December 2007 - BBClist - maillist.psb.ugent.be

PhD studentship in structural bioinformatics
by Tom Lenaerts 21 Dec '07

21 Dec '07

One PhD studentship in Structural Bioinformatics (1 year) Project: Structural analysis of mutations and polymorphisms in human cancers and the effect of these changes on the signaling properties of proteins. We offer a PhD position in the context of a collaborative project in the Brussels region. The project focusses on the relationship between single-nucleotide polymorphisms and protein structure and function in cancer. The aim is to predict the effects that single-nucleotide polymorphisms (SNPs) and haplotypes have on both the expression levels and structural properties of cancer-related proteins. The best candidates will have a strong background in computational chemistry or structural bioinformatics. Experience with SNP arrays and/or data mining is a serious plus. For further information contact Joost Schymkowitz (joost.schymkowitz(a)vub.ac.be) or Tom Lenaerts (tlenaert(a)vub.ac.be) SWITCH, VIB Vrije Universiteit Brussel http://switch.vub.ac.be/

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postdoc position: computational chemistry/structural bioinformatics
by Tom Lenaerts 21 Dec '07

21 Dec '07

Postdoc computational chemistry/structural bioinformatics (2 yrs) Project: Parametrisation of an all-atom force field with non-natural amino acids The laboratory has significant expertise in the development of empirical force fields predicting mutational changes in the free energy of folding or binding of proteins. The aim of the current project is to extend the capabilities of the force field towards non- natural amino acids. This work involves obtaining good estimates of atomic parameters such as volumes, charges, hydrophobicity and compound properties such as backbone and sidechain entropy, from datamining and first principle simulations. You will need a good understanding of the physicochemistry of organic compounds and their interaction with proteins. The candidate will have a strong background in computational chemistry or structural bioinformatics and experience with c++ programming will be considered a serious plus. For more information contact Prof. Joost Schymkowitz (joost.schymkowitz(a)vub.ac.be)

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Postdoc position: Integrative cancer bioinformatics
by Lodewyk Wessels 20 Dec '07

20 Dec '07

======================================= Integrative cancer bioinformatics: Postdoc position. ======================================= About the position: ============== Basic cancer research through the development of appropriate model systems such as mice, rats and cell lines is a field of special interest within the Netherlands Cancer Institute. Ultimately, the goal is to combine this information with human tumor data in order to deliver personalised treatment to patients. Recent developments in high-throughput genomic technologies have made it possible to significantly further this research by unraveling the role of large numbers of genes in important cellular processes. These technologies include, amongst other, high-throughput high content screening (HTHCS) and insertional mutagenesis screens. In HTHCS, a large RNAi library in combination with cell-based assays, fluorescence-based reagents, automated fluorescence microscopy and image analysis are employed to study complex cellular phenotypes. In HTHCS one can study the consequence of inactivation of large numbers of individual genes, in a collection of individual cells, measured by multiple cellular parameters. In retroviral insertional mutagenesis, retroviruses integrate in the genome of (genetically manipulated) mice, causing tumors by either activating oncogenes of de-activating tumor suppressors. By studying the genomic distribution patterns of the viral integration sites and the gene expression of associated tumors, valuable information about genes and pathways involved in tumorigenesis can be obtained. Each of these technologies generates large, heterogeneous, complex datasets. Currently, many of these datasets are simply employed to extract an interesting new hit (e.g. a putative new oncogene) from a screen. By performing an integrative analysis of the data we want to work towards developing a 'systems level' understanding of the pathways and processes involved in tumorigenesis. The computational challenges that need to be addressed include the development of: 1) integrative models for 'experiment specific' data and 'experiment independent' data to identify pathways and interactions between pathways relevant to tumor development; 2) approaches to associate (perturbations to) the identified pathways to phenotypic outcomes; 3) cross-species comparisons to translate findings from model systems (cell lines and mouse models) to the human system, and integration of the findings from model systems with data from human tumors to predict outcome and therapy response. About the candidate - requirements: =========================== Ph.D in a relevant computational discipline such as Computer Science, Statistics, Engineering, Applied Mathematics or Physics with experience in Bioinformatics and/or Machine learning. Applicants that hold a Ph.D in the life sciences, but with substantial experience in bioinformatics are also encouraged to apply. The researcher appointed in this position will function as a liaison between the Bioinformatics group and the research groups within the Netherlands Cancer Institute performing the screens. About the employer: =============== The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) This group closely collaborates with the groups of Drs Rene Bernards, Roderick Beijerbergen, Anton Berns, Maarten van Lohuizen and Laura van 't Veer on the topics listed above. The candidate will also be closely interacting with these groups on the relevant topics. Research in the Netherlands Cancer Institute covers all major areas of cancer research, with special emphasis on mouse models, mouse (reverse) genetics, cell biology, immunology, translational research requiring close collaboration between clinical and basic scientists and epidemiology and psychosocial cancer research. Employment conditions: ================= The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience. Want to find out more? ================= For further information about the position please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl How to apply: ========== Applications for this position should include a Curriculum Vita with the names and contact information of two professional references that can be contacted for further information. Send applications to: The Personnel Department The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital Plesmanlaan 121 1066 CX Amsterdam The Netherlands, or via email to work(a)nki.nl. L.F.A.Wessels, Ph.D Bioinformatics and Statistics The Netherlands Cancer Institute Plesmanlaan 121, 1066 CX Amsterdam The Netherlands Tel: +31 (0)20 5127987 Fax: +31 (0)20 6691383 Mobile: +31 (0)634485714 http://bioinformatics.nki.nl/

