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

EMBL Practical Bioinformatics Course Protein Sequence Analysis
by Wouter Van Gool 30 Nov '09

30 Nov '09

Hi All, I'd like to draw your attention to some nice bioinformatics course about protein sequence analysis organized at the EMBL, this next January. You can find more information and register online at: http://www.embl.de/training/courses_conferences/course/2010/EMP10-01/ Or read below for a short course summary. Best Regards, Wouter Van Gool EMPA2010 - Protein Sequence Analysis Practical Bioinformatics Course EMBL-Heidelberg Tuesday 19th - Friday 22nd January 2010 This 3.5 day practical bioinformatics course, aimed at wet-lab biologists with only limited experience, will focus on protein sequence analysis, and analysis/prediction of protein modular architecture. www.embl.de/courses/empa2010 The deadline for applications is Friday 4 December 2009, and there is an application fee of 250 euros (which also covers meals and accommodation). The course is aimed at wet-lab biologists who are looking to exploit bioinformatic tools in their work - setting the scene by introducing the biological concepts behind protein architecture modules and providing extensive hands-on application of the relevant bioinformatics tools with appropriate example proteins. The power - but also the limitations, which remain substantial - of the currently available software will be examined. People should feel free to get in touch with Aidan (budd(a)embl.de) if they've any questions about the course.

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(no subject)
by Bogaert, D. 27 Nov '09

27 Nov '09

Dear Madam/Dear Sir, Would you please be so kind to inform all your list members about this vacancy (see text below) at the University Medical Centre (UMC) Utrecht Kind regards, Debby Bogaert Vacancy: Postdoc Bio-informatics We are a microbiology and infectious diseases group in The Netherlands, investigating microbial flora in health and disease in relation to prevention of bacterial infections. We are looking for a postdoctoral fellow bioinformatics/-statistics who will help us to analyze complex metagenomic data in relation to epidemiological parameters. Besides the complex problem of interpreting phylogenetic data of microbiota, we find there are currently no generally accepted statistical methods available to analyze complex communities in relation to epidemiological determinants, especially not in multivariate ways. Our final goal is to model complex microbiota with the help of environmental and individual characteristics, with the ultimate goal to predict when disease will develop and to design preventive strategies. We are looking for someone with experience in the field of metagenomics, bio-informatics, or adjacent fields, who does not dislike statistics and epidemiology, is not afraid of developing new tools, is creative, efficient, independent, and likes to work in a multi-disciplinary team. The position is guaranteed for at least 3 years. The salary is depending on previous experience and according to the CAO for university medical centres (CAO-UMC: salary scale 10). If you are interested, please contact: Debby Bogaert d.bogaert(a)umcutrecht.nl <mailto:d.bogaert@umcutrecht.nl> . Tel. +31-88-7551754 D. Bogaert, MD, PhD UMC Utrecht-WKZ Department of Pediatric Immunology Lundlaan 6 (room KC.03.068.0) 3584 EA Utrecht, The Netherlands Phone: +31-88-7551754 E-mail: dbogaert(a)umcutrecht.nl ------------------------------------------------------------------------------ De informatie opgenomen in dit bericht kan vertrouwelijk zijn en is uitsluitend bestemd voor de geadresseerde. Indien u dit bericht onterecht ontvangt, wordt u verzocht de inhoud niet te gebruiken en de afzender direct te informeren door het bericht te retourneren. Het Universitair Medisch Centrum Utrecht is een publiekrechtelijke rechtspersoon in de zin van de W.H.W. (Wet Hoger Onderwijs en Wetenschappelijk Onderzoek) en staat geregistreerd bij de Kamer van Koophandel voor Midden-Nederland onder nr. 30244197. Denk s.v.p aan het milieu voor u deze e-mail afdrukt. ------------------------------------------------------------------------------ This message may contain confidential information and is intended exclusively for the addressee. If you receive this message unintentionally, please do not use the contents but notify the sender immediately by return e-mail. University Medical Center Utrecht is a legal person by public law and is registered at the Chamber of Commerce for Midden-Nederland under no. 30244197. Please consider the environment before printing this e-mail.

