January 2009 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc, Amsterdam, NL
by Lodewyk Wessels 05 Aug '09

05 Aug '09

BIOINFORMATICS POSTDOC Topic: Pathway-based tumour characterisation by alignment against cell panels along multiple molecular dimensions. Research: Astra Zeneca Oncology has constructed large cell panels to serve as in vitro models for drug response. These cell panels have been extensively characterized by mutation analysis, mRNA expression, aCGH, response to a wide variety of drugs, micro-RNA expression and phosphoprotein characterization. In parallel, the same measurements are being performed on a collection of colorectal samples. In this project two aims are pursued. First, a comparative analysis will be performed between the cell line data and the tumor data to determine the multi-dimensional molecular states spanned by the cell lines and whether these states faithfully recapitulate the space spanned by a representative and clinically relevant selection of tumor samples. Guided by this mapping and by following a pathway-based approach, integrative modeling will be applied on the cell line panel data to construct models predictive of resistance. Job description: The successful candidate will be responsible for the bioinformatics analysis of the cell line and tissue data. More specifically, these tasks include 1) constructing a comprehensive gene list of the PI3K and ERK network; 2) Molecular characterisation of the colorectal cell panel and tumour samples through integrative analysis of the various data sources within the space spanned by the identified network genes and 3) Pathway-based alignment of cell panel to tumours to determine the extent to which the cell panel recapitulates the heterogeneity in the tissue set. Location: The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan to have regular meetings, and the postdoc will also spend time at both locations. Requirements: Candidates should fulfill the following criteria. - MSc or PhD in one of the following areas: bioinformatics, engineering, computer science, statistics, physics, biotechnology, or biology. - Knowledge of fundamental aspects of cancer biology, especially signalling pathways. - Knowledge of fundamental aspects of computer science (algorithms and data structures, programming languages). - Knowledge or experience of informatics. - Knowledge of statistics, artificial intelligence or bioinformatics is highly desirable. Conditions of Employment: The successful candidate will be employed by the Netherlands Cancer Institute. 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. Contact and Applications: Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922 or e-mail: Tim.French(a)AstraZeneca.com. Applicants should send a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Website: http://bioinformatics.nki.nl Closing date: 30 January 2009 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/ 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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Joint PhD position at CWI and NKI, Amsterdam
by Gunnar W. Klau 30 Jan '09

30 Jan '09

The National Centre for Mathematics and Computer Science (CWI) and the Netherlands Cancer Institute (NKI), both located in Amsterdam, The Netherlands, invite applications for a jointly advised PhD position on Subnetwork module construction for improved diagnostic classiﬁcation and subtyping CWI is the national research institute for mathematics and computer science in the Netherlands. CWI performs frontier research in mathematics and computer science and transfers new knowledge in these fields to society in general and trade and industry in particular. The newly established Life Sciences group develops algorithms, theory, and models, and performs simulations for a wide range of biological topics with a strong focus on systems biology. The Netherlands Cancer Institute is the only dedicated cancer center in the Netherlands and maintains an important role as a national and international center of scientific and clinical expertise, development and training. Research within the Netherlands Cancer Institute covers all major areas of cancer research, with a strong emphasis on translational research. The Bioinformatics and Statistics group closely collaborates with basic scientists and clinicians and conducts research on a wide range of topics, focusing on integrative bioinformatics. The opening is a research position within the field of bioinformatics/ computational biology and will be a joint appointment between the two institutes. The research will be carried out in close collaboration of the involved partners. The successful candidate will contribute to building better predictors of disease outcome based on functional interaction network modules, which are predictive of a speciﬁed phenotype, e.g., outcome in cancer. To this end, development of new algorithms to detect these modules given a complex interaction graph has to be combined with protocols for building predictive classiﬁers given the activation patterns of the retrieved modules. The ideal candidate has a background in bioinformatics, computer science, statistics, physics, or biology, strong algorithmic and/or machine learning skills, and experience with the analysis of high- throughput data. Applications consisting of motivation letter, Curriculum Vitae, a list of publications, and a list of references should be send by email before 15 March 2009 to Dr. G.W. Klau or Dr. L.F.A. Wessels, who can also supply further information about this position. Please see the website http://www.cwi.nl/en/node/961 for further details.

