- BBClist - maillist.psb.ugent.be

Call for participation PRIB 2011
by Thomas Abeel 18 Aug '11

18 Aug '11

6th IAPR Conference on Pattern Recognition in Bioinformatics November 2-4 2011, Delft, The Netherlands Website: http://prib2011.tudelft.nl/ Early Bird Registration August 24, 2011 Registration October 12, 2011 We invite you all to join the Pattern Recognition in Bioinformatics conference series. It aims to bring together researchers, practitioners and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology and systems biology. For the 2011 program we carefully selected an interesting mix of topics, with 5 great keynote speakers and (almost) 30 presenters from the community. The preliminary program and the registration can be found on the webpage: http://prib2011.tudelft.nl

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Mini-symposium Ghent - September 28: Bioinformatics: tools in research
by Maté Ongenaert 01 Aug '11

01 Aug '11

Bioinformatics: tools in research WOUD, a research group of the Ghent University Association organises a mini-symposium: Bioinformatics: tools in research. During this meeting, researchers not trained in bioinformatics should get an idea how bioinformatics can be a tool for their research. More details and registration on http://mellfire.ugent.be/public/woud The program is included below. September 28th 2011, Congress Center Het Pand, Gent, Belgium Program 13:30 Welcome reception 14:00 Introduction: WOUD and bioinformatics (prof. dr. Bruno Verhasselt, prof. dr. Jo Vandesompele) 14:05 Investigating the human gut flora using metagenomics (prof. dr. Jeroen Raes, VUB) 14:25 The post-genomic era: epigenetic sequencing applications and data integration (dr. ir. Maté Ongenaert, CMGG - UGent) 14:45 Visualisation of large datasets (drs. Geert Trooskens, BIOBIX - UGent) 15:00 Race against the sequencing machine: processing of raw DNA sequence data at the Genomics Core (dr. Luc Dehaspe, Genomics Core - UZLeuven) 15:20 Coffee break 15:45 Integrative transcriptomics to study non-coding RNA functions (dr. ir. Pieter Mestdagh, CMGG - UGent) 16:05 Large scale machine learning challenges for systems biology (dr. Yvan Saeys, VIB - UGent) 16:25 Pathway analysis: example from the bench (drs. Jolien Vermeire, HIVlab, Department of Clinical Chemistry, Microbiology and Immunology - UGent) 16:40 Proteomics and cross-omics integration (prof. dr. Lennart Maertens (VIB - UGent) 17:00 Closure

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POSTDOC: COMPUTATIONAL CANCER BIOLOGY
by Lodewyk Wessels 04 Jul '11

04 Jul '11

POSTDOC: COMPUTATIONAL CANCER BIOLOGY TAILORING TREATMENT FOR COLORECTAL CANCER THROUGH MOLECULAR REDEFINITION OF THE DISEASE VIA INTEGRATED IN SILICO AND IN VITRO ANALYSES OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, in order to identify and validate new activated pathways and specific drug targets for defined CRC patient populations, and to identify molecular markers that can be used to select patients most likely to benefit from drugs active against these targets. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam) PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling and extensive clinical annotation data from a collection of 400 CRC tumors to identify and prioritize pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group (Wessels lab.) provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. The candidate will also spend time at Agendia BV, Amsterdam, The Netherlands. Frequent visits to AstraZeneca Oncology, Alderley Park, UK will be undertaken. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. Knowledge of biology, particularly signaling pathways and cancer is a strong recommendation. EMPLOYMENT CONDITIONS The temporary employment will be for a period of two years. The gross monthly salary for a Postdoc will range from €3140,- to €3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of ‘Best Employers’ in 2010 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. http://bioinformatics.nki.nl CLOSING DATE 1 September 2011

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Vacancy: bioinformatics programmer at Applied Maths NV
by Koen Janssens 01 Jul '11

01 Jul '11

Dear all, Applied Maths is currently looking for a BIOINFORMATICS PROGRAMMER for its office in Sint-Martens-Latem (Ghent area). More information about the job description can be found in attachment. Please feel free to forward this to any interested party. Kind regards, Koen Janssens ____________________________ Koen Janssens Applications Manager Applied Maths NV Keistraat 120 | B-9830 Sint-Martens-Latem | Belgium Tel: +32 9 22 22 100 | Fax: +32 9 22 22 102 www.applied-maths.com

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postdoc bioinformatics at PSB-VIB/UGent
by Stefanie De Bodt 30 Jun '11