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NBIC PhD Course Algorithms for Biological Networks open for registration
by Celia van Gelder 23 Nov '09

23 Nov '09

Dear researcher, The third course of the NBIC PhD School is now open for registration: PhD-Course: Algorithms for Biological Networks Date: 11-15 January 2010 Location: Delft, the Netherlands Course Credits: 3 EC Course Coordinator: Dick de Ridder, TUD, Delft *Short course description* In this course, we will first give a brief overview of molecular biology, the advent of high-throughput measurement techniques and large databases containing biological knowledge, and the importance of networks to model all this. We will highlight a number of peculiar features of biological networks. Next, a number of basic network models (linear, Boolean, Bayesian) will be discussed, as well as methods of inferring these from observed measurement data. A number of alternative network models more suited for high-level simulation of cellular behavior will also be introduced. Building on the network inference methods, a number of ways of integrating various data sources and databases to refine biological networks will be discussed. Finally, we will give some examples of applications of graph mining algorithms (dense subgraph extraction, small recurring subgraph enumeration, graph alignment) to learn about biology. More information about the course can be found on the course website: http://inpc55.et.tudelft.nl/nbic/abn/ *Registration* You can register via the registration form on http://www.nbic.nl/education/nbic-phd-school/enrolment/. Please note: the course is free for PhD students working in a BioRange (including matching) or BioAssist project. Others can participate as well when paying a course fee (see Enrolment page). This course is part of the Education Programme of the NBIC PhD School. The PhD School is an initiative of NBIC together with a number of universities to organize high level education and training for PhD-students in bioinformatics. More information about the latest developments of the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl> -> Education -> NBIC PhD School). Best regards, Celia van Gelder Netherlands Bioinformatics Centre (NBIC) Dr. Celia van Gelder Projectleader Education NBIC +31 (0)24 3666120 (direct) +31 (0)24 36 19500 (office) -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Fwd: CNIO International PhD and Postdoctoral Programmes_2010 call
by Jacques van Helden 16 Nov '09

16 Nov '09

Begin forwarded message: From: "Training Cnio" <training(a)cnio.es> Date: 16 November 2009 16:42:09 CET To: <Jacques.Van.Helden(a)ulb.ac.be> Subject: CNIO International PhD and Postdoctoral Programmes_2010 call Dear Dr. VAN HELDEN , I would like to draw your attention to the 2010 calls for the International PhD and Postdoctoral Programmes at the Spanish National Cancer Research Centre (CNIO). We would greatly appreciate if you could forward the information about these exciting programmes to potential candidates. The CNIO offers excellent training and research opportunities in cutting edge basic and applied cancer research. The programmes are open to outstanding young graduates from all over the world who want to pursue ambitious research projects. The CNIO International Postdoctoral Programme offers up to 6 very competitively funded two-year postdoc positions to outstanding junior scientists. Applications are considered at regular intervals, this call closes on December 31st, 2009. The CNIO International PhD Programme each year supports 10 candidates for a 4-year PhD. We have one selection per year. The deadline for applications is March 15th, 2010. Our webpage provides further information on both programmes and the application procedure: - Postdoc Programme: www.cnio.es/postdoc To print a copy of the poster: http://www.cnio.es/es/cursos/descargas/postdoctorado/Poster_postdoc_2009.pdf - PhD Programme: www.cnio.es/phd To print a copy of the poster: http://www.cnio.es/es/cursos/descargas/doctorado/Poster_PhD_2010.pdf Please feel free to distribute this message on your local institute network and thank you very much in advance for advertising our programmes in your institution. Best regards, Mar Pérez, PhD Training Manager Fax: +34 912246980 E-mail: phd(a)cnio.es or postdoc(a)cnio.es Website: www.cnio.es/phd and www.cnio.es/postdoc In compliance with the Spanish Law on Personal Data Protection (“Ley Organica” 15/1999 of December 13), we inform you that your data, collected from databases and sources of public access, has been incorporated into an automated confidential file, duly registered with the Spanish Agency for Data Protection and owned by the Spanish National Cancer Research Centre (CNIO), for the communication of professional training activities, future events and of publications. You may exert your rights to oppose such treatment, as well as your rights to access, cancel or amend as acknowledged by the mentioned law on matters of protection of data of a personal nature by sending a request to the following address: unsubscribe(a)cnio.es **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.

