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statphysStatistical Physics GaussDCA: Multivariate Gaussian Inference of Protein Contacts from Multiple Sequence Alignment
This is the code which accompanies the paper "Fast and accurate multivariate Gaussian modeling of protein families: Predicting residue contacts and proteininteraction partners" by Carlo Baldassi, Marco Zamparo, Christoph Feinauer, Andrea Procaccini, Riccardo Zecchina, Martin Weigt and Andrea Pagnani, (2014) PLoS ONE 9(3): e92721. doi:10.1371/journal.pone.0092721 The code comes in two versions, one for Julia and one for MATLAB. They provide nearly identical funcitionality. The Julia code is slightly faster, and doesn't require compilation of external modules. Julia codeYou can download the Julia code from the attached file "GaussDCAjulia.tgz"; however, the recommended way to obtain the code is by using the command Matlab codeYou can download the MATLAB code from the attached file "GaussDCAmatlab.tgz", or from https://github.com/carlobaldassi/GaussDCA.matlab. See the README.md file for instructions. The patientzero problem with noisy observationThe patientzero problem consists in finding the initial source of an epidemic outbreak given observations at a later time. In this seminar, I will describe a Bayesian method which is able to infer details on the past history of an epidemics based solely on the topology of the contact network and a single snapshot of partial and noisy observations. The method is built on a Bethe approximation for the posterior distribution, and is inherently exact on tree graphs. Moreover, it can be coupled to a set of equations, based on the variational expression of the Bethe free energy, to find the patientzero along with maximumlikelihood epidemic parameters. Date:
Thu, 30/10/2014  14:30
Speaker:
Alessandro Ingrosso
Place:
HuGeF, Via Nizza 52
A cavitymethod based approach to the Steiner tree problem on graphsThe minimum weight Steiner tree problem (MST) is an important combinatorial optimization problem over networks that has applications in a wide range of ﬁelds. I will mainly focus my attention on two variants of the problem: Date:
Thu, 23/10/2014  14:30
Speaker:
Anna Paola Muntoni
Signal localization as a phase separation processIt is well known that ultrasensitivity (Goldbeter & Koshland, 1981) is the core of many bistable switches in biological systems. It is not as well recognized that when ultrasensitive selfamplifying circuits are diffusively coupled in a spatially distributed system such as the cell plasmamembrane, they may induce its dynamic separation into distinct signaling phases. This basic mechanism lays behind the process of cell membrane polarization in many, diverse biological systems. Cell membrane polarization is implicated in basic biological phenomena such as differentiation, proliferation, migration and morphogenesis of unicellular and multicellular organisms. Physical models based on the coupling of membrane diffusion with bistable enzymatic dynamics can reproduce a broad range of symmetrybreaking events, such as those observed in eukaryotic directional sensing, the apicobasal polarization of epithelial cells, the polarization of budding and mating yeast. Date:
Thu, 16/01/2014  14:30
Speaker:
Andrea Gamba
Perturbation Biology: Inferring Signaling Networks in Cellular Systems
Perturbation Biology: Inferring Signaling Networks in Cellular Systems. PLoS Computational Biology. 2013;9(12):e1003290.
Optimizing spread dynamics on graphs by message passing
Optimizing spread dynamics on graphs by message passing. Journal of Statistical Mechanics: Theory and Experiment. 2013;2013(09):P09011.
Large deviations of cascade processes on graphs
Large deviations of cascade processes on graphs. Phys. Rev. E. 2013;87:062115.
Multisurface coding simulations of the restricted solidonsolid model in four dimensions
Multisurface coding simulations of the restricted solidonsolid model in four dimensions. Physical Review E. 2013;87(1).
Spatial disorder in the Voter ModelWhen we try to study the organization and the properties of ecological systems, nonequilibrium statistical physics is a natural candidate to develop a unified framework for understanding the emergent properties of these kind of systems. Simple interacting particle systems, such as the Voter Model (VM), have found a surprisingly good agreement with empirical data and proved to be a useful nullmodel that can be treated analytically. Despite the recent progress in this field, still a major issue in ecology and conservation ecology is to understand the effects of habitat fragmentation and heterogeneities on the biodiversity of an ecosystem. Motivated by this open problem, we study the effects of quenched spatial disorder on the longtime behavior of the VM and its nonlinear generalizations. Date:
Wed, 12/12/2012  15:00
Speaker:
Claudio Borile
Palettecolouring: a belief propagation approach
Palettecolouring: a belief propagation approach. Journal of Statistical Mechanics: Theory and Experiment. 2011;2011:P05010.