30 Jun '11

Dear all, We have a job opening for a postdoctoral scientist in Bioinformatics who will be involved in the integrative analysis of RNA-seq data and growth phenotype data. More detailed information can be found in attach. Please forward to any interested colleagues. Kind regards, Stefanie De Bodt (our apologies for multiple posting) -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ==================================================================

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2 Ph.D. student positions in Systems Biology for Tissue Engineering
by Liesbet Geris 30 Jun '11

30 Jun '11

Two PhD student positions in Systems Biology for Tissue Engineering (4 years, fully funded by ERC starting grant) are available immediately in the group of Prof. Liesbet Geris at the University of Liège, Belgium. Work in our group focuses computational modeling for bone tissue engineering. The PhD students will work on the development and evaluation of computation models of the in vitro bone formation process in order to enhance robustness and predictability of the in vitro culture process and the resulting in vivo bone formation. The models range from mechanistic (differential equations) to more phenomenological (Boolean networks, empirical modeling). Dedicated experimental work will be executed at the University of Leuven (Belgium). Candidates should have a strong background in biomedical engineering, systems biology and/or computational modeling. The work will be carried out in a interdisciplinary research environment. Strong communication skills (English) and an open attitude towards other scientific disciplines are necessary. Applications (including a CV and contact details of 3 referees) should be sent by e-mail to: Prof. Dr. Lies Geris Biomechanics Research Unit, U.Liège Chemin des Chevreuils 1 - BAT 52/3|4000 Liège 1|Belgium tel.: +32 4 3669587 | fax : +32 4 3669505 e-mail (1): liesbet.geris(a)ulg.ac.be e-mail (2): liesbet.geris(a)mech.kuleuven.be Additional information : http://www.ltas.ulg.ac.be/cmsms/uploads/File/RESEARCH%20biomedical_GERIS.pdf <http://www.kuleuven.be/prometheus> http://www.kuleuven.be/prometheus http://orbi.ulg.ac.be/browse?type=author <http://orbi.ulg.ac.be/browse?type=author&value=Geris%2C+Liesbet+p084700> &value=Geris%2C+Liesbet+p084700 _______________________________________________ Prof. Liesbet Geris, PhD Biomechanics Research Unit, U.Liège Chemin des Chevreuils 1 - BAT 52/3|4000 Liège 1|Belgium tel.: +32 4 3669587 fax : +32 4 3669505 e-mail (1): liesbet.geris(a)ulg.ac.be e-mail (2): liesbet.geris(a)mech.kuleuven.be <http://www.kuleuven.be/prometheus> http://www.kuleuven.be/prometheus _______________________________________________

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job opening
by Tobias Verbeke 27 Jun '11

27 Jun '11

L.S. OpenAnalytics is an international company based in Belgium that provides data analysis services and products across geographies and industrial sectors. We currently have an open position for a molecular or computational biologist with strong experience in R / BioConductor. More detailed information on the position is available from http://www.openanalytics.eu/jobs Kind regards, Tobias Verbeke -- Tobias Verbeke Manager OpenAnalytics BVBA Kortestraat 30A 2220 Heist-op-den-Berg Belgium E tobias.verbeke(a)openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

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Postdoc or Ph.D. student in Computational Systems Biology (Network analysis of diseases)
by Antony Le Béchec 24 Jun '11

24 Jun '11

Dear all, The Computational Biology Research Unit of the Luxembourg Centre for Systems Biomedicine in collaboration with the Systems Biology Institute (Tokyo, Japan) has the following vacancy Postdoc or Ph.D. student in Computational Systems Biology (Network analysis of diseases) • Fixed-term contract 1 year, 40h/week, may be extended up to 5 years. • Employee status (start date: as soon as possible) • Research will be carried out in Luxembourg and Tokyo Area: Multidisciplinary project in systems biology approaches to model diseases. Tasks/Mission: • Modeling and analysis of biological networks (e.g. gene regulatory networks, metabolic networks, protein-protein interaction networks) will be used to elucidate disease mechanism and development. The goal of this project is the study of different aspects of these networks, including topology, dynamics, and perturbations by combining concepts from different areas of mathematics, such as graph, information and game theories, which then allows a better prediction of how some of major diseases (in particular neurodegenerative diseases, such as Parkinson’s and Alzheimer’s diseases) can be prevented or treated. Collaboration with different medical and clinical research groups will be essential. Profile: • A Ph.D. or Master in Bioinformatics, Computer Science, Biology or a related discipline • Strong computational skills • High interest in researchers with prior experience in mathematical modelling of biological systems especially in network construction and statistical analysis • Excellent working knowledge in English. . Offer: • Opportunity to participate in the development of a newly created LCSB in collaboration with SBI Japan • An exciting international environment • A competitive salary For further information, please contact: Prof. Dr. Antonio del Sol E-mail: antonio.delsol(a)uni.lu Prof. Dr. Hiroaki Kitano E-mail: kitano(a)sbi.jp Applications should contain the following documents: • A detailed curriculum vitae • cover letter mentioning the reference number • list of publications • description of past research experience and future interests • name and addresses of three referees All applications should be sent preferably in electronic version until August 1st , 2011 to the following address: Luxembourg Centre for Systems Biomedicine Universite' du Luxembourg Campus Limpertsberg 162a Rue de la Faiencerie L-1511 Luxembourg Tel: +352-466644-6982 Email: antonio.delsol(a)uni.lu Best regards, Antony Le Béchec -- Dr. Antony Le Béchec University of Luxembourg FSTC - Faculty of Sciences, Technology and communication Campus Limpertsberg 162a, avenue de la Faïencerie L-1511 Luxembourg Tel: (+352) 46 66 44 6581 Email: antony.lebechec(a)uni.lu<mailto:antony.lebechec@uni.lu> www.uni.lu

