2010

25 June 2010

SIB honours two young bioinformaticians for their outstanding research work     

Today, during the 8^th [BC]² Computational Biology Conference in Basel, SIB Swiss Institute of Bioinformatics announced the two winners of the SIB Awards 2010.

The winner of the SIB Young Bioinformatician Award is SIB Member Aitana Morton de Lachapelle, 27, PhD student in the Computational Biology Group led by Prof. Sven Bergmann at the Department of Medical Genetics of the University of Lausanne, which she joined after graduating in Physics from the EPFL (Swiss Federal Institute of Technology in Lausanne). During her PhD thesis, she has been investigating how robust pattern formation can be achieved during development.

The Young Bioinformatician Award is given yearly by SIB Swiss Institute of Bioinformatics. It recognises a graduate student or young researcher who has carried out a research project centered on the in silico analysis of biological sequences, structures and processes. The award is given competitively by a jury of experts and is doted with a cash prize of CHF 10'000.

The winner of the 2010 SIB Best Graduate Paper Award is Rajesh Ramaswamy, 27, PhD student in the MOSAIC Group of Prof. Ivo Sbalzarini at ETH Zurich (Swiss Federal Institute of Technology). The title of his award paper is «A new class of highly efficient exact stochastic simulation algorithms for chemical reaction networks».

The Best Graduate Paper Award is given yearly by SIB Swiss Institute of Bioinformatics. It recognises outstanding contributions to the fields of bioinformatics and computational biology made by young researchers who have not yet completed their PhD. The award is given competitively by a jury of experts and is doted with a cash prize of CHF 5'000. 
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21 June 2010

Sequencing of the human body louse Genome: an important step towards the control of this disease-vector insect

The results of the sequencing and analysis of the human body louse genome, which were published on June 21 in the Proceedings of the National Academy of Sciences (PNAS), offer new insights into the intriguing biology of this disease-vector insect. The project involved more than 70 international scientists led by Professor Evgeny Zdobnov at the University of Geneva Medical School and the SIB Swiss Institute of
Bioinformatics, with Professor Barry Pittendrigh at the University of Illinois and Professor Ewen Kirkness at the J. Craig Venter Institute.
The human body louse, Pediculus humanus humanus, is an obligate human parasite responsible for the transmission of bacteria that cause relapsing fever, trench fever, and epidemic typhus. The sequencing and comparative analysis of the body louse genome with other sequenced species revealed many features that will enhance our understanding of the relations between disease-vector insects, the pathogens they
transmit, and the affected human hosts.
Full media release  

16 April 2010

Scientists discover new genetic sub-code

In a multidisciplinary approach, Professor Yves Barral, from the Biology Department at ETH Zurich and the computer scientists Dr. Gina Cannarozzi and Professor Gaston Gonnet, from the Computer Science Department of ETH Zurich and the SIB Swiss Institute of Bioinformatics, joined forces to chase possible sub-codes in genomic information. The study, which will be published in today’s issue of the journal Cell, led to the identification of novel sequence biases and their role in the control of genomic expression.
Full media release

29 January 2010

New computational tool for cancer treatment

Docking Algorithm EADock allows successful design of new inhibitors for an anti-cancer target

Many human tumors express indoleamine 2,3-dioxygenase (IDO), an enzyme which mediates an immune-escape in several cancer types. Researchers in the Molecular Modelling group at the Swiss Institute of Bioinformatics (SIB) and Dr. Benoît J. Van den Eynde’s group at the Ludwig Institute for Cancer Research Ltd (LICR) Brussels Branch developed an approach for creating new IDO inhibitors by computer-assisted structure-based drug design. The study was presented in the January 2010 online issue of the Journal of Medicinal Chemistry.
The docking algorithm EADock, used for this project, was developed by the Molecular Modeling Group over the last eight years. It provides solutions for the “lock-and-key” problem, wherein the protein active site is regarded as a “lock”, which can be fitted with a “key” (usually a small organic molecule) able to regulate its activity. Once an interesting molecule has been obtained, synthesis and laboratory experiments are necessary to confirm or reject the prediction. This algorithm will soon be made available to the scientific community worldwide.
The scientists obtained a high success rate. Fifty percent of the molecules designed in silico were active IDO inhibitors in vitro. Compounds that displayed activities in the low micromolar to nanomolar range, made them suitable for further testing in tumor cell experiments and for in vivo evaluation in mice. If these studies are successful, scientists can begin evaluating these new compounds in patients undergoing cancer-immunotherapy.
According to Olivier Michielin, Assistant Member at the Lausanne Branch of LICR and leader of the SIB Swiss Institute of Bioinformatics Molecular Modelling group, “This is a satisfactory proof of principle showing that computational techniques can produce very effective inhibitors for specific cancer targets with high yield. This is very encouraging for future drug developments in the academic environment.”

