International Summer School in Methods in Bioinformatics (SSMBio 2012)

General info

Date 

27 Aug 2012 - 31 Aug 2012 

Location

Tarragona, Spain

Website

http://grammars.grlmc.com/SSMBio2012/

Keywords

Human Protein Variants, Bioinformatics, Spectrometry, Reconciliations

Contact(s)

Florentina Lilica Voicu

Description

Course Description

Rita Casadio (U Bologna), [advanced, 8 hours]

Human Protein Variants: Structural and Functional Annotation

Technological advancements constantly increase the number of mutations that need annotation in translated regions of the human genome. Single residue mutations in proteins are known to affect protein stability and function. As a consequence, they can be disease associated. Available computational methods starting from protein sequence/structure predict whether residue mutations are conducive to disease or alternatively to instability of the protein folded structure. However, the relationship among stability changes in proteins and their involvement in human diseases still needs to be established. Here we will address relevant problems of protein structural and functional annotation in relation to the putative involvements of protein variations and their stability perturbation in human diseases. Specifically we will try to rationalize in a nutshell the complexity of the question by generalizing over information already stored in public databases. Then we will revise available methods for structural and functional annotation of protein variants and benchmark them on real cases of single amino acid polymorphism annotation as detected from transcriptomic data.

Syllabus:

How to annotate protein variants.

How to predict protein stability upon residue change.

How to annotate disease related single amino acid polymorphisms.

Real cases of transcriptome analysis.

Translational Bioinformatics: From Genomes to Diseases and Drugs

This course is an introduction to translational bioinformatics, more specifically how bioinformatics methods for analyzing genomes, diseases, and drugs can be used for the benefits of health and society. An important aspect of bioinformatics is its ability to integrate different types of data and knowledge. The integration can be done by considering the molecular networks of interactions and reactions that are related to various types of cellular processes and organismal behaviors. This integrated approach has enabled functional interpretation of genomes and other high-throughput experimental data. Furthermore, this has enabled diseases and drugs to be considered in terms of the perturbed molecular networks. I will first give an overview of all diseases known to be associated with genes and other factors and all drugs marketed in USA, Europe and Japan. I will then discuss how disease and drug information can be analyzed as part of the molecular network information, especially focusing on drug interactions.

Bin Ma (U Waterloo), [introductory/intermediate, 6 hours]

Mass Spectrometry Data Analysis for Proteomics

Mass spectrometry has become the primary method for protein identification and characterization in proteomics. The tutorial will begin with the necessary background of mass spectrometry for proteomics. Then the computational challenges and algorithms for solving various proteomics problems are introduced, including: peptide de novo sequencing, database search, statistical validation of the results, homology search with de novo tags.

Luay Nakhleh (Rice U), [introductory/intermediate, 4 hours]

Gene Tree Reconciliations: Incomplete Lineage Sorting, Duplication/Loss, and Reticulation

Comparative analysis of biological data across species is a powerful method for understanding biological data and their properties. Such an analysis requires knowledge of the evolutionary histories of species, or populations, from which the data is acquired. Traditionally, such an evolutionary history would be constructed, or inferred, using a gene, or a genomic region, of interest. However, evolutionary analyses in the post-genomic era have highlighted the issue of gene tree incongruence: that gene trees may disagree with each other, as well as with the evolutionary history of the species. In this course, we will discuss three main mechanisms of gene tree incongruence, namely incomplete lineage sorting, gene duplication/loss, and reticulation, and review mathematical models and algorithmic techniques for inferring evolutionary histories under these mechanisms. The models and algorithms we discuss involve combinatorial optimization and probability.

Gajendra P.S. Raghava (Institute of Microbial Technology, Chandigarh), [intermediate/advanced, 8 hours]

Bioinformatics Approach for Designing Therapeutic Peptides, particularly Subunit Vaccines

Traditionally small molecules are used as drugs; in recent years, the number of approved drugs based on small molecules is decreasing, thus pharmaceutical R&D industries are looking for an alternative strategy. One of the alternative strategies to small molecules is a peptide-based drug. In addition, there is a tremendous change in the field of medicine in the last twenty years. Earlier, discovering new drugs or vaccines was the domain of biologists, pharmacists and medical professionals. Today the field is dominated by computer professionals, who are not only assisting the research in discovering new drugs and optimizing the process of drug/vaccine development. In this course, the application of peptides in therapeutics and the role of peptide bioinformatics in designing effective drugs/vaccines against dread diseases will be discussed. Major emphasis will be on the following topics:

Analysis and prediction of tertiary structure of peptides.

Prediction and design of antibacterial peptides.

Half-life and toxicity of peptides.

Application of cell penetrating and tumor homing peptides in drug delivery.

Designing of epitope/peptide-based vaccine design (integrative approaches for prediction of B-/T- cell epitopes).

Joachim Selbig (University of Potsdam & Max Planck Institute of Molecular Plant Physiology), [intermediate/advanced, 6 hours]

Integrative 'Omics' Data and Network Analysis

We will focus on specific aspects of metabolite profile and network analysis: the evaluation of the interactions between metabolites, the uncovering of the connection between metabolism and the phenotype (e.g. as measured by the biomass or morphological properties) and the establishment of relationships between gene expression and metabolite profiles. The latter is to date the most difficult task because the number of observations is often much smaller than the number of investigated genes. For the same reason, the uncovering of relationships between gene expression and physiological properties is difficult (Steinfath et al. 2008, Jozefczuk et al. 2010, Larhlimi et al. 2011, Basler et al. 2012, Girbig et al. 2012). To date, more than 100,000 different metabolites of broad biochemical complexity have been discovered in the plant kingdom and typical non-plant eukaryotic organisms are estimated to contain 4,000 to 20,000 metabolites (Fernie et al. 2004). The high number of metabolites, together with their biochemical complexity and a wide dynamic range of abundances, hampers a comprehensive analysis. The technical and analytical challenges in metabolome analysis have been recently reviewed in detail (Goodacre et al. 2004).

Wing-Kin Sung (National U Singapore), [introductory/intermediate, 6 hours]

Extracting Information from Next Generation Sequencing Data

During the last few years, next generation sequencing (NGS) becomes a popular research tool. People identified more and more NGS applications. At the same time, the throughput of NGS is improving exponentially. It becomes a challenging bioinformatics problem on how to process and analyze NGS data.

This course has three parts. The first part studies methods on processing NGS data. We will discuss techniques to reduce the processing time and how to reduce the NGS datasize. The second and third parts study two specific applications of NGS, namely genome assembly and binding site analysis.

Michael Zhang (U Texas Dallas), [intermediate, 6 hours]

From Computational -Omics to Systems Biology

These lectures will introduce typical computational biology problems in genomics and epigenomics. They will describe basic ideas and computational approaches to study transcriptional and post-transcriptional gene regulatory networks in molecular systems biology.