiple Signaling Pathways via the Prize-Collecting Steiner Forest Problem

Christian Borgs, Jennifer T. Chayes, Ernest Fraenkel, 2012, J. Comput. Biol..

An analytic approximation of the feasible space of metabolic networks

Alfredo Braunstein, Andrea Pagnani, Anna Paola Muntoni, 2017, Nature Communications.

Aligning biological sequences by exploiting residue conservation and coevolution

Andrea Pagnani, Anna Paola Muntoni, Martin Weigt, 2020, bioRxiv.

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Weiqing Wang, Chris Sander, Riccardo Zecchina, 2013, PLoS Comput. Biol..

Regularization and decimation pseudolikelihood approaches to statistical inference inXYspin models

Andrea Pagnani, Luca Leuzzi, Alessia Marruzzo, 2016, 1603.05101.

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

Andrea Pagnani, 2013, CiE.

Predicting protein functions with message passing algorithms

Andrea Pagnani, Michele Leone, W. Kibbe, 2004, Bioinform..

Sharing Information to Reconstruct Patient-Specific Pathways in Heterogeneous Diseases

Christian Borgs, Jennifer T. Chayes, Ernest Fraenkel, 2013, Pacific Symposium on Biocomputing.

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

Andrea Pagnani, Paolo Marcatili, Guido Uguzzoni, 2016, PLoS Comput. Biol..

Improving Contact Prediction along Three Dimensions

Marcin J. Skwark, Erik Aurell, Andrea Pagnani, 2014, PLoS Comput. Biol..

Expectation propagation for the diluted Bayesian classifier

Alfredo Braunstein, Andrea Pagnani, Mirko Pieropan, 2020, Physical review. E.

adabmDCA: adaptive Boltzmann machine learning for biological sequences

Andrea Pagnani, Anna Paola Muntoni, Francesco Zamponi, 2021, BMC Bioinform..

Identifying All Moiety Conservation Laws in Genome-Scale Metabolic Networks

Andrea Pagnani, Roberto Mulet, Daniele De Martino, 2014, PloS one.

Classification and sparse-signature extraction from gene-expression data

Andrea Pagnani, Francesca Tria, Martin Weigt, 2009, 0907.3687.

A stochastic local search approach to language tree reconstruction

Vittorio Loreto, Emanuele Caglioti, Andrea Pagnani, 2010 .

Alfredo Braunstein, Andrea Pagnani, Roberto Mulet, 1991, Nature.

RNAs competing for microRNAs mutually influence their fluctuations in a highly non-linear microRNA-dependent manner in single cells

Carlo Baldassi, Riccardo Zecchina, Francesco Sgrò, 2017, Genome Biology.

Kinetic Modelling of Competition and Depletion of Shared miRNAs by Competing Endogenous RNAs.

Andrea Pagnani, Carla Bosia, Araks Martirosyan, 2018, Methods in molecular biology.

A stochastic local search algorithm for distance-based phylogeny reconstruction.

Vittorio Loreto, Emanuele Caglioti, Andrea Pagnani, 2010, Molecular biology and evolution.

Finite size corrections to random Boolean networks

Giorgio Parisi, Andrea Pagnani, Michele Leone, 2006 .

Inverse problem for multi-body interaction of nonlinear waves

Andrea Pagnani, Luca Leuzzi, Alessia Marruzzo, 2016, Scientific Reports.

Statistical mechanics of sparse generalization and graphical model selection

Andrea Pagnani, Martin Weigt, Alejandro Lage-Castellanos, 2009 .

Stability of the replica symmetric solution in diluted perceptron learning

Andrea Pagnani, Alejandro Lage-Castellanos, A. Pagnani, 2013 .

Fast and Accurate Multivariate Gaussian Modeling of Protein Families: Predicting Residue Contacts and Protein-Interaction Partners

Carlo Baldassi, Riccardo Zecchina, Andrea Pagnani, 2014, PloS one.

Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon

Andrea Pagnani, Martin Weigt, Christoph Feinauer, 2015, PloS one.

The space of feasible solutions in metabolic networks

Alfredo Braunstein, Andrea Pagnani, Roberto Mulet, 2008 .

ceRNA crosstalk stabilizes protein expression and affects the correlation pattern of interacting proteins

Andrea Pagnani, Araks Martirosyan, E. Marinari, 2017, Scientific Reports.

The importance of dilution in the inference of biological networks

Andrea Pagnani, Martin Weigt, Alejandro Lage-Castellanos, 2009, 2009 47th Annual Allerton Conference on Communication, Control, and Computing (Allerton).

Modelling Competing Endogenous RNA Networks

Riccardo Zecchina, Andrea Pagnani, Carla Bosia, 2013, PloS one.