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Dataflows in het Labo - Studiedag KVCV Sectie Analytische Chemie 08/12/2009
by Tony Houthaeve 13 Nov '09

13 Nov '09

Beste, Op dinsdag 8 december 2009 plant de Sectie Analytische Chemie van KVCV (www.kvcv.be) een studiedag met als thema ‘Dataflows in het labo’. Hoofddoel van de studiedag is problemen & oplossingen én de nieuwste trends rond alle mogelijke dataflows in het laboratorium aan te kaarten en te bespreken aan de hand van cases uit de praktijk en de recente producten van de leveranciers ter zake. Items als: upgraden LIMS & CDS, globale versus lokale oplossingen, interfacing van apparatuur, ELN & PDA & RFID, evolutie van de markt, kosten, auditeren van datasystemen, etc… wensen we tijdens deze dag aan bod te laten komen. De dag bestaat uit een combinatie van: - Plenaire voordrachten; waarin algemene thema’s worden gebracht alsook een aantal cases van gebruikers uit de praktijk. - Twee parallelle breakout-sessies; één specifiek rond LIMS en één rond de interfacing van alle apparatuur & datastromen. Daarnaast bieden wij leveranciers de mogelijkheid om hun producten voor te stellen (voordrachten, exhibitie, demo's). Alle info en het programma staat op http://analytische.kvcv.be/agenda.html Graag uw medewerking voor deelname en verspreiding aan de collega's binnen de labowereld, bv VIB voor wie dit een meerwaarde kan betekenen (bv BITS commitee, ...). Alvast bedankt & Met vriendelijke groeten, Mit freundliche Grüsse, Sincerely yours, Hi, On Tuesday 08 December 2009, the section Analytical Chemistry of the KVCV organizes, for the Benelux, a Symposium 'Dataflows in the lab' in Grobbendonk. Presentations feature: - Labsoftware (LIMS, ELN, CDS), PDA, RFID & barcode scanning, interfacing lab equipment, lab-KPI, evolutions & trends of dataflows in the labmarket, ... - cases & experiences brought by end-users & vendors With the collaboration of : Starlims, Thermo Fisher Scientific, LabVantage Solutions, Siemens, LabWare, Waters, Agilent Technologies, DatAction, LabFactor, Raak Lab Informatics, Dionex, Labwing, Atos Origin, IS-X, Agfa, VMW, FAVV, ... See for more information: http://analytische.kvcv.be/agenda.html for more information & http://events.linkedin.com/Dataflows-het-labo/pub/128457 We hope to meet you there. If not applicable, please do pass on this information to a colleague. Met vriendelijke groeten, Mit freundliche Grüsse, Sincerely yours, Dr. Ing. Tony Houthaeve BASF Antwerpen lid bestuur Sectie Analytische Chemie KVCV Ijsvogelstraat 80-82 B-2170 Merksem tel: (32)-3-290.82.44 Tony.Houthaeve(a)telenet.be http://www.linkedin.com/in/tonyhouthaeve

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BBC 2009 - Call for posters and participation
by Pierre Geurts 12 Nov '09