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Two postdoc vacancies for toxicogenomics bioinformatics at the National Institute for Public Health and the Environment (RIVM)
by Jeroen Pennings 23 Jan '09

23 Jan '09

Please feel free to forward this mail to suitable candidates or to bring them to our attention. Two postdoc vacancies for toxicogenomics bioinformatics at the National Institute for Public Health and the Environment (RIVM) Within the context of the Netherlands Toxicogenomics Centre (NTC), a multidisciplinary research effort will be executed. We aim to develop novel genomics-based methods for assessing human health risk associated with chemical exposures. The project is broken up in different work packages according to specific endpoints of toxicity (carcinogenesis, immune toxicity, reproductive toxicity, organ toxicity), and an overarching work package devoted to bioinformatics. The two postdocs will provide bioinformatics support for the analysis of transcriptomics data as well as emerging omics data (e.g. proteomics, metabolomics, SNPs, miRNA). Multi-platform experimental and literature data will be integrated to identify genes and pathways involved in toxicological mechanisms. This will be used to develop in silico systems biology models for toxicology prediction in research models appropriate for the other work packages. Systems toxicology models will be validated regarding translation to humans and applicability in regulatory decision making. We offer an exciting working environment in a fast developing scientific field. Experience with bioinformatics, and the ability to connect mathematical approaches with biology are prerequisites. The work place will be Bilthoven; affiliations will be with Maastricht University. The salary will be at the level 10 according to the Collective Employment Agreement of the Dutch Universities. For more general information, please visit http://www.toxicogenomics.nl. For more specific information contact: Dr. J. Pennings, 030-2742214, jeroen.pennings(a)rivm.nl Please send applications ultimately February 9, 2009, to: Prof. dr. H. van Loveren, RIVM PO Box 1 3720 BA Bilthoven the Netherlands ---------------------------------------------------------------------------------------------------- Jeroen Pennings National Institute for Public Health and the Environment (RIVM) Laboratory for Health Protection Research (GBO) P.O.Box 1, 3720 BA Bilthoven, The Netherlands T: +31 (0)30 - 274 2214 F: +31 (0)30 - 274 4446 E: Jeroen.Pennings(a)rivm.nl ---------------------------------------------------------------------------------------------------- Disclaimer RIVM

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L'Evolution aujourd'hui: à la croisée de la biologie et des sciences humaines
by Jacques van Helden 22 Jan '09

22 Jan '09

L'Académie Royale de Belgique organise un colloque de 3 jours sur le thème de l'Evolution. Attention, le nombre de places est restreint, si vous désirez y assister il vaudrait mieux ne pas traîner pour vous inscrire. Cordialement, Jacques van Helden Jacques van Helden <Jacques.van.Helden(a)ulb.ac.be> http://www.bigre.ulb.ac.be/Users/jvanheld/ Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) Laboratory of Genome and Network Bioinformatics Université Libre de Bruxelles.

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Vacancy Genomics Database Developer
by Roland Siezen 21 Jan '09

21 Jan '09

Dear all, We have a vacancy for a Genomics Database Developper which needs to be filled urgently. Interested candidates are invited to send in their CV, including names of referees. Please also kindly forward this email to your colleagues who are interested. many thanks Prof. Roland J. Siezen Bacterial Genomics Group CMBI 260, room 21 Radboud University NIjmegen Medical Centre / NCMLS PO Box 9101, 6500HB Nijmegen Tel: 31-24-3619559 Fax: 31-24-3619395 email: r.siezen(a)cmbi.ru.nl <mailto:r.siezen@ncmls.ru.nl> www.ncmls.ru.nl/cmbi <http://www.ncmls.ru.nl/cmbi>

