Seminars
News and materials about the seminars held at OptLab in Crema.
Business Analytics - La matematica che crea valore
2011, June 21
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Past Seminars (click to expand)
The minimum evolution problem
2008, May 16, 11:00 am || Speaker: Daniele Catanzaro, G.O.M., ULB, Brussels
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the video WMV (skip the first 15 minutes).
Abstract: Molecular phylogenetics studies the hierarchical evolutionary relationships among organisms by means
of molecular data. These relationships are typically described by means of weighted trees, or phylogenies,
whose leaves represent the observed organisms, internal vertices the intermediate ancestors, and edges the
evolutionary relationships between pairs of organisms. Molecular phylogenetics provides several criteria
for selecting one phylogeny from among plausible alternatives. Usually, such criteria can be expressed
in terms of objective functions, and the phylogenies that optimize them are referred to as optimal. One
of the most important criteria is the Minimum Evolution (ME) criterion, which states that the optimal
phylogeny for a given set of organisms is the one whose sum of edge weights is minimal. Finding the
phylogeny that satisfies the minimum evolution criterion involves solving an optimization problem, called
the Minimum Evolution Problem (MEP), which is notoriously NP-Hard. Here we offer an overview
of the minimum evolution problem and discuss the different versions of it that occur in the literature.
Structural Alphabets: from geometric to string representations of protein structures
2009, December 17, 4:30 pm || Speaker:
Alessandro Pandini
National Institute for Medical Research, London
Abstract
A detailed understanding of the biological function of proteins requires knowledge of their molecular structures. The increased availability of experimental data has shown that protein structures have a hierarchical and partially redundant nature: they can be seen as composed of short fragments representing frequently occurring local conformations. This has stimulated the development of successful computational approaches based on fragment assembly. Methods relying on relatively large libraries of fragments have been developed to analyze, predict and design protein structures.
A parallel interest has arisen in developing sets of fragments that can describe the most typical local conformations with the smallest number of representatives. These are generally called Structural Alphabets and form a bridge between the string-oriented methods of sequence analysis and the coordinate-oriented methods of protein structure analysis.
During the talk, an introduction will be provided to protein structures and their geometric representations. Then Structural Alphabets will be described in detail and their advantages to string representation will be discussed. Finally the development of a new Structural Alphabet suitable for studies of protein dynamics will be presented.
Haplotype Inference problems based on the parsimony principle
2010, February 08, 4:30 pm || Speaker:
Yuri Pirola
BIMIB, Universita` di Milano Bicocca
Abstract
After the first human genome draft has been published in 2000, a lot of research efforts have been devoted to the discovery of genetic differences among same-species individuals and to the characterization of their impact to the expression of different phenotypic traits such as disease susceptibility or drug resistance.
Haplotype Inference (HI) is one of the pivotal computational problems of this area because it provides an inexpensive method for obtaining the genetic sequences that each individual of a population has inherited from his parents starting from "raw" genetic data extracted by wet-lab experiments.
Since different populations or datasets may have different characteristics, several formulations of the HI problem have been proposed in the literature.
In this talk, the optimization problems underlying parsimony-based formulations of Haplotype Inference on two kinds of populations (namely unstructured and structured populations) will be presented. In particular, the main results and the most recent advances for each problem will be reviewed, and some possible lines of future research will be discussed.