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probabilityEffects of migration and stochasticity in subdivided populationsAbstract: In mathematical models of subdivided populations (or metapopulations) migration acts together with selection and genetic drift to determine their evolution. In order to study the coupled dynamics of these populations, I will develop a selfconsistent meanfieldlike method that hinges on the presence of a separation of time scales between local and global dynamics and catches the effects of migration on relevant nonequilibrium properties, such as the mean fixation time. As an result, I will show that when the evolution strongly favors coexistence of species (e.g., balancing selection), the mean fixation time develops an unexpected minimum as a function of the migration rate. I will also discuss possible generalizations of the method to include sparseness effects on random graphs. Date:
Thu, 22/01/2015  14:30
Speaker:
Luca Dall'Asta (Polito)
Place:
HuGeF, Via Nizza 52, Old Building, First floor, aula affrescata
Protein contact prediction: prospects and realityRecent developments in coevolution based contact prediction have been recently widely adopted by the structure prediction community, as evidenced in CASP11, a recently finished commnitywide experiment in blind protein structure prediction.. According to organisers’ opinion, contact prediction was one of the “winners” of CASP this year. In this talk I will present how did the field of contact prediction progress recently and how are the inferred couplings applied to solving problems in biological settings. This talk will particularly focus on my contactdriven CASP method “my protein&me”, which ranked as 4th most group worldwide and was claimed as one of more unexpected developments in this years’ experiment. I will also discuss several success stories for contact prediction, in which successful contact inference allowed for discovering structural information that has not been attainable by other means. Finally, the talk will discuss the potential impact of introducing additional biological information in the inference process and prospective ways of increasing the applicability of these methods. Date:
Thu, 15/01/2015  14:30
Speaker:
Marcin J. Skwark (The Finnish Centre of Excellence in Computational Inference)
Place:
HUGEF, old building 1st floor "Aula Affrescata"
Bayesian inference of epidemics on networkI study inference problems for irreversible stochastic epidemic models on network via Belief Propagation algorithm. Previous works derive equations which allow to compute posterior distributions of the time evolution of the state of each node given some observation. It has already been shown that this method outperforms previous ones in the particular case of finding "patient zero" of a SIR epidemic given an observation at a later unknown time. I study performances of this method on the inference of the time evolution of a SIR epidemic subsequent a given observation. Date:
Thu, 16/10/2014  14:30
Speaker:
Jacopo Bindi
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).
Palettecolouring: a belief propagation approach
Palettecolouring: a belief propagation approach. Journal of Statistical Mechanics: Theory and Experiment. 2011;2011:P05010.
Statistical physics approach to graphical games: local and global interactions
Statistical physics approach to graphical games: local and global interactions. Eur. Phys. J. B. 2011;81(3).