12 Nov '09

************** Call for Posters and Participation *************** Fifth Benelux Bioinformatics Conference December 14-15, 2009, Liège, Belgium ******************************************************************* http://www.montefiore.ulg.ac.be/services/stochastic/bbc09 CALL FOR POSTERS Abstract submission for oral presentation is now closed but participants are still cordially invited to submit an abstract for poster presentation before November 23. Submissions can be done using the form at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/ submission.php. CONFIRMED INVITED SPEAKERS Thomas Sauter Life Sciences Research Unit, Université du Luxembourg "Modeling and Analysis of Metabolic and Signaling Networks using Bottom-Up Approaches" M. Madan Babu MRC Laboratory of Molecular Biology, University of Cambridge "Intrinsically Unstructured Proteins: Regulation and Disease" Pierre Rouzé BioInformatics & Systems Biology, VIB Department of Plant Systems Biology, Ghent, Belgium "From protists to plants, fungi and animals : eukaryote genomes are not born equal" REGISTRATION Registration is now open: http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/registration.php The deadline for early registration is November 23. SPONSORS The conference is sponsored by the Netherlands Bioinformatics Center (NBIC), the Alma in Silico project (Interreg IV Program), PEPITe, Sciforma and KeyGene. It is organized within the framework of the Belgian Network BIOMAGNET (Bioinformatics and Modeling: from Genomes to Networks), funded by the Interuniversity Attraction Poles Programme, initiated by the Belgian State, Science Policy Office.

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Fwd: Announcing postdoc positions in MIT Computational Biology group
by Stein Aerts 08 Nov '09

08 Nov '09

Hi all, Several very interesting postdoc positions are available at MIT, in Manolis Kellis' group. Best, Stein Aerts Begin forwarded message: > From: Manolis Kellis <manoli(a)MIT.EDU> > Date: Sun 8 Nov 2009 15:04:27 GMT+01:00 > To: Stein Aerts <Stein.Aerts(a)med.kuleuven.be> > Subject: Announcing postdoc positions in MIT Computational Biology > group > Reply-To: "manoli(a)MIT.EDU" <manoli(a)MIT.EDU> > > > -------- > > Subject: Postdoctoral positions available in MIT Computational > Biology group > > The MIT Computational Biology group (compbio.mit.edu) is seeking > highly motivated postdocs to undertake exciting new projects in > computational and regulatory genomics. We seek applicants with a > strong background in machine learning, algorithm development, > statistical methods, and their applications to computational > biology, gene regulation, epigenomics, and integration of large- > scale biological datasets. > > Our group is part of the MIT Computer Science and Artificial > Intelligence Lab, and of the Broad Institute of MIT and Harvard, > leading to a truly interdisciplinary environment. We have numerous > ongoing collaborations with experimental and biological groups, and > are part of the NIH ENCODE, modENCODE, and Epigenome Roadmap > collaborative projects where our group plays a leadership role in > data analysis and integration. > > For more information about the group, please visit: http://compbio.mit.edu/ > > Applicants are sought for the following ongoing projects: > > (1) Integrative analysis of genomic and epigenomic datasets in the > human genome, in the context of the NIH Epigenome Roadmap and ENCODE > projects. Goal is to use many chromatin marks in multiple cell types > in order to discover and interpret chromatin states, understand > their biological roles, and their dynamics in differentiation and > disease (NIH RC1-HG005334, NIH U54-HG004570). > > (2) Integrative analysis of the Drosophila modENCODE project. Goal > is to systematically understand the functional elements encoded in > the fly genome, and the regulatory logic defining transcription > factor binding and chromatin domains, and guiding developmental > programs (NIH RC2-HG005639, NIH U54-HG004555). > > (3) Regulatory genomics in human and fly genomes. Goal is to > discover regulatory motifs, enhancers, and cis-regulatory modules in > the human and fly genomes, and develop predictive models of gene > regulation using comparative genomics and large-scale experimental > datasets (NIH R01-HG004037). > > (4) Role of non-coding RNAs in chromatin. Goal is to understand the > role of small and large non-coding RNAs in directing, establishing, > and maintaining chromatin modifications in human embryonic stem > cells and during differentiation and cancer (Collaborative work with > Ron Hart at Rutgers and John Rinn at HMS). > > (5) Additional projects are available in comparative genomics, > genome interpretation, microRNA regulation, phylogenomics, image > analysis, RNA structure, and applicants are welcome to define their > own projects within the context of ongoing activities in the group > (NSF 0644282, NIH U01-HG004264, NSF 0936234). > > For more information about open positions, please visit: > http://compbio.mit.edu/positions.html > or contact Prof. Manolis Kellis directly at <manoli(a)mit.edu>. Prof. Dr. Stein Aerts Laboratory of Computational Biology Center for Human Genetics University of Leuven Herestraat 49, P.O. Box 602 3000 Leuven, Belgium Tel +32 16 330132 Mobile +32 486 659003 http://med.kuleuven.be/lcb/