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PhD studentship or postdoctoral research assistant in Luxembourg
by Antony Le Béchec 23 Jun '11

23 Jun '11

Dear all, Luxembourg Centre for Systems Biomedicine in collaboration with Center for Neurogenomics in Amsterdam is currently seeking a postdoctoral research assistant or PhD student to work in the group of prof. Antonio del Sol. The aim of the project is to investigate novel statistical and data mining techniques to analyze high-throughput high-content functional image data of neuronal proteins implicated in Parkinson’s disease (PD). Human SH-SY5Y neuroblastoma cells are used as an in vitro cell model to study the effects of candidate PD susceptibility genes on dopamine neuron differentiation and viability. Successful candidate will be responsible for the development of scientific methodologies and computational solutions for the interpretation of high-throughput imaging data. Experience in network analysis will be an important asset. QUALIFICATIONS • PhD (or Msc) in bioinformatics, computational biology, computer sciences, statistics or molecular biology; • Excellent verbal and written communication skills; • Experience in the large-scale data analysis and software programming skills; • Experience with machine-learning, feature-selection techniques and network analysis is a definite asset; • Good background in statistics; • Experience with Unix/Linux environment The position is for 3 years for postdoc or 4 years for PhD student and is funded by an FNR Luxembourg grant. The successful candidate will actively participate in grant preparation process. For further information, please contact: prof. dr. Antonio del Sol E-mail: antonio.delsol(a)uni.lu Best regards, Antony Le Béchec -- Dr. Antony Le Béchec University of Luxembourg FSTC - Faculty of Sciences, Technology and communication Campus Limpertsberg 162a, avenue de la Faïencerie L-1511 Luxembourg Tel: (+352) 46 66 44 6581 Email: antony.lebechec(a)uni.lu<mailto:antony.lebechec@uni.lu> www.uni.lu

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Postdoc or Ph.D. position for a position in Computational Systems Biology
by Antony Le Béchec 23 Jun '11

23 Jun '11

Dear all, The Computational Biology Research Unit of the Luxembourg Centre for Systems Biomedicine in collaboration with the Institute for Systems Biology (Seattle, United States) is looking for a postdoc or a Ph.D. candidate in the field of in Computational Systems Biology. The goal is to model and analyze various types of biological networks (e.g. gene regulatory networks, metabolic networks, protein-protein interaction networks) in order to explain mechanisms involved in metastasis of cancer. For this purpose the candidate will explore different aspects of these networks, including topology, dynamics, and perturbations by combining concepts from areas of mathematics including graph theory, information theory and game theory. Collaboration with experimental research group in ISB, Seattle, is essential and the candidate will be given a unique possibility to complement the computational skills with biological knowledge and wet lab practice. Therefore candidates with strong commitment for exploring a fascinating research area and obtaining valuable experience are especially encouraged to contact us for further details. Profile: • Ph.D. or Master in Bioinformatics, Computer Science, Biology or a related discipline • Strong computational skills • Excellent working knowledge in English. For further information, please contact: prof. dr. Antonio del Sol E-mail: antonio.delsol(a)uni.lu Best regards, Antony Le Béchec -- Dr. Antony Le Béchec University of Luxembourg FSTC - Faculty of Sciences, Technology and communication Campus Limpertsberg 162a, avenue de la Faïencerie L-1511 Luxembourg Tel: (+352) 46 66 44 6581 Email: antony.lebechec(a)uni.lu<mailto:antony.lebechec@uni.lu> www.uni.lu

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