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4th INTERNATIONAL SUMMER SCHOOL
ON COMPUTATIONAL BIOLOGY
2008

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4th International Summer School on COMPUTATIONAL BIOLOGY

Statistical Methods for Genetic and Molecular Data

Thursday 29.5.2008: Genetic and Molecular Data Processing

9-11

Opening by Prof. J. Hřebíček, the guarantee of Computational Biology

Introduction into multivariate data analysis (T. Pavlík)

Development of molecular biology techniques in the last decade is characterized by production of vast amount of data. This holds true also for the DNA microarray technology which enables scientists to monitor tens of thousands of genes at the same time. However, for relevant medical inference there is the need for appropriate evaluation and interpretation of this large quantity of experimental data. This lecture is dedicated to statistical methods that can be used for the evaluation of gene expression data, especially those for multivariate stochastic methods used for data exploration and classification. Data exploration can be performed using clustering methods that are used for identification of homogeneous groups of patients or genes with similar expression profile. Such pattern recognition can lead to discovery of to this day unknown classes among patients suffering from certain disease or hidden relations and dependencies among specific genes. On the other hand, classification techniques are used for setting up a discrimination rule for sorting newly diagnosed patients into one of previously defined classes. This task is particularly important for future practice because the utilization of genomic data for precise diagnostics of serious diseases is a great challenge.

12-18

Practical training in analysis of genomic profiles (E. Budinská, T. Pavlík)

The presentation will guide the participants through the analysis of the data from microarray experiments (both expression and genomic), with using the state of the art methods. After brief introduction, participants will have the opportunity to follow the presentation by simultaneously analyzing the example dataset. Following SW will be used: Excel, R, SPSS Clementine.

Bioinformatics - tool for solving biological problems (E. Chovancová, J. Damborský)

Bioinformatics covers different computer applications in biological sciences and in its broadest sense the bioinformatics means information technology applied to the management and analysis of biological data. In recent years, bioinformatics has become essential for basic molecular biology research as well as for many areas of biotechnology and biomedical sciences. The aim of this lecture is to introduce selected areas of bioinformatics including biological databases, sequence alignments and analyses, molecular phylogenetics and structural bioinformatics. The topic will be presented using examples from real biological research.

Practical training in bioinformatics (E. Chovancová, J. Damborský)

The practical training aims to familiarize students with selected bioinformatics tools commonly used in biological research. These will include the tools for database searches, sequence analysis, prediction and visualization of protein structures.

Friday 30.5.2008: Applied phylogenetics

9-13

Basic phylogenetic methods (P. Vallo)

Reconstruction of phylogeny from DNA sequences plays an important role in present-day science. Therefore aim of this lecture is to introduce basic methods of phylogenetic analysis including initial processing of DNA sequences. Approaches to phylogenetic inference, commonly used methods of tree reconstruction, and models of DNA evolution will be presented. Particular attention will be given to interpretation of results in the relationship to methods used.

Phylogenetic applications (G. Heckel)

"Phylogenetic trees in evolutionary and medical research: enthusiasm and caution"
Phylogenetic reconstructions have found their application in a wide range of scientific fields from linguistics to systems biology. This lecture will emphasize on the application of phylogenetic inference in evolutionary, ecological and medical sciences. Examples from various organisms and their pathogens will illustrate important issues for practical research in terms of sampling, marker choice, levels of molecular divergence and peculiarities of evolutionary histories.
Applications of phylogenetic trees in human research include not only the identification of the origin of modern humans but also the tracing of our movements across the planet. Interestingly, important insights into the recent history of our own and other species are often derived from phylogenetic analyses of molecular data from "surrogate" organisms.

14-18

Tutorial in phylogenetic analyses (N. Martínková)

Phylogenetic analysis evolves dynamically, and new methods or advanced optimisation of current methods arise frequently. This tutorial will provide tools for identifying the crucial steps in phylogenetic DNA sequence analysis that can be applied universally across the plethora of computational approaches. This includes sequence alignment, haplotype/allele identification, model selection and phylogenetic tree reconstruction.

Saturday 31.5.2008: Processing of Genetic data and their Role in Diagnostics

9-13

Application and role of genetic and molecular data in clinical research (J. Mužík, L. Dušek)

Cytogenetic and molecular genetic tests become key component in diagnostics and follow-up control of oncology diseases. The clinical registries incorporating these data can thus play important role in analysis of treatment results and scientific research on this field. The clinical registries collect complex data on diagnosis, treatment, achieved treatment goals, characteristics of patient and tumour etc. and their goal is to provide sufficient information for process of diagnosis and treatment standardisation and optimization. The main aim of this work is the presentation of technological, management and data analysis background for the multicentric standardised data collection and analysis of clinical and laboratory data. This solution is documented on case studies of international clinical registries for patients with chronic myelogenous leukaemia (project CAMELIA) and acute leukaemia (project ALERT).

Genetic and molecular data in predictive medicine (L. Dušek, J. Mužík, K. Chroust)

IBA 4th International summer school on COMPUTATIONAL BIOLOGY is organized by
Institute of Biostatistics and Analyses, Faculty of Science and Faculty of Medicine, Masaryk University, Kamenice 126/3 Brno, Czech Republic, http://www.iba.muni.cz