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ECCB'14 - workshop on the Dual Benefit of Bioinformatics Training - Call for abstracts
by Celia.vanGelder＠radboudumc.nl 27 Jun '14

27 Jun '14

Dear colleagues, Besides our work in research, many of us are also involved (in greater or lesser extent) in helping out / training / collaborating with our colleague researchers in the life sciences. We are organising a one-day workshop on on 7 September 2014, as a satellite event of ECCB'14 in Strasbourg, France, entitled: The Dual Benefit of Bioinformatics Training - Empowering Life Scientists and freeing more time for your research The workshop will be a forum to hear from the bioinformaticians themselves about their experiences and perspectives in "helping" life scientists in their bioinformatics tasks, being asked to collaborate or do the actual analysis for projects. How do they cope with this challenge (both time-wise and content-wise)? Are there best approaches, methodologies and even further existing materials and efforts that we can use, share and expand to tackle several of these topics and challenges, some of which are probably shared across many Institutes and groups worldwide? We invite you to share your experiences with us and encourage you to send in an abstract for a talk. We will be receiving abstracts for talk contributions until 18 July. You will find all the information about this workshop at: http://www.eccb14.org/program/workshops/dbbt. We are looking forward to meet several of you at the workshop and/or at ECCB! Best regards Celia van Gelder (NL) Also on behalf of: Patricia Palagi (CH) Vicky Schneider (UK) Michelle Brazas (CA) Dr. Celia W.G. van Gelder Projectleader Education NBIC/BioSB Coordinator Education CMBI Programme Manager Learning DTL tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl, www.dtls.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre PO Box 9101 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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Bioinformatician, Division of Clinical Infectiology, Faculty of Veterinary Medicine of Utrecht University
by Berend Snel 26 Jun '14

26 Jun '14

Bioinformatician (1,0 fte) *Functie* As a bioinformatician in the Division of Clinical Infectiology (KLIF) of the Department of Infectious Diseases & Immunology, your main job is applied bioinformatics. You work in a research team with molecular microbiologists and veterinarians with focus on the genomics of selected pathogens (in particular *Campylobacter *and Staphylococci) and on the analysis of complex microbiota (nose and gut) in relation to colonization and environmental cues (e.g. antimicrobial usage). Genomic approaches are considered to be applied in our routine diagnostic microbiology in close collaboration with the University Medical Center Utrecht. Your main task as bioinformatician will be to set up and implement existing tools and pipelines for analysis of high-throughput scale next-generation sequencing (NGS) of bacterial genomes with focus on bacterial environmental adaptation and dissemination of antibiotic resistance among bacterial populations. The NGS-based analysis includes phylogenetic reconstructions, estimations of mutation rates, detection of gene gain / loss and single nucleotide positions, gene annotation and the identification of mobile genetic elements, such as drug-resistant plasmids. Metagenomic and metatransciptomic analysis of the microbiota during colonization and environmental pressure requires computational analysis of sequence data to characterize ecological communities and identify the flow of resistance genes. You will assist in the design of sequencing experiments catered to the research projects, and in the development of new tools for mining, analyzing and visualizing sequence data. You will advise the team on the use of bioinformatics in running projects, and will be given the possibility to explore and develop own research ideas The position will be linked to the ‘Evolutionary Genomics and Integrative Bioinformatics’ group of Theoretical Biology & Bioinformatics. The Division has a close collaboration with the bioinformaticians of the department of Medical Microbiology of the UMC Utrecht. *Profiel* - A PhD in microbiology with a proven strong affinity for bioinformatics and hands-on programming experience. Alternatively, you hold a PhD in bioinformatics or computer science with proven experience in solving microbiological questions. - Experience with Linux command line and programming languages such as Python, Perl, C, or Java are required. - Experience with Next-Generation Sequencing data, preferably in the context of microbial genomics is recommended. - Experience with large-scale data management or data visualization is recommended. - You are a dedicated and flexible team player with excellent communicative skills to work with scientists from different domains. *Aanbod* We offer a position of 1.0 fte initially for a period of two years with possibilities for extension and potentially a permanent position. The gross salary depends on qualifications and experience and ranges between € 3.259,- and € 5.070 per month for a full time employment of 38 hours per week. The salary is supplemented with an annual holiday pay of 8% and an end-of-year bonus of 8.3% per year. Additionally, we offer a pension scheme, a collective health insurance and flexible employment conditions <http://www.uu.nl/en/informationfor/jobseekers/working-for-utrecht-universit…>. Conditions are based on the Collective Labor Agreement of the Dutch Universities. *Over de organisatie* Utrecht University <http://www.uu.nl/En/Pages/default.aspx> has great ambitions for its teaching quality and study success rates. This also applies to its clear research profiles which are centred around four themes: Sustainability, Life Sciences, Youth & Identity, and Institutions. Utrecht University plays a prominent role in our society and contributes to finding the answers to topical and future societal issues and is the only Dutch university and in fact the only university in continental Europe in the Times Higher Education Ranking of the Top 50 Social Sciences Universities 2012/2013. The Faculty of Veterinary Medicine of Utrecht University <http://www.uu.nl/faculty/veterinarymedicine/en/Pages/default.aspx> (FVM-UU) is the only Veterinary School in the Netherlands and belongs to the international top in education, research and patient care. FVM-UU is one of the few European veterinary schools accredited by the American and Canadian Veterinary Medical Associations. The faculty employs approximately 800 veterinarians, scientists and support staff and counts 1,500 students. Detailed information about the FVM-UU and Utrecht University is available via the website www.uu.nl *Aanvullende informatie* For more information about this position, please contact Dr Birgitta Duim: b.duim(a)uu.nl, telephone: +31 30 253 3603 or Prof Dr Jaap Wagenaar: j.wagenaar(a)uu.nl, telephone:+31 30 253 4376. Please do *NOT *send your application to these addresses. *Solliciteren* Please send your application accompanied by a letter of motivation, a curriculum vitae and the names of at least two persons to be contacted for professional reference. You can apply via http://www.peoplexs.com/Peoplexs22/CandidatesPortalNoLogin/Vacancy.cfm?Port… *Reageren uiterlijk* 13/07/2014

