ICARIS 2012
Taormina Taormina Taormina Taormina Taormina

Tutorial Speakers



Computational Immunology, Immuno-informatics, Theoretical Immunology, & Systems Immunology

NGS: From the sequencing machine to the data archive

Heiko Muller, Italian Institute of Technology - Center of Genomic Science, Italy

Heiko Muller - NGS: From the sequencing machine to the data archive
Abstract

New generation sequencing (NGS) is becoming routine in life sciences and new applications are being developed at increasing speed. The generation, analysis, interpretation, and storage of NGS data poses a number of technical challenges. Here, the computational infrastructure and the analysis pipelines used at the Center of Genomic Science in Milan (Italian Institute of Technology) are described. Furthermore, meta-analysis approaches that can aid in the interpretation of NGS data are being discussed.

Short Bio

Heiko Muller studied Biophysics at the Humboldt University in Berlin and obtained a Ph.D. in Molecular Biology in 1995. His post-doctoral work was carried out at the Danish Cancer Society in Copenhagen and at the European Institute of Oncology in Milan, where he studied cell cycle regulation. In particular, he collaborated with Affymetrix in 1999 to use microarray technology for the identification of E2F target genes. The analysis of these data has triggered his moving from the bench into the field of bioinformatics. In 2002 he became an independent researcher at the European Institute of Oncology and in 2010 he joined the Italian Institute of Technology in Milan as head of the Computational Research.


A database for the analysis of mutation spectra in human cancer and immune systems

Luca Zammataro, Italian Institute of Technology - Center of Genomic Science, Italy

Luca Zammataro - A database for the analysis of mutation spectra in human cancer and immune systems
Abstract

Cancer is a multifactorial disease in which the genetic material of a cell can become damaged, producing mutations that affect normal cell growth and division. When this happens, damaged cells (that not die when they should) may form a mass of tissue called "tumor". In this tutorial we will explain how instruments are useful to produce and collecting genomic mutations regarding cancer cell, from several kind of tumors. An explanatory introduction on cancer origin theory will occur, together to a detailed description of wet and in silico tools, for new cancer mutations identification (bioinformatics tools, databases etc). Finally, a case study will be explained, singling out mutations in immune system genes related to cancer developing.

Short Bio

Luca Zammataro is Senior-Post-Doc at Computational Research Unit, Center of Genomic Science of IIT@SEMM, in Milan. He graduated in Medicine in 1998. From 2008 to 2011 he has been Bioinformatician in the Department of Immunology and Inflammation, Clinical Institute Humanitas, Milan. From 2001 to 2008 he has been fellow at Laboratory of Molecular Angiogenesis of University of Turin, where he got his specialization in Clinical Pathology in 2003, and his PhD degree in 2006, studying the role of Semaphor- ins and CRMP-1 in angiogenesis and cell movement. Since 2004 he is a strong collaborator of Wolfram Research Group, Champaign, USA, developing algo- rithms for reproducing of embryonic patterns and structural biology. Today, his principal investigations regard functional genomics, systems biology applied to tran- scriptional profiles and microarrays analysis.

Immunological Computation, Immune-inspired Engineering, Immune-inspired Heuristics

Swarm Intelligence

Christian Blum, Universitat Politècnica de Catalunya, Spain

Christian Blum - TBA
Abstract

Swarm intelligence is concerned with the design of intelligent multiagent systems by taking inspiration from the collective behavior of social insects such as ants, termites, bees, and wasps, as well as from other animal societies such as flocks of birds or fish schools. Colonies of social insects have mesmerized reseachers for many decades, and the mechanisms that govern their behavior has remained unknown for a long time. Even though the single members of these colonies are non-sophisticated individuals, they are able to achieve complex tasks in cooperation. Coordinated colony behavior emerges from relatively simple actions or interactions between the colonies' individual members.
Optimization techniques based on swarm intelligence have become increasingly popular during the last decade. They are characterized by a decentralized way of working that mimics behaviors found in nature. The advantage of these approaches over traditional techniques is their robustness and flexibility. These properties make swarm intelligence a successful algorithm design paradigm in order to cope with increasingly complex problems. After a general introduction, this tutorial will focus on well-known swarm intelligence techniques for optimization (such as ant colony optimization and particle swarm optimization), but also on more recent examples of swarm intelligence such as the self-organized (de-)synchronization that is found in ant colonies and certain species of frogs.

Short Bio

Christian Blum received the doctoral degree in 2004 from the Free University of Brussels (Belgium). He currently holds an Associate Professor position at the Universitat Politècnica de Catalunya in Barcelona (Spain). Current subject of his research is the use of swarm intelligence techniques for the management of large-scale mobile ad-hoc and sensor networks, as well as the hybridization of metaheuristics with more classical artificial intelligence and operations research methods. In the context of these research lines he has published more than 100 papers in journals and conference proceedings. He is a member of the editorial boards of international journals such as Computers & Operations Research, Swarm Intelligence, Applied Soft Computing and Neural Computing & Applications. As a co-founder, he initiated the series of International Workshops on Hybrid Metaheuristics (HM). Finally, he presented invited tutorials at conferences such as PPSN, GECCO, and HIS, and keynote talks at international conferences such as ANTS 2008 and BIOMA 2010.