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vacancy postdoc computational systems biology Amsterdam
by Hans van Beek 20 Jan '09

20 Jan '09

*Postdoc Position Computational Systems Biology 'Systems Bioinformatics: Computational Modelling Methods' f/m * * VU University Amsterdam, the Netherlands * *Research project * The goal of the project is to develop and implement computer methods for computational modelling of biological systems. This encompasses methods for computational model assembly, execution, analysis and parameter estimation. This means collaboration with several experimental groups which work among others on metabolism in micro-organisms, animals and humans, on plant biology, nutrition and disease processes such as cancer. We also interact with the mathematical modelling group of the Netherlands Institute for Systems Biology. In this way this project is part of the core activity in Dutch systems biology. The project focuses on developing and implementing computational methods generically useful for computational modelling of biological systems. This encompasses computational model assembly, modification, maintenance, execution, simulation, optimisation, parameter estimation etc. Parameter sensitivity spectrum analysis, ensemble simulation, model-based data analysis techniques, multiscale modelling, 'e-BioScience' approaches and data assimilation methods may be part of the project. Demonstration of the effectiveness of developed methods by application to modelling of some of the example biological systems is desirable. This Systems Bioinformatics project is funded by The Netherlands Consortium for Systems Biology (NCSB) and in total involves six Dutch bioinformatics centres. In addition, the Systems Bioinformatics group is part of the BioAssist programme of the Netherlands Bioinformatics Centre. The VU group coordinates the six centres involved in the Systems Bioinformatics project. The Postdoc plays an active role in coordination of the project with the bioinformatic and experimental partners. Further information: see website : http://www.vu.nl/nl/werken-bij-de-vu/vacatures/1-2008-00278.asp -- Hans van Beek ADDRESS : Section Medical Genomics Department of Clinical Genetics VU University Medical Centre Phone: +31 20 5987460 Contact details: Dr JHGM van Beek Mail address: van der Boechorststraat 7 1081 BT Amsterdam The Netherlands Visiting address: Faculty of Earth and Life Sciences (W&N building) De Boelelaan 1085 Amsterdam Room B-423 http://vumc.nl; http://ibivu.nl; http://home.hccnet.nl/jhgm.van.beek e-mail: hans.van.beek(a)falw.vu.nl secondary e-mail: hans.vanbeek(a)vumc.nl (checked infrequently) FOR YOUR INTEREST freely downloable scientific article on dynamics of energy conversion in the heart : Click http://home.hccnet.nl/jhgm.van.beek/prod02.htm#download and click on "Freely downloable article in American Journal of Physiology"

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The BBC mailing list
by BEN 08 Jan '09

08 Jan '09

Dear colleagues, Some of you will have received a wellcome message for the BBC mailing list. This is because each year we add the E-mail addresses of the attendants of the Benelux Bioinformatics Conference. The BBC list is hosted on the Mailman server of the Belgian Biodiversity Facility (http://www.biodiversity.be) and is moderated by the staff of the Belgian EMBnet Node (http://www.be.embnet.org) You can send a mail to this this list (BBClist(a)biodiversity.be) if you want to announce a public lecture or a job opening, if you have a question or if you want to start a discussion about bioinformatics in the Benelux. Note that only members of the list are allowed to post and that, because of the moderation, the messages are delivered with some delay (usually te next day in the morning). You can unsubscribe or customize the way you receive messages at http://mailman.biodiversity.be/mailman/listinfo/bbclist (do use the password mentioned in the wellcome message). On the same site you can consult archived messages and interested friends of yours can subscribe. In case of problems you can send an Email to the moderator at ben(a)vub.ac.be. Enjoy biocomputing, Guy Bottu, Belgian EMBnet Node ---------------------------------------------------------------------------- BEN - Belgian EMBnet Node at the Brussels Free Universities Computing Centre Marc Colet - Guy Bottu 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 ----------------------------------------------------------------------------

