SWISS BIOINFORMATICS A newsletter published twice a year by SIB Swiss Institute of Bioinformatics July 2009 Welcome It is with pleasure that I introduce Swiss Bioinformatics Contents which we will issue twice a year. In this inaugural edition, we welcome four new Group Leaders and their Groups to Welcome 1 SIB, we introduce the new President of the SIB Foundation Snippets 1 Council and a new member of the SIB Executive Board, and SIB welcomes new Group Leaders 2 we congratulate the winners of the 2009 SIB Awards. The Editorial 3 main scientific article showcases the work from the MOSAIC group of Ivo Research in brief 4 Sbalzarini from the first half of 2009. [BC]2 2009 6 Research spotlight 6 Since the beginning of this year we have introduced a new SIB logo, the new-look SIB institutional website has gone online at www.isb-sib.ch, and now, with the first edition of our external newsletter, we launch a regular information channel with external stakeholders. I hope that you find this newsletter an informative and interesting read! Ron Appel Director, SIB Swiss Institute of Bioinformatics Snippets ● Martine Brunschwig Graf, Swiss National Councillor from Geneva, has been nominated to the SIB Executive Board from January 1, 2009. She replaces Christiane Langen- Martine Brunschwig Graf Peter Malama berger who left the Executive Board at the end of Decem- ber 2008 after a decade-long association with the SIB. ● The SIB Swiss Institute of Bioinformatics is pleased to announce the re-launch of GlycoSuiteDB http:// ● Peter Malama became the new President of the SIB glycosuitedb.expasy.org, a product of Tyrian Diagnostics Foundation Council on July 1, replacing Johannes Ltd (formerly Proteome Systems Ltd). The glycan data- Randegger who held the post for three years. base is available in open access mode on the ExPASy website. ● The new Centre Universitaire de Bioinformatique (CUB) at the University of Geneva has been approved by uni- ● The Concept Web Alliance CWA, an international non- versity administration. It will coordinate and deliver pre- profit organisation aimed at harnessing semantic web ap- and post-graduate bioinformatics courses, strengthen the proaches to disseminate life science data, held its inaugu- coordination of bioinformatics research, and ral meeting in mid-May. A goal of the alliance facilitate access to bioinformatics tools and is to pull together existing academic projects, databases for other Unige groups. as well as seek new ideas and methods to address the challenges associated with ● Ron Appel and Ernest Feytmans have high-volume scholarly and professional data edited a new book, Bioinformatics: A Swiss production, storage, interoperability, and Perspective. It covers both research and analyses. Founding members of the CWA major infrastructure efforts in genome and include Barend Mons of the Erasmus Medi- gene expression analysis, investigations cal Centre at the University of Rotterdam on proteins and proteomes, evolutionary and Leiden University Medical Center, and bioinformatics and modelling of biological Amos Bairoch and Frédérique Lisacek from systems. Bioinformatics: A Swiss Perspec- the Swiss Institute of Bioinformatics. tive, published by World Scientific press, is available at www.worldscibooks.com/ ● Coming events: 8th [BC]2 Basel Compu- lifesci/7181.html and other outlets such as tational Biology Conference June 24-25, www.amazon.com. 2010. 2 SWISS BIOINFORMATICS SIB welcomes new Group Leaders Welcome to four new Group Leaders, whose nominations University, New York. Simon was a post-doc fellow in the were ratified by the SIB Foundation Council on July 1, 2009. Structural Biology Division, Biozentrum of the University The SIB now consists of 29 groups and 320 members and of Basel from 2003 to 2006, and subsequently he was collaborators. At the same time, the SIB has announced a research scientist in Olivier Michielin’s Molecular Modelling new group for functional characterisation of human proteins Group at the SIB. Since April 2008, he is Assistant Professor and a new head of Swiss-Prot. SNF in core programs, Computational & Systems Biology and Structural Biology & Biophysics, at the Biozentrum, UniBS. Canadian by origin, Simon has received numerous Niko Beerenwinkel academic awards and fellowships and he has authored D-BSSE, ETH Zurich, studied more than twenty research articles. mathematics and biology at the University of Bonn and computer His group focuses on the structure-function relationship of science at Saarland University in membrane proteins. By explicitly simulating the dynamics Saarbrücken where he obtained of the proteins in their physiological environment, the group his PhD summa cum laude. He has aims to elucidate the microscopic mechanisms that underlie worked as