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NBIC/BioSB course RNAseq data analysis course (4th edition), 7-9 July 2014
by Celia.vanGelder＠radboudumc.nl 25 Jun '14

25 Jun '14

NBIC/BioSB RNA- seq data analysis course (4th edition) Date: 7-9 July, 2014 Location: Leiden, the Netherlands Course coordinators: Peter-Bram 't Hoen (LUMC), Jan Oosting (LUMC), Andrew Stubbs (ErasmusMC), Celia van Gelder (NBIC/BioSB, education(a)biosb.nl<mailto:education@biosb.nl> ) Course website: http://biosb.nl/education/course-portfolio/rna-seq/ . Registration: http://biosb.nl/education/enrollment-rna-seq-advanced-data-analysis-course-… More information: education(a)biosb.nl<mailto:education@biosb.nl> Course description BioSB/NBIC and partners LUMC and ErasmusMC are organizing a 3-day course on RNA-seq. This is an expert course for people with experience in NGS and a follow-up course on the general NBIC NGS data analysis course (coordinator Jeroen Laros, LUMC). The course will consist of seminars and hands-on command line, Galaxy and R practicals and will focus on data preprocessing, quality control, alignment, visualization and statistics for differential transcript expression. Examples will be taken from human and mouse studies. The course does not cover prokaryotic RNA profiling nor plant- and metagenomics aspects. Course topics RNA-seq experimental approaches Alignment and de novo assembly Statistics for differential gene expression eQTL analysis and allele specific expression Variant calling and RNA editing Small RNA profiling Software for RNA-seq data analysis The tentative programme can be found here: http://biosb.nl/wp-content/uploads/2014/03/RNAseq_preliminary_programme_29-… Target audience Participants for the RNA-seq course should preferably have participated in the general NGS course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend. Registrations will be handled on a first-come-first-served basis but experience and motivation will be reviewed. Seats have been reserved for participants in the FP7-funded project RD-Connect and Marie Curie European Training Network TranCYST. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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ESCS2014 Abstract Submission Extended Deadline!
by Thomas Abeel 24 Jun '14