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Januray 12: CINBIOS program
by Marianne Rooman 08 Jan '09

08 Jan '09

Dear all, Here is the final program (attached) of the CINBIOS meeting (centre de BioInformatique et BioModélisation, ULB), which will take place on Monday January 12 at the ULB. Everybody is wellcome ! All the best, Marianne Rooman -- --------------------------------------------------------- Marianne Rooman Unité de Bioinformatique génomique et structurale Service de BioSystèmes, BioModélisation & BioProcédés Université Libre de Bruxelles 50 avenue Roosevelt, CP 165/61, 1050 Bruxelles, Belgium Tel : 32-2-650 2067 Email: mrooman(a)ulb.ac.be ---------------------------------------------------------

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BioSapiens European School of Bioinformatics in Brussels
by Jacques van Helden 07 Jan '09

07 Jan '09

The Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) from the Université Libre de Bruxelles is organizing the 9th Biosapiens European School of Bioinformatics The course will run from January 26th to 30th 2009, at ULB (Brussels , Belgium). The goal of the school is to initiate biologists to the utilization of bioinformatics software tools. The course will cover the following topics: Mon Jan 26 Analysis tools and databases for protein sequences Teacher: Jennifer McDowall (InterPro team, EBI, UK). Tools: UniProt, InterPro, InterProScan. Tue Jan 27 Browsing and comparing genomes with EnsEMBL Teacher: Giulietta Spudich (EnsEMBL team, EBI, UK). Topics: browsing genomes, comparing multiple genomes, variation, functional elements, ... Tools: EnsEMBL genome browser, BLASTZ, PECAN, ENREDO, ORTHEUS, tBLAT, BLAST, ... Wed Jan 28 Analysis of regulatory sequences Teachers: Morgane Thomas-Chollier, Jean-Valéry Turatsinze, Olivier Sand, Matthieu Defrance (BiGRe team, ULB, Belgium) Topics: Detection of cis-acting elements in genomic sequences. Discovering motifs from promoters of co-regulated genes. Tools: Regulatory Sequence Analysis Tools Thu Jan 29 Protein structures Teacher: Oliver Redfern (CATH group, University College London, UK) Topics: accessing and handling protein structures from databases. Modelling protein structures. Tools: CATH Biomolecular networks and pathways Teacher: Sylvain Brohée (BiGRe team, ULB, Belgium) Topics: bioinformatics approaches to analyze biomolecular networks (protein interactions, regulatory networks, metabolic pathways). Tools: Network Analysis Tools, CytoScape, STRING. Fri Jan 30 Systems biology Teachers: Florian Reisinger (EBI, UK), Hedi Peterson (Quretec, Estonia) Topics: the ENFIN data integration, workflow management. Network reconstruction using gene expression, network visualisation with expression data, network combining and mining. Tools: EnCORE, KEGGAnim, GraphWeb. More information and registration form are available from the Web site: http://www.bigre.ulb.ac.be/9esb/ Registrations are restricted to a maximum of 40 participants. The deadline for applications is January 15th 2009. Contact: Olivier Sand <oly(a)bigre.ulb.ac.be> Myriam Loubriat <mloubria(a)ulb.ac.be> Please spread this information around.

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Protein folds in infectious and neurodegenerative diseases
by Marianne Rooman 06 Jan '09

06 Jan '09

Here attached is the announcement of the conference: Protein folds in infectious and neurodegenerative diseases which will take place in Aussois (Savoie), France, from 25-29 April 2009 ------------------------------------------------------------------------- Marianne Rooman Unité de BioInformatique génomique et structurale Service de BioSystèmes, BioModélisation & BioProcédés (3BIO) Université Libre de Bruxelles avenue Roosevelt 50, CP 165/61, 1050 Bruxelles, Belgium Tél: +32-2-650 2067 Email: mrooman(a)ulb.ac.be -------------------------------------------------------------------------

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