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VIB User Group Meeting
by Torik Ayoubi 06 Nov '09

06 Nov '09

Dear Listers, The VIB MicroArray Facility (MAF) is organizing a User Group Meeting, this time focusing on miRNA expression analysis. Other topics covered are: AGRONOMICS1, a new tiling array for Arabidopsis, DamID, an alternative for ChIP-chip, Breast cancer gene expression profiling, Toxicogenomics, nCounterR analysis system, and many more. Attendance is completely free but as space is limited you are required to register and attendance will be acknowledged on a "first come first served" principle. Check out the preliminary program below and at: www.microarrays.be You may register at: torik.ayoubi(a)vib.be, do not forget to state "registration" in the subject header. In the body of the email please give your - -Name -Affiliation Torik Ayoubi (PhD) Research Manager VIB MicroArray Facility, K.U. Leuven Herestraat 49 O&N 1, Post Box 816 3000 Leuven, Belgium email: <mailto:torik.ayoubi@vib.be> torik.ayoubi(a)vib.be tel: 0032-16347939 web site: http://www.microarrays.be/ <https://vibportal.vib.be/f5-w-68747470733a2f2f7765626d61696c2e6d61617374726 9636874756e69766572736974792e6e6c$$/owa/redir.aspx?C=79d0788ad2864e59b7182fa dcb4db57e&URL=http%3a%2f%2fwww.microarrays.be%2f> , http://www.vib.be/ <https://vibportal.vib.be/f5-w-68747470733a2f2f7765626d61696c2e6d61617374726 9636874756e69766572736974792e6e6c$$/owa/redir.aspx?C=79d0788ad2864e59b7182fa dcb4db57e&URL=http%3a%2f%2fwww.vib.be%2f> personal web site: http://www.biomedicalgenomics.org <https://vibportal.vib.be/f5-w-68747470733a2f2f7765626d61696c2e6d61617374726 9636874756e69766572736974792e6e6c$$/owa/redir.aspx?C=79d0788ad2864e59b7182fa dcb4db57e&URL=http%3a%2f%2fwww.biomedicalgenomics.org> 9.30-10.00 Registration 10.00-10.30 New developments at VIB MicroArray Facility; More, Better, Faster, Cheaper, Torik Ayoubi, VIB MAF 10.30-11.00 MicroRNAs: A comparison of different platforms, Hinrich Goehlmann, Johnson & Johnson, Beerse 11.00-11.15 MicroRNA data analysis, Rudy van Eijsden, VIB MAF 11.15-11.30 Microarray analysis of microRNA profiles in a mouse model of left ventricular hypertrophy, Peter Pokreisz, Department of Cardiovascular Diseases, KU Leuven and Vesalius Research Center, VIB. 11.30-11.45 MicroRNAs in heart progenitor cells, Stefania Crippa, Maurilio Sampaolesi, Stem cell Institute, K.U.Leuven 11.45-12.15 MicroRNA profiling and targets genes in normal and malignant B cells, Anke Van den Berg, Pathology & Medical Biology, University Medical Center Groningen 12.15-13.20 Lunch 13.20-13.40 Extracting knowledge from your microarray experiment, Joke Allemeersch, VIB MAF 13.40-14.00 AGRONOMICS1, a new tiling array for Arabidopsis transcriptome profiling, Pierre Hilson, Functional Genomics, VIB Department of Plant Systems Biology, Ghent University 14.00-14.20 High resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region, Jan De Rijck, Moleculaire Virologie en Gentherapie, K.U.Leuven 14.20-14.40 Prediction of lymph node involvement in breast cancer from primary tumor tissue using gene expression profiling, Ann Smeets, Multidisciplinary Breast Centre Leuven 14.40-15.10 Coffee 15.10-15.30 Toxicogenomics in an in vitro estrogenic screening context: added value to classical single endpoint estrogenicity screens , Caroline Vanparys, Laboratory of Ecophysiology, Biochemistry and Toxicology, University of Antwerp 15.30-15.50 Mapping gene regulatory networks in Drosophila, Stein Aerts, Laboratory of Computational Biology, Center for Human Genetics, KULeuven 15.50-16.10 nCounterR, multiplex transcript quantification using a molecular barcoding detection system, Frederik Coppens, VIB Department of Plant Systems Biology, Ghent University 16.10-16.25 End Remarks