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Research pogrammer position
by Lodewyk Wessels 20 Dec '07

20 Dec '07

=========================================================== High-throughput, high-content support platform: research programmer position. =========================================================== About the position: ============== The recent developments in functional genomic technologies have made it possible to unravel the role of large numbers of genes in important cellular processes. A powerful new technology is based on RNA interference (RNAi) by which the expression of individual genes can be silenced through small interfering RNAs (siRNAs). The combination of RNAi with cell-based assays in high- throughput screening (HTS) will yield valuable new insights for the detection and treatment of disease. Several platforms have been developed to systematically examine the consequence of inactivation of individual genes in cell-based assays. In order to study more complex cellular phenotypes, High-Content Screening (HCS) was introduced. HCS defines the role of targets in cellular processes by combining fluorescence-based reagents, automated fluorescence microscopy and image analysis to automatically extract temporal and spatial information about multiple parameters within single cells. By combining HCS and HTS, it is now possible to study the consequence of inactivation of large numbers of individual genes, in large numbers of individual cells, measured by multiple cellular parameters. The implementation of HCS in HTS generates a wealth of data that will require a dedicated support platform. The challenges involved in this project include 1) efficient handling of the sheer volume of data (a relatively small screen already produces 150 000 images, each 1.4 Mb in size) and to do this across different locations; 2) processing of the images to extract the relevant parameters; 3) the integration of these parameters with other high-throughput data sources to extract new biological knowledge and 4) providing capabilities to enable users to effectively visualize and browse the database. It is essential that the platform include a flexible database or data warehouse infrastructure. The platform will provide web services, support for software development, and set software standards. The support platform will be developed based on the GRID and VL-e infrastructure as established by the Netherlands Bioinformatics Centre. To help build this support platform we are looking for a scientific programmer, who will participate in the design and implementation of the platform and the required software tools. About the candidate - Requirements: =========================== 1. HBO, Bachelor or Masters degree in either informatics or biology with a clear programming component; 2. Experience with dfatabases, webservices and workflow management systems, programming (C, Java, Python, Perl and/or Shell programming, Unix) and/or experience with bioinformatics / biostatistics software (R, Matlab) is preferred; 3. Good communication and interpersonal skills to facilitate collaboration with clinicians and biologists with very diverse scientific and statistical background. 4. Good command of English. About the employer: =============== The position is embedded within the groups of Dr Roderick Beijersbergen who is head of the NKI Robotics and Screening Center (NRSC) (http://www.screeninc.nl) and the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) These groups closely collaborate with the Central Microarray facility at the NKI-AvL, which has ample experience in constructing databases for expression data. Research in the Netherlands Cancer Institute covers all major areas of cancer research, with special emphasis on mouse models, mouse (reverse) genetics, cell biology, immunology, translational research requiring close collaboration between clinical and basic scientists and epidemiology and psychosocial cancer research. Employment conditions: ================= The employment conditions follow general employment rules as laid down in the CAO for hospitals. The salary will be determined depending on education and experience. Want to find out more? ================= For further information about the position please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl How to apply: ========== Applications for this position should include a Curriculum Vitae with the names and contact information of two professional references that can be contacted for further information. Send applications to: The Personnel Department The Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital Plesmanlaan 121 1066 CX Amsterdam The Netherlands, or via email to work(a)nki.nl.

