March 27,2007 — Joint ICM UW/LCB UU Seminar

The joint ICM LCB bioinformatics seminar will be held on March 28 at 10:15. Seminar will be transmitted by Marratech software. Due to technical problems in Uppsala only one way communication will be possible..
Professor Ron D. Appelds, a member of Proteome Informatics Group, Swiss Institute of Bioinformatics, Geneva, Computer Science Department at Geneva University and Geneva Bioinformatics (GeneBio) SA, Geneva, Switzerland, will deliver the lecture :
“Analytical bioinformatics: from data to knowledge”

Bioinformatics is the application of computer sciences to molecular biology, and in particular to the study of macromolecules such as proteins, nucleic acids and oligosaccharides. It encompasses many diverse aspects, such as the development and annotation of protein or DNA sequence databases, the development of programs to analyse the intrinsic properties of DNA or protein sequences, or three-dimensional structure visualisation and modelling tools. Analytical bioinformatics focuses on the computational analysis of experimental biological data, such as micro-array data, genome sequencing data or proteomics data. The proteome is the protein complement of the genome, i.e. the set of expressed genes (proteins) in a given organism, at a given point in time, in a given situation. Proteomics deals with the qualitative and quantitative analysis and comparison of proteomes under different conditions to further unravel biological processes. Proteomics experiments typically separate proteins in biological samples using techniques such as two-dimensional gel electrophoresis (2-DE) or liquid chromatography (LC), followed by high resolution mass spectrometry (MS) analysis. These experiments produce up to thousands of mass spectra per day that must be analysed on efficient informatics platforms in order to extract pertinent biological knowledge. Analytical bioinformatics provides imaging tools to analyse the results of the protein separation step (2-DE or LC), powerful identification and characterisation software from MS data, as well as databases containing annotated data resulting from the analysis of experimental data.

The Swiss Institute of Bioinformatics (SIB) coordinates the activities of currently eighteen bioinformatics groups throughout Switzerland in association with seven universities and research institutes, carrying out services, education and research in many areas of bioinformatics. At the Proteome Informatics Group (PIG) of SIB and its sister company Geneva Bioinformatics (GeneBio) SA, in collaboration with the Biomedical Proteomics Research Group (BPRG) at Geneva University, we have been developing several platforms for high-confidence analysis of proteomics data. Melanie is a software architecture for image analysis that served as the basis for two software packages. One is ImageMaster for 2-DE image analysis, the other one is MSight, a comprehensive package for the analysis of MS data obtained after protein or peptide separation, such as LC-MS or electrophoresis-MS. The software allows for differential analysis as well as for quality control of experimental design, data exploration and linking to identification results. Phenyx provides efficient identification of proteins from MS-MS data. A new platform, swissPIT, is designed for the analysis of MS-MS data using several identification engines (currently Phenyx and X!Tandem) and two characterization software (Popitam and InsPecT), giving access to automated protein identification and characterization through a unique Web portal. The platform runs on the SwissBioGrid environment for high-throughput usage. The various tools offer tight integration among themselves and with external data sources.

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January 23, 2007 — Joint ICM UW/LCB UU Seminar

The joint ICM LCB bioinformatics seminar will be held on 23.01.2007.
Prof. Piotr Zielenkiewicz, from University of Warsaw, will deliver the lecture :
“Modules in protein-protein interaction networks.”

Doc. Dr. David Ardell, from LCB, Uppsala University, will deliver the lecture :
“Structure and Evolution of Noncoding RNA.”

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January 17, 2007 — Joint ICM UW/LCB UU Seminar

We would like to inform you that ICM Bioinformatics Centre and The Linnaeus Centre for Bioinformatics Joint Seminars are back. Every seminar will be broadcasted over internet. We have implemented some new technologies in order to improve quality of the broadcast. All the persons that are interested in taking part in the seminars, are kindly requested to contact Dr. Witold Rudnicki. Seminars will be held on Tuesdays (at least one seminar per month), 15:00 at the ICM new conference room (Faculty of Geology Building, room 3075). During the first seminar that will be held on January 23, 2007:

  • Doc Dr. David Ardell (The Linnaeus Centre for Bioinformatics) will present his talk on: “Structure and Evolution of Noncoding RNA”.
  • Prof. Piotr Zielenkiewicz (University of Warsaw) will talk about “Modules in protein-protein interaction networks”.
  • Details can be accessed here. W E L C O M E !

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January 17, 2007 — New servers at the Centre

A cluster devoted exclusively to the needs of the bioinformatics community has been acquired by ICM. The initial configuration consists of four servers with four dual core Opterons on board, 16 GB of memory and 1.2 TB of hard disks each. The system is being configured and will be available to the users of the HPC Centre in February. Later during the year the access through the WWW interface and grid technology will be offered.

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January 2007

The European Molecular Biology Organization has singled out 10 talented life scientists to receive EMBO Installation Grant. We are happy to inform that Dr. Krzysztof Ginalski from our Centre is among these awarded scientists. The grants will help the scientists to relocate and set up their research groups. Each scientist will receive 50,000 euro annually for three to five years, giving them the extra resources they need to get their groups started and establish themselves in the European scientific community. More information on the grant itself can be accessed here. More information about EMBO can be found here.

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December 1, 2006

We are proud to announce that Dr. Joanna Trylska received prestigious research grant from Fogarty International Research Collaboration Award (FIRCA) National Institutes of Health, Fogarty Intl. Center, USA. The research will be focused on: “Association of elongation factors and antibiotics with the ribosome.”

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June 2006

Dr. Joanna Trylska received research grant from Polish Ministry of Science and Higher Education. Her research topic is: “Development and optimisation of mesoscopic methods for modelling of nanomolecular systems and their application to ribosome modelling.”

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April 24th, 2006 — Joint ICM UW/ LCB UU Seminar

The joint ICM LCB bioinformatics seminar will be held on April 24th, 2006.
Urszula Mazurek, Agnieszka Witkowska, from Department of Molecular Biology and Medical Genetics Medical University of Silesia in Katowice, will deliver the lecture :
“Analysis of gene expression connected with immortalisation in neoplasm cells – as a challenge in asking questions and looking for answers”

Jacek Koronacki, from Institute of Computer Science, Polish Academy of Sciences, will deliver the lecture :
“On unsupervised and supervised classification of high-dimensional data”

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April 10th, 2006 — Joint ICM UW/ LCB UU Seminar

The joint ICM LCB bioinformatics seminar will be held on April 10th, 2006.
Professor Claes Wadelius, from Rudbeck Laboratory, Uppsala University, will deliver the lecture :
“Genomic studies of transcription regulation using ChIP-chip and other novel methods”

Adam Ameur, from The Linnaeus Centre for Bioinformatics, Uppsala University, will deliver the lecture :
“Base pair localization of in vivo transcription factor binding from low resolution ChIP-chip data”

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March 20th, 2006 — Joint ICM UW/ LCB UU Seminar

The joint ICM LCB bioinformatics seminar will be held on March 20th, 2006.
Professor Piotr Stepien, from Institute of Genetics and Biotechnology, Warsaw University, will deliver the lecture :
“Modelling of the 3′-end of RNA”

Dr Krzysztof Ginalski, from ICM Warsaw University, will deliver the lecture :
“Consensus approaches to protein structure prediction”

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