Research Assistant at the protein functions. The approach thus complements the Max Planck Institute for Informatics, information obtained by X-ray crystallography which can only before doing a PostDoc at the University of California at provide limited information on the dynamics and energetics Berkeley from 2004 to 2006, and at Harvard University from of proteins. This simulation work, while being quite different 2006 to 2007. He joined ETH Zurich in 2007 as Assistant in nature compared to the work pursued in the -omics fields, Professor for Computational Biology in the Department shares the goal of building a strong theoretical framework of Biosystems Science and Engineering and heads the to advance our understanding and interpretation of large Computational Biology Group (CBG). He is author of experimental datasets. more than 40 research articles on computational biology, bioinformatics, biostatistics, virology, and cancer biology The long-term goal of the research pursued in the labora- and was awarded the Otto Hahn Medal of the Max Planck tory of Simon Bernèche is to establish a bridge between Society and the Emmy Noether Fellowship of the German microscopic properties of membrane channel systems and National Science Foundation. macroscopic properties of single excitable cells. His research is at the interface of mathematics, statistics, See: Computational Biophysics Group www.isb-sib.ch/groups/ computer science, biology and medicine. His current re- basel/computational-biophysics-s-berneche.html search activities deal with applying computational methods to biomedical problems, namely using mathematical models to predict the behavior of biological systems and designing Dagmar Iber efficient algorithms to aid in the diagnosis and treatment of D-BSSE, ETH Zurich, studied diseases. Current research projects developed by his team mathematics and biochemistry in include the use of algorithms to analyse the HIV genome for Regensburg, Germany, Cambridge the selection of optimal drug treatment combinations, the and Oxford, UK. She holds Master use of deep sequencing to characterise the genetic diver- degrees and PhDs in both disciplines. sity of pathogen populations, the use of evolutionary models After three years as a Junior and statistics to study cancer progression, and the analy- Research Fellow in St John’s College, sis of host cellular pathways activated by viral or bacterial Oxford, Dagmar became a lecturer in infection to identify host proteins that could serve as potential Applied Mathematics at Imperial College London. Dagmar targets for future drug therapies. has joined ETH Zurich in 2008 after returning from an See: Computational Biology Group www.isb-sib.ch/groups/ investment bank where she worked as an oil option trader basel/computational-biology-group-n-beerenwinkel.html for one year. Dagmar Iber’s research involves the development of quan- Simon Bernèche titative, predictive models for cellular signaling networks. Biozentrum, University of Basel, has Close collaborations with experimental laboratories permit a Bachelor of Engineering in physics a cycle of model testing and improving. The ultimate goal and bio­­medical enginee ring from the of her research is a comprehensive understanding of the École Polytechnique de Montréal dynamics and evolution of complex cellular signaling net- and a Masters in Biophysics from the works. Université de Montréal. He obtained See: Computational Biology Group www.isb-sib.ch/groups/ his PhD in physiology and biophysics basel/computational-biology-group-d-iber.html from Weill Medical College, Cornell July 2009 3 A new roadmap for Jacques Rougemont bioinformatics in Switzerland is head of the Bioinformatics and Bio- statistics Core Facility (BBCF) of the Bioinformatics resources are needed to sustain life EPFL School of Life Sciences since science research – biologists need bioinformaticians 2007 and does research on statistical to develop new methods and software and to maintain analysis of large-scale genomic data. large biological encyclopaedias in the form of curated He studied physics and mathematics databases. They also need the computational infra- at the University of Geneva and ob- structure to store and process their data, specialised tained his PhD in 1999, followed by high-level bioinformatics competencies and support postdoctoral training in numerical analysis and stochastic to analyse data and infer pertinent information that processes at the Mathematics Department, Heriot-Watt Univer- eventually will be used to develop innovative solutions sity in Edinburgh. He then worked on microarray data analysis to improve our daily lives. at the TAGC la boratory at INSERM, Marseille, before joining the SIB’s Vital-IT group as a computer analyst in 2004. Since the