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[Fwd: Postdoc in computational bioNMR in Utrecht]
by BEN 14 Dec '07

14 Dec '07

-------- Original Message -------- Subject: Postdoc in computational bioNMR in Utrecht Date: Fri, 14 Dec 2007 11:52:17 +0100 From: Alexandre M.J.J. Bonvin <a.m.j.j.bonvin(a)uu.nl> To: ben(a)vub.ac.be Please find below an advertisement for a post-doc position which I would like to advertise via the bbclist. Best regards Alexandre ----------------------------------------------------------------------- Dr. Alexandre M.J.J Bonvin, Associate Professor NMR, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands Phone: +31-30-2533859 Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl http://www.nmr.chem.uu.nl/~abonvin ----------------------------------------------------------------------- =================================== Post-doc in computational biomolecular NMR =================================== Description of the Faculty / Research group ---------------------------------------------------------- The new Faculty of Science consists of six departments: Biology, Pharmaceutical Sciences, Information and Computing Sciences, Physics and Astronomy, Mathematics and Chemistry. The Faculty is home to 3500 students and nearly 2000 staff and is internationally renowned for the quality of its research. The NMR Research Group (http://www.nmr.chem.uu.nl) headed by Prof. R. Boelens, is part of the Chemistry Department (http:// www.chem.uu.nl) and belongs to the Bijvoet Center for Biomolecular Research (http://www.bijvoet-center.nl) The research within the NMR group is focused on the structure determination of proteins and protein complexes by high-resolution NMR spectroscopy and bio- computational modelling. The group has strong research lines on protein-DNA and protein-protein complexes in transcription and DNA repair and modelling of bio-molecular complexes. The NMR Research group also belongs to the European NMR Research Infrastructures (www.eu-nmr.eu) providing experimental NMR access to European groups. We are searching for a researcher (post-doc) in computational biomolecular NMR. Job description --------------------- You will be part of a European team working toward the deployment and unification of the NMR computational infrastructure in system biology, a project funded under the 7th framework programme of the European Union (Contract no. 213010 – eNMR). NMR plays an important role in life sciences (bio-NMR), and structural biology in particular, at both European and international levels. The main objective of this project is to optimize and extend the use of the NMR Research Infrastructures of EU-NMR through the implementation of an e-Infrastructure in order to provide the European bio-NMR user community with a platform integrating and streamlining the computational approaches necessary for bio-NMR data analysis (e-NMR). The e-NMR infrastructure will be based on the Grid infrastructure. For this, you will work on the development of a uniformed and integrated e-NMR platform that will form the core of the e-NMR infrastructure. The work will be carried in close collaboration with our European partners. Qualifications ------------------- You should have a Ph.D. degree in chemistry, physics, bioinformatics, computational biology or a related field. You should possess a strong research background in the computational aspects of biomolecular NMR and structure calculations, experience with Linux and programming skills, and are expected to show initiative and be able to work independently. Terms of employment ------------------------------ We offer initially a position for two years with a possible extension by one year. Salary is dependent on qualifications and experience and ranges from €2740.- to €3597.- gross per month (salary scale 10). The salary is supplemented with a holiday bonus of 8% per year and a year-end bonus of 3% per year. We also offer a pension scheme. Employment conditions are according to the Collective Labour Agreement of Dutch Universities. Further details -------------------- For further information contact Dr. Alexandre M.J.J. Bonvin (Phone: +31-30-2533859 Fax: +31-30-2537623 Email: a.m.j.j.bonvin(a)uu.nl) How to apply ------------------ Your application, referring to vacancynumber 65720, including a CV with contact information of two referees, should be sent to Science.PenO(a)uu.nl or: Faculty of Science, Personnel department, PO Box 80010, 3508 TA Utrecht.

