Biomedical subjects

Andrea Pagnani

Publications and source records attributed to Andrea Pagnani.

3 recordsLinked to original sources

PubMed2004

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

We consider the problem of coloring Erdös-Rényi and regular random graphs of finite connectivity using q colors. It has been studied so far using the cavity approach within the so-called one-step replica symmetry breaking (1RSB) ansatz. We derive a general criterion for the validity of this ansatz and, applying it to the ground state, we provide evidence that the 1RSB solution gives exact threshold values c(q) for the transition from the colorable to the uncolorable phase with q colors. We also study the asymptotic thresholds for q>>1 finding c(q) =2q ln q-ln q-1+o (1) in perfect agreement with rigorous mathematical bounds, as well as the nature of excited states, and give a global phase diagram of the problem.

Journal Article↗

PubMed2004

Predicting protein functions with message passing algorithms.

MOTIVATION: In the last few years, a growing interest in biology has been shifting toward the problem of optimal information extraction from the huge amount of data generated via large-scale and high-throughput techniques. One of the most relevant issues has recently emerged that of correctly and reliably predicting the functions of a given protein with that of functions exploiting information coming from the whole network of proteins physically interacting with the functionally undetermined one. In the present work, we will refer to an 'observed' protein as the one present in the protein-protein interaction networks published in the literature. METHODS: The method proposed in this paper is based on a message passing algorithm known as Belief Propagation, which accepts the network of protein's physical interactions and a catalog of known protein's functions as input, and returns the probabilities for each unclassified protein of having one chosen function. The implementation of the algorithm allows for fast online analysis, and can easily be generalized into more complex graph topologies taking into account hypergraphs, i.e. complexes of more than two interacting proteins. RESULTS: Benchmarks of our method are the two Saccharomyces cerevisiae protein-protein interaction networks and the Database of Interacting Proteins. The validity of our approach is successfully tested against other available techniques. CONTACT: leone@isiosf.isi.it SUPPLEMENTARY INFORMATION: http://isiosf.isi.it/~pagnani

Algorithms↗

PubMed2002

Zero-temperature properties of RNA secondary structures.

We analyze different microscopic RNA models at zero temperature. We discuss both the most simple model, which suffers a large degeneracy of the ground state, and models in which the degeneracy has been removed in a more or less severe manner. We calculate low-energy density of states using a coupling perturbing method, where the ground state of a modified Hamiltonian, that repels the original ground state, is determined. We evaluate scaling exponents starting from measurements of overlaps and energy differences. In the case of models without accidental degeneracy of the ground state we are able to clearly establish the existence of a glassy phase with theta approximately 1/3. 87.15.Aa, 64.60.Fr

Freezing↗