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Thursday October 16, 2014, 9:15 AM
Interactomics: Computational Analysis of Novel Drug Opportunities
Ram Samudrala,
University of Washington, Seattle, USA

Ram Samudrala is professor of computational biology and bioinformatics at the University of Washington. He researches protein and proteome structure, function, interaction, design, and evolution spanning atomic to organismal levels of description. He published more than 110 works and he is author of free software and web servers for molecular and systems modelling.
He has developed the Computational Analysis of Novel Drug Opportunities (CANDO) platform to analyse compound-proteome interaction signatures.
For further details see Ram Samudrala Talk page.

Thursday October 16, 2014, 2:20 PM
Biomodel engineering with Petri nets
Wolfgang Marwan,
Otto-von-Guericke Universität, Magdeburg, Germany

Wolfgang Marwan got a Degree in Biology, University of Erlangen, in 1985 and a PhD in Biochemistry, University of Munich in 1989. Since 2005 he is Full Professor at the Otto-von-Guericke Universit$auml;t Magdeburg. Cofounder of the Magdeburg Centre for Systems Biology in 2007.

With Petri nets as formal language for biomodel engineering, we describe the general concept of a modular modelling approach that considers the functional coupling of modules representing components of the genome, the transcriptome, and the proteome in the form of an executable model.

For details see Wofgang Marwan Talk page.

Friday October 17, 2014, 9:00 AM
Modeling protein structures and complexes using evolutionary information
Torsten Schwede,
SIB Swiss Institute of Bioinformatics & Biozentrum University of Basel, Switzerland
Torsten Schwede got a degree in Biochemistry at Albert Ludwigs Universität, Freiburg i.Br., Germany, in 1994, and a PhD in protein crystallography in 1998 in the group of G.E. Schulz, in the same University.
After his initial reasearch activity in Geneva at GWER GlaxoWellcome Experimental Research first and at GSK GlaxoSmithKline R&D later, he moved to the Biozentrum, University of Basel, in 2001, where he has been Assistant professor since 2001 and then Associate professor since 2007 in Structural Bioinformatics. Since 2002 he also is Group leader at the SIB Swiss Institute of Bioinformatics.

Traditionally the focus of structure modelling has been on predicting the 3-dimensional structure of a single protein chain – ignoring the fact that the majority of proteins in a living cell exist as part of complexes and quaternary structure assemblies. Frequently, ligand binding sites and enzyme active sites are located between protein chains, and mutations in protein-protein interfaces are often related to diseases. We have therefore developed an approach for comparative protein quaternary structure modelling using an evolutionary interaction fingerprint profile.

For details see Torsten Schwede Talk page.

Friday October 17, 2014, 2:00 PM
Crystallizing macromolecular complexes: the ribosome
Ada Yonath,
Weizmann Institute of Science, Rehovot, Israel

Ada Yonath CV and research interests will be added here.
Talk abstract to be added here.
For details see Ada Yonath Talk page.

Special Guest

Thursday October 16, 2014, 12:00 PM
Understanding protein–protein contacts on a PDB-wide scale
Guido Capitani,
Paul Scherrer Institute, Villigen, Switzerland

Guido Capitani is a project leader in the department of Biology and Chemistry at the Paul Scherrer Institute in Switzerland and a lecturer in Bioinformatics at the department of Biology of the ETH Zurich.
He is interested both in protein structure determination by crystallography and other techniques and in structural bioinformatics. He carried out extensive research work in structural enzymology, on bacterial and plant glutamate decarboxylase and on sphingosine-1-phosphate lyase.
His current research focus is on protein structure analysis, with the goal of extracting as much information as possible from protein structures with the help of sequence information. This approach is being applied to the problem of identifying biologically relevant contacts in crystal structures (EPPIC server) and to the analysis of membrane protein oligomeric interfaces.
For details see Guido Capitani Talk page.

Thursday October 16, 2014, 1:30 PM
From genes to networks and to dynamic models
Lilia Alberghina,
SYSBIO Centre of Systems Biology, University of Milano-Bicocca, Italy

Lilia Alberghina is the Director of SYSBIO, Centre of Systems Biology, Milan, Italy.
Emeritus Professor at the University of Milano-Bicocca.
The present grand challenge in biomedicine aims to reach full understanding on relations of genes to function in complex biological processes. These functions, in fact, emerge as system-level properties from the dynamic ordered interactions of a large number of gene products and of small molecules, derived from environment or from metabolism.
For details see Lilia Alberghina Talk page.

Friday October 17, 2014, 12:00 PM
ELIXIR technical coordinators: who we are and what we are trying to do
Federico Zambelli,
University of Milan and Institute of Biomembrane and Bioenergetics (IBBE), National Research Council, Italy

Federico Zambelli is the technical coordinator of ELIXIR-Italy, the Italian ELIXIR node.
He obtained his PhD in Cellular and Molecular Biology at the University of Milan in 2009. From 2009 to 2014, he got a Postdoc position at the Department of Life Science at the University of Milan. Since April 2014, he is technical coordinator of ELIXIR-Italy and he works both at the University of Milan and at the Institute of Biomembranes and Bioenergetics of CNR in Bari.
He participated in the development of several tools for the identification of regulatory elements in Eukaryotic genomic sequences. His main scientific interests focus on Next Generation Sequencing data analysis. As ELIXIR-Italy technical coordinator he is involved in many activities related to his role.
The amount of biological data that needs to be analyzed, stored and retrieved is growing at a “more than exponential” rate. No single institution can cope with this challenge without joining forces.
ELIXIR’s mission is to provide the necessary infrastructure for the European life science needs of the future. Storage, services availability and interoperability, cloud, training, standards, are the main topics that ELIXIR technical coordinators are discussing in order to propose viable solutions.
This talk will provide a brief summary of such activities and future projects.
For details see Federico Zambelli Talk page.

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