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Vacancy for 2 PhD positions at Bioinformatics and Evolutionary Genomics division (VIB/UGent)
by Klaas Vandepoele 10 Dec '07

10 Dec '07

Dear, currently, we have 2 PhD positions open. The Research Group Bioinformatics and Evolutionary Genomics of the Department of Plant Systems Biology at VIB/Ghent University is currently looking for * a PhD student in Bioinformatics to work on an Interuniversity Attraction Pole (IAP) Research Project entitled BioMaGNet (Bioinformatics and Modelling: from Genomes to Networks) * a PhD student in Bioinformatics to work on an Research Project focusing on the integration of sequence and expression data in plants For more information and full job descriptions, please visit: http://bioinformatics.psb.ugent.be/jobs best regards, Klaas Vandepoele -- ================================================================== Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.ugent.be Website: http://bioinformatics.psb.ugent.be/ ==================================================================

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nature biotech assistant editor position
by jeroen raes 07 Dec '07

07 Dec '07

there's worse places in the world than New York... cheers, jeroen -- Jeroen Raes, PhD EMBL - Computational Biology Unit (Bork group) Meyerhofstrasse 1, D-69117 Heidelberg, Germany Tel: +49 6221 387372 jeroen.raes(a)embl.de http://www.embl.de/~raes/ http://www-db.embl.de/jss/EmblGroupsHD/g_27.html

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[Fwd: Mathematics and Informatics in Evolution and Phylogeny]
by BEN 06 Dec '07

06 Dec '07

We were asked to diffuse this message. ---------------------------------------------------------------------------- BEN - Belgian EMBnet Node at the Brussels Free Universities Computing Centre Marc Colet - Guy Bottu - David Coornaert Tel. +32/2/6505146 | Address BEN ULB CP 257 Fax +32/2/6505124 | Boulevard du Triomphe email ben(a)vub.ac.be | B-1050 Bruxelles ---------------------------------------------------------------------------- -------- Original Message -------- Subject: Mathematics and Informatics in Evolution and Phylogeny Date: Thu, 6 Dec 2007 09:22:25 +0100 (CET) From: gascuel(a)lirmm.fr To: ben(a)vub.ac.be Mathematics and Informatics in Evolution and Phylogeny June 10-12, 2008 France, Montpellier area: Hameau de l'Etoile Conference web site http://www.lirmm.fr/MIEP08/ Theme ----- The subject is evolution, which is considered at different scales: sequences, genes, gene families, organelles, genomes, and species. The focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies. Recent years have witnessed rapid progress in this area, with models becoming more realistic, and complex, and with fast algorithms able to deal with the large datasets that are available today. Non-exhaustive list of topics: phylogenetics, evolutionary genetics and genomics, molecular evolution of pathogens and epidemiology, biodiversity, statistical modelling, algorithmics, and software development. The program will include short talks (typically 20 minutes) and plenty of time for discussions. If you are planning to attend, you have to register on this web site. As the number of attendees will be limited, we recommend registering quickly, and to submit a title and abstract if you are willing to talk. Poster sessions will be organized if we have too many propositions. This conference is a continuation of: * Mathematics of Evolution and Phylogeny (2003 and 2005) * Dumont D'Urville Workshop on Applied Evolutionary Bioinformatics (2007) * Phylogenetics programme at Isaac Newton Institute (2007) Scientific committee -------------------- Elisabeth Allman: University of Alaska, US. Vincent Berry: CNRS, FR. David Bryant: University of Auckland, NZ. Frantz Depaulis: CNRS, FR. Laurent Duret: CNRS, FR. Nicolas Galtier: CNRS, FR. Olivier Gascuel: CNRS, FR, chair. Mike Hendy: Massey University, NZ. Daniel Huson: University of Tübingen, DE. Vincent Moulton: University of East Anglia, UK. David Posada: Universidad de Vigo, ES. Allen Rodrigo: University of Auckland, NZ, co-chair. Noah Rosenberg: University of Michigan, US. Charles Semple: University of Canterbury, NZ. Mike Steel: University of Canterbury, NZ. Organizing committee -------------------- Céline Berger, Samuel Blanquart, Olivier Gascuel, Vincent Lefort (LIRMM). Location and Online Registration -------------------------------- The conference will be held in the Hameau de l'Etoile, a small village dedicated to seminars and conferences, which is located at about 30 km in the north of Montpellier (south of France). Buses will be arranged for transportation, the 10th in the morning and the 12th just after the workshop end. The conference is free. Full accommodation including breakfast, lunch and dinner will be from 130 euros to 190 euros, depending on the room type (single, double, dormitory), to be payed to the Hameau de l'Etoile. The number of participants is limited. Please register at: http://www.lirmm.fr/MIEP08/ -------------------------------------------------------------- SMBE meeting is June 5-8 at Barcelona (400 km from Montpellier --------------------------------------------------------------

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