15 January 2010

Parasitic Wasps’ Newly Sequenced Genomes Reveal New Avenues for Pest
Control, Provides Insights into Evolution, Genetics

Researchers from the University of Geneva and the SIB Swiss Institute of Bioinformatics led an analysis of the sequenced genomes of parasitic wasps. Generally unknown to the public, the parasitic wasps kill pest insects. They are like ‘smart bombs’ that seek out and kill only specific kinds of insects. Harnessing their full potential would thus be vastly
preferable to chemical pesticides, which broadly kill or poison many organisms in the environment, including humans. The results of this large study are featured in today’s issue of Science. Professor Evgeny Zdobnov from the University of Geneva Medical School and the SIB Swiss Institute of Bioinformatics directed the comparative evolutionary genomics studies as part of this international project, which revealed many features that could be useful to pest control and medicine, and to enhance our understanding of genetics and evolution.
Full media release

2009

Lausanne, September 17

Statement regarding the EpiFlu database

This document is the SIB’s statement in response to recent allegations made by the GISAID Foundation in relation to the EpiFlu Database. More

Lausanne, July 1

Announcing "Bioinformatics: A Swiss Perspective"

Ron D. Appel and Ernest Feytmans of the Swiss Institute of Bioinformatics have edited a new book, Bioinformatics: A Swiss Perspective. With contributions from SIB group leaders and members, it covers both research work and major infrastructure efforts in genome and gene expression analysis, investigations on proteins and proteomes, evolutionary bioinformatics, and modelling of biological systems.
Full media release

Basel, June 19

The SIB recognises the next generation of bioinformaticians

The SIB Swiss Institute of Bioinformatics announced the winners of the 2009 SIB Best Graduate Paper Award and the SIB Young Bioinformatician Award at the 7th annual [BC]2 Basel Computational Biology Conference. Lukas Burger (Erik van Nimwegen Group, Biozentrum Basel) was awarded the 2009 SIB Young Bioinformatician Award for his outstanding work on predicting protein residue interactions using homologous protein sequences. The 2009 SIB Best Graduate Paper Award was won by Julien Roux (Marc Robinson-Rechavi Group, University of Lausanne) for his paper entitled “Developmental Constraints on Vertebrate Genome Evolution” (PLoS Genetics, December 2008), which was immediately recognised as an important contribution to the general understanding of evolution.

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Geneva, June 09

SIB Swiss Institute of Bioinformatics establishes new group for functional characterisation of human proteins and announces new head of Swiss-Prot

The SIB Swiss Institute of Bioinformatics announced today that Professor Amos Bairoch, the creator of the world-renowned protein database Swiss-Prot (now known as UniProtKB/Swiss-Prot ), has been proposed to direct a new SIB group, CALIPHO, as of July 1, 2009. This new group’s main project is to develop an innovative knowledge resource centred on human proteins, building on the expertise gained by the Swiss-Prot group. Prof. Bairoch will remain senior scientific advisor to the Swiss-Prot group. Dr. Ioannis Xenarios, who is also Group Leader of Vital-IT at SIB, will become the Director of Swiss-Prot, from July 1, 2009.  Full media release  English   French  German

Geneva/Lausanne, April 23

Sequencing the cow's genetic code – a new agricultural era dawns

Researchers from the Universities of Geneva and Lausanne, as well as the Swiss Institute of Bioinformatics have been part of a major international project to sequence the bovine (cow) genome, a female Hereford cow named L1 Dominette. Sequencing the bovine genome is now complete, paving the way for research into more sustainable food production, taking into account the needs of an increasing world population.   Full media release  English  French  German
 

New York, February 26

New Tool for Genome-Wide Association Studies

Modern genotyping technologies offer opportunities to explore the influence of genes on health and disease, with the challenge of analysing huge amounts of genetic and clinical data. Investigators at the Lausanne Branch of the international Ludwig Institute for Cancer Research (LICR), the Swiss Institute of Bioinformatics (SIB) and the University Hospital of Lausanne have developed AssociationViewer, a computational tool that displays genetic differences between individuals on a large scale. Full media release   Full scientific article

Lausanne, February 3

Stroma genomic signature predicts resistance to anthracyclin-based – chemotherapy in breast cancer patients: One step closer to personalized medicine

Researchers at the Swiss Institute of Bioinformatics and the Swiss National Center of Competence in Research in Molecular Oncology in Lausanne have developed a new test to predict how breast cancer patients respond to chemotherapy, which could help change how treatment is delivered in the future. In an article, A stroma-related gene signature predicts resistance to neoadjuvant chemotherapy in breast cancerⁱ, published in this month’s Nature Medicine, Drs Pierre Farmer, Mauro Delorenzi, and Pratyaksha Wirapati and the study team showed the potential of the reactive stroma to modulate tumor phenotype and the clinical response to treatment. This is a major step forward in the field as identifying factors that influence response to cancer chemotherapy is crucial for improving its efficacy. Full media release