24 Jun '14

Dear Colleagues, Due to popular demand, we have decided to extend the abstract submission deadline for the 3rd European Symposium of the International Society for Computational Biology Student Council until the 30th of June. We welcome abstracts covering scientific studies as well as novel tools and applications in the fields of computational biology and bioinformatics. As in previous editions, awards will be given to outstanding posters and presentations. *All abstracts accepted for oral presentation will be published in a special issue of the BMC Bioinformatics journal.* ESCS2014 is to be held on September 6th 2014 in Strasbourg, France, as a satellite meeting of the European Conference on Computational Biology (ECCB) and will bring together young computational biologists from several research areas and regions of the world. This is your chance to present your work to an international audience of young scientists! In addition, we are proud to host three keynotes from distinguished scientists: Dr. Lennart Martens from the University of Ghent, Dr. Jeroen de Ridder from the Delft University of Technology and Dr. Lars Juhl Jensen from Technical University of Denmark. Submission information: http://escs2014.iscbsc.org/escs-submission General information and program: http://escs.iscbsc.org/ Important dates April 24, 2014: Abstract submission opens *June 30, 2014: Abstract submission closes EXTENDED!* July 15, 2014: Abstract acceptance notifications We look forward to receiving your abstract! On behalf of the ESCS organizers, Pieter Meysman Chair, 3rd European Student Council Symposium 2014 Margherita Francescatto Co-Chair, 3rd European Student Council Symposium 2014

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ESCS2014 Abstract Submission Extended Deadline!
by ISCBSC announcement 24 Jun '14

24 Jun '14

Dear Colleagues, Due to popular demand, we have decided to extend the abstract submission deadline for the 3rd European Symposium of the International Society for Computational Biology Student Council until the 30th of June. We welcome abstracts covering scientific studies as well as novel tools and applications in the fields of computational biology and bioinformatics. As in previous editions, awards will be given to outstanding posters and presentations. *All abstracts accepted for oral presentation will be published in a special issue of the BMC Bioinformatics journal.* ESCS2014 is to be held on September 6th 2014 in Strasbourg, France, as a satellite meeting of the European Conference on Computational Biology (ECCB) and will bring together young computational biologists from several research areas and regions of the world. This is your chance to present your work to an international audience of young scientists! In addition, we are proud to host three keynotes from distinguished scientists: Dr. Lennart Martens from the University of Ghent, Dr. Jeroen de Ridder from the Delft University of Technology and Dr. Lars Juhl Jensen from Technical University of Denmark. Submission information: http://escs2014.iscbsc.org/escs-submission General information and program: http://escs.iscbsc.org/ Important dates April 24, 2014: Abstract submission opens *June 30, 2014: Abstract submission closes EXTENDED!* July 15, 2014: Abstract acceptance notifications We look forward to receiving your abstract! On behalf of the ESCS organizers, Pieter Meysman Chair, 3rd European Student Council Symposium 2014 Margherita Francescatto Co-Chair, 3rd European Student Council Symposium 2014

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SMBM 2014 submission June 30
by José Luis Oliveira 23 Jun '14

