2010

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