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Invitation: Seminar Extreme Desktop Virtualization with VirtualStorm
by Axio Systems 05 Nov '09

05 Nov '09

Open this mail in your browser: http://tools.emailgarage.com/Pub/42gpCwAAAAA~/RadYa0BQJ0m2gT1mw5EFrA~~/Text… http://tools.emailgarage.com/Pub/42gpCwAAAAA~/SCcehdPcTEm_0KNcLramFA~~/Text… Invitation: Seminar Extreme Desktop Virtualization with VirtualStorm Dear , Axio Systems and partners DinamiQs and VMware invite you to a seminar about VirtualStorm: Extreme Desktop Virtualization! VirtualStorm is all about reducing management tasks to the absolute minimum. VirtualStorm is software you add to your dekstop virtualization software in order to: - reduce your entire IT environment requirements to an absolute minimum - reduce storage needs by 80 to 90% - save on all levels: hardware, licenses, bandwith, power, administration, support, maintenance... - lower desktop management costs Compared to a classic PC, the end user experience is the same with VirtualStorm. The end user can customize his own Windows desktop and all applications are fully installed and integrated. Ready to use with an improved user productivity! Agenda: 09h00: Welcome & registration 09h30: Our view on the future of VDI - Mr Gert Van der Jeugt - Axio Systems 09h45: Announcing VMware View 4 and the new PC over IP protocol - Mr Jan Tiri - VMware 10h15: View 4 & PCoIP demo - Mr Jan Tiri - VMware & Mr Wouter Coppens - Axio Systems 10h45: Coffee Break 11h00: Extreme Desktop Virtualization with VirtualStorm - Mr Mike Jansen - DinamiQs & Mr Wouter Coppens - Axio Systems 12h00: VirtualStorm reference case: SAP - Mr Jean Paul Beerens - SAP IT Infrastructure Services EMEA 12h15: Q&A 12h30: Networking lunch Date: November 24, 2009, 09h00 - 12h30 Location: Van der Valk hotel Brussels Airport, Culliganlaan 4b, B-1831 Diegem Don't miss this unique event and register now http://tools.emailgarage.com/Pub/42gpCwAAAAA~/k2xvl7lM7kq8qiiCx4JZzQ~~/Text… We are looking forward to meeting you there! If you do not want to receive any emails on the products and services of Axio Systems, you can unsubscribe here http://tools.emailgarage.com/Pub/42gpCwAAAAA~/7PmMiv80eke5Vp5YtMHSzA~~/Unsu…

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Post-doc / PhD position at Netherlands Metabolomics Center
by Alkema, W.B.L. (Wynand) 03 Nov '09

03 Nov '09

Dear colleagues, A 3-years post-doc position or 4-years PhD student position is available within the Netherlands Metabolomics Center, in a joint project between Schering-Plough, Leiden/Amsterdam Center for Drug Research (LACDR), TNO Zeist and Radboud University Medical Center Nijmegen. Please see the attachment for more details. Regards, Wynand Alkema <<project_description_NMC.pdf>> This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.

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