23 Jun '14

** Apologies if you received multiple copies of this CFP. Please kindly forward to those who may be interested. ** Sixth International Symposium on Semantic Mining in Biomedicine (SMBM 2014) http://www.smbm.org/ Important Dates • Full paper submission deadline: June 30th 2014 • Poster and system demonstration paper submission deadline: July 4th 2014 • Notification of acceptance for full papers: July 21st 2014 • Notification of poster and system demonstration papers: July 28th 2014 • Symposium dates: October 6-7th 2014 Venue: October 6th and 7th, University of Aveiro, Portugal SMBM 2014 aims to bring together researchers from text and data mining in biomedicine, medical, bio- and chemoinformatics, and researchers active in biomedical ontology design and engineering, and the Semantic Web. The combined research helps to promote full integration of data and factual content from large text collections, biological databases, ontological and terminological resources, and from the Web. We are inviting papers from a full range of topics (see below), emphasizing in particular work on methods deployed in a production-like research environment, user-facing applications of text mining technology, the integration of text with domain resources such as content from reference databases (e.g., UniProt, EntrezGene, OMIM) and semantic resources such as GO, UMLS etc. We also welcome contributions from across the biomedical domains, including genomics, translational medicine, clinical practice, and public health. Topics of interest include (but are not limited to): • Development and use of biomedical semantic resources • Terminology and ontology development for biomedical information systems including terminology evolution • Integration of text and data mining in the biomedical domain • (Semantic) Web mining of biomedical information • Text mining, information extraction, and information retrieval for the biomedical domain • Evaluation techniques and standards for text mining solutions • Annotation schemes for biomedical corpora • Text mining for resource building, e.g. ontologies, and resource enrichment, e.g., biomedical databases • Representation and discovery of biomedical domain knowledge • Image/caption processing in relation to content extraction • Domain-specific reasoning processes, e.g., to infer non-explicit information, validation (trust-worthiness, believability, safety) of extracted information • Integration of text mining in biological database curation workflows All accepted papers will be published in the conference proceedings that will be available online. We invite three categories of papers: full research papers, short papers and system papers. Research papers will be given an oral presentation, short papers a poster presentation, and systems papers will be presented in systems demonstration sessions. System papers should describe an implemented system related to a topic of interest that the authors will demonstrate live during the symposium. The final modality of presentation will be decided by the organizing committee. Authors of selected papers will be invited to submit an extended version for publication in a special issue of the Journal of Biomedical Semantics (JBMS), an open-access journal published by BioMed Central (BMC). Submissions should follow the ACL instructions for authors, with a maximal limit of 8 pages. The recommended length for system papers and poster submissions is four (4) pages. Manuscripts will be submitted electronically as PDF files. Reviewing will be double-blind, and submissions should therefore NOT contain author names or other obviously identifying information. Authors of selected papers will be invited to submit an extended version for publication in a special issue of the Journal of Biomedical Semantics (JBMS), an open-access journal published by BioMed Central (BMC). Scientific chairs Fabio Rinaldi, University of Zurich, Switzerland Olivier Bodenreider, National Library of Medicine, USA Program chair José Luis Oliveira, University of Aveiro, Portugal Local organization committee Andreia Davide, University of Aveiro, Portugal David Campos, BMD Software, Portugal Pedro Lopes, University of Aveiro, Portugal Program committee Adrian Shepherd, Birkbeck University of London, UK David McClosky, Stanford University, USA Dietrich Rebholz-Schuhmann, University of Zurich, Switzerland Dina Demner-Fushman, National Library of Medicine, USA Florian Leitner, CNIO, Spain Francisco Couto, University of Lisbon, Portugal Gerold Schneider, University of Zurich, Switzerland Goran Nenadic, University of Manchester, UK Gwan-Su Yi, KAIST, South Korea Hongfang Liu, Georgetown University Medical Center, USA Hyunju Lee, GIST, South Korea Jin-Dong Kim, Database Center for Life Science, Japan Jong C. Park, KAIST, South Korea Jung-Jae Kim, Nanyang Technological University, Singapore Karin Verspoor, NICTA, Australia Kevin Cohen, University of Colorado, USA Makoto Miwa, NaCTeM and University of Manchester, UK Mariana Neves, Hasso-Plattner Institut, Germany Martin Krallinger, CNIO, Spain Michael Krauthammer, Yale University School of Medicine, USA Mike Conway, University of Pittsburgh, USA Naoaki Okazaki, Tohoku University, Sendai, Japan Nigel Collier, National Institute of Informatics, Japan Patrick Lambrix, Linköping University, Sweden Patrick Ruch, University of Applied Sciences, Geneva Pierre Zweigenbaum, LIMSI-CNRS, France Rune Sætre, University of Science and Technology, Trondheim, Norway Sampo Pyysalo, NaCTeM and University of Manchester, UK Sérgio Matos, University of Aveiro, Portugal Sophia Ananiadou, NaCTeM and University of Manchester, UK Stefan Schulz, Medical University Graz, Austria Tomoko Ohta, NaCTeM and University of Manchester, UK Udo Hahn, University of Jena, Germany Wendy Chapman, University of Pittsburgh, USA Yutaka Sasaki, Toyota Technological Institute, Nagoya, Japan

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The 4th VIB International PhD Symposium-Registration deadline: 31 July 2014
by Şule Yılmaz 19 Jun '14

