List of works - Andrea Pagnani

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

scientific article

A discrete model of water with two distinct glassy phases

article

A stochastic local search algorithm for distance-based phylogeny reconstruction

scientific article

An analytic approximation of the feasible space of metabolic networks ⬇️

scientific article

Bridging the gaps in systems biology

scientific article published on 13 April 2014

Classification and sparse-signature extraction from gene-expression data

article

Coloring random graphs.

scientific article published on 9 December 2002

Core percolation and onset of complexity in boolean networks.

scientific article published on 4 January 2006

Critical exponents of the KPZ equation via multi-surface coding numerical simulations

article by Enzo Marinari et al published 9 November 2000 in Journal of Physics A

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

scientific article

Estimating the size of the solution space of metabolic networks.

scientific article

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

Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners ⬇️

scientific article

Finite size corrections to random Boolean networks

Gene-network inference by message passing

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells

scientific article

Glassy Transition in a Disordered Model for the RNA Secondary Structure

scientific article published in Physical Review Letters

Identifying all moiety conservation laws in genome-scale metabolic networks

scientific article (publication date: 2014)

Improving contact prediction along three dimensions ⬇️

scientific article

Inference algorithms for gene networks: a statistical mechanics analysis

article

Inference for interacting linear waves in ordered and random media ⬇️

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

scientific article

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

scientific article

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments

scientific article published on 27 March 2013

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

scientific article

Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes.

scientific article published in September 2013

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

scientific article

Metastable configurations on the Bethe lattice

Modelling Competing Endogenous RNA Networks

scientific article (publication date: 2013)

Multisurface coding simulations of the restricted solid-on-solid model in four dimensions

scientific article published on 14 January 2013

Near-optimal configurations in mean-field disordered systems

article

Numerical estimate of the Kardar-Parisi-Zhang universality class in (2+1) dimensions ⬇️

scientific article published on 2 July 2015

Perturbation biology: inferring signaling networks in cellular systems

scientific article (publication date: 2013)

Polynomial iterative algorithms for coloring and analyzing random graphs.

scientific article published on 3 September 2003

Predicting protein functions with message passing algorithms

scientific article published on 17 September 2004

Propagation of external regulation and asynchronous dynamics in random Boolean networks

scientific article published on 01 June 2007

Protein 3D structure computed from evolutionary sequence variation

scientific article published in 2011

SLAMF1 regulation of chemotaxis and autophagy determines CLL patient response

scientific article published on 30 November 2015

Scalings of Domain Wall Energies in Two Dimensional Ising Spin Glasses

scientific article published in Physical Review Letters

Sharing information to reconstruct patient-specific pathways in heterogeneous diseases

scientific article published on January 2014

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

article published in 2012

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. ⬇️

scientific article

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem

scientific article published on February 2013

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

scientific article published on 23 February 2018

Stability of the replica symmetric solution in diluted perceptron learning

Statistical mechanics of sparse generalization and graphical model selection

article published in 2009

The computational core and fixed point organization in Boolean networks

article published in 2006

The enzymatic activities of CD38 enhance CLL growth and trafficking: implications for therapeutic targeting.

scientific article published on 3 July 2014

The importance of dilution in the inference of biological networks

The intrinsic dimension of protein sequence evolution

The space of feasible solutions in metabolic networks

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

scientific article published on 29 October 2004

Width distributions and the upper critical dimension of Kardar-Parisi-Zhang interfaces.

scientific article published on 23 January 2002

Zero-temperature properties of RNA secondary structures

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

scientific article published on 07 March 2017

List of works by Andrea Pagnani

A critical assessment of Mus musculus gene function prediction using integrated genomic evidence

A discrete model of water with two distinct glassy phases

A stochastic local search algorithm for distance-based phylogeny reconstruction

An analytic approximation of the feasible space of metabolic networks ⬇️

Bridging the gaps in systems biology

Classification and sparse-signature extraction from gene-expression data

Coloring random graphs.

Core percolation and onset of complexity in boolean networks.

Critical exponents of the KPZ equation via multi-surface coding numerical simulations

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

Estimating the size of the solution space of metabolic networks.

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

Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners ⬇️

Finite size corrections to random Boolean networks

Gene-network inference by message passing

Genome-wide analysis identifies a functional association of Tet1 and Polycomb repressive complex 2 in mouse embryonic stem cells

Glassy Transition in a Disordered Model for the RNA Secondary Structure

Identifying all moiety conservation laws in genome-scale metabolic networks

Improving contact prediction along three dimensions ⬇️

Inference algorithms for gene networks: a statistical mechanics analysis

Inference for interacting linear waves in ordered and random media ⬇️

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

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

Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments

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

Inter-individual variation in nucleotide excision repair pathway is modulated by non-synonymous polymorphisms in ERCC4 and MBD4 genes.

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

Metastable configurations on the Bethe lattice

Modelling Competing Endogenous RNA Networks

Multisurface coding simulations of the restricted solid-on-solid model in four dimensions

Near-optimal configurations in mean-field disordered systems

Numerical estimate of the Kardar-Parisi-Zhang universality class in (2+1) dimensions ⬇️

Perturbation biology: inferring signaling networks in cellular systems

Polynomial iterative algorithms for coloring and analyzing random graphs.

Predicting protein functions with message passing algorithms

Propagation of external regulation and asynchronous dynamics in random Boolean networks

Protein 3D structure computed from evolutionary sequence variation

SLAMF1 regulation of chemotaxis and autophagy determines CLL patient response

Scalings of Domain Wall Energies in Two Dimensional Ising Spin Glasses

Sharing information to reconstruct patient-specific pathways in heterogeneous diseases

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

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis. ⬇️

Simultaneous reconstruction of multiple signaling pathways via the prize-collecting steiner forest problem

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Stability of the replica symmetric solution in diluted perceptron learning

Statistical mechanics of sparse generalization and graphical model selection

The computational core and fixed point organization in Boolean networks

The enzymatic activities of CD38 enhance CLL growth and trafficking: implications for therapeutic targeting.

The importance of dilution in the inference of biological networks

The intrinsic dimension of protein sequence evolution

The space of feasible solutions in metabolic networks

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

Width distributions and the upper critical dimension of Kardar-Parisi-Zhang interfaces.

Zero-temperature properties of RNA secondary structures

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