19 Jun '14

Dear Ph.D. students, Ph.D. students from VIB, Belgium, are organizing the “*VIBes in Biosciences 2014*” symposium which aims to bring together Ph.D. candidates from different areas in life sciences. This symposium is organized to stimulate networking, listen to renowned speakers, including a *Nobel laureate,* and transfer skills through workshops. The closing speaker is *Jorge Cham from PHD Comics*! The symposium will take place *from* *17 to 19 September 2014* in the Horta venue in *Antwerp, Belgium.* The symposium offers an exciting scientific program with topics that concern every doctoral student. In addition, workshops are offered that provide hands-on practicals on key skills to help Ph.D. candidates during their studies. In order to reach as many Ph.D. students as possible, we would appreciate it very much if you could forward this e-mail to everyone whom it may concern. In attachment, you can also find the poster announcing the symposium. There is also CELLFIE competition - *"Let me take a cellfie"*! You can *win a cool prize* by participating! Detailed information can be found on www.vibes2014.org <http://www.vibes2014.org> Please check our web site to see more details about program. You can *register *here: http://vibes2014.org/registration.html. *The final registration deadline is the **31st of July*! Please do not hesitate to contact us for more information. Follow us on Facebook (VIBesSymposium), Twitter (@VIBesSymposium) and check out our YT movies: https://www.youtube.com/watch?v=1LicxBaOXQ0 https://www.youtube.com/watch?v=mI43rwJUC6A&feature=youtu.bebbc With kind regards, The VIBes 2014 Organizing Committee Liesbeth Aerts, Özden Akay , Alice Borghi , Michaela Conrad, Sylvester Holt, Nevena Hristozova, Michal Janiak, Michiel Krols, Marie Lork, Laura Meloni, Esther Meersman, Raffaele Mori, Ehsan Sabaghian, Karolina Slowicka, Giel Tanghe, Kevin Titeca, Niels Vandamme, Lana Vandersarren, Tessa Vermeire, Elke Ydens and Şule Yılmaz

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PhD position Bioinformatics/NGS/MS/sORF detection @ BioBix
by Gerben Menschaert 18 Jun '14

18 Jun '14

Dear colleagues, We have a vacancy for a PhD position in our lab for someone with a background in bioinformatics and data analysis and a keen interest in sequencing and mass spectrometry, for a project exploring small ORFs and micropeptide translation products. (see description in attachment)! I would very much appreciate it if you could circulate the attached advertisement to any relevant candidates or advertise the position within your institute. Kind regards, Gerben dr. ir. Gerben Menschaert Post-doctoral fellow FWO Lab of Bioinformatics and Computational Genomics FBE - Ghent University Coupure Links 653 9000 Ghent, Belgium MAIL Gerben.Menschaert(a)ugent.be PHONE +32 9 264 99 22 SKYPE gerben.menschaert WEB www.biobix.be/gerben-menschaert/

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Fwd: Postdoc position working on sRNAs - please circulate
by Yao-Cheng Lin 13 Jun '14

13 Jun '14

---------- Forwarded message ---------- From: Nathaniel Street <nathaniel.street(a)umu.se> Date: Fri, Jun 13, 2014 at 4:20 PM Subject: Postdoc position working on sRNAs - please circulate Hi I have an open postdoc position for a project exploring the relationship between sRNA, methylation and repeats in Norway spruce. I would very much appreciate it if you could circulate the attached advertisement to any relevant candidates or advertise the position within your institute. Kind regards Nat -- Yao-Cheng Lin Bioinformatics and Systems Biology VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, B-9052 Ghent, Belgium TEL: +32 (0)9 33 13 821 GSM: +32 (0)472 480 968 http://bioinformatics.psb.ugent.be

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NBIC/BioSB Course Algorithms for Biological Networks (3th edition) - still some seats open!!
by Celia.vanGelder＠radboudumc.nl 13 Jun '14

13 Jun '14

NBIC/BioSB Course Algorithms for Biological Networks (3rd edition) - still some seats open! Date: 30 June - 4 July, 2014 Course coordinators: Dick de Ridder (WUR), Jeroen de Ridder (TUD), Celia van Gelder (NBIC/BioSB) Location: Delft University of Technology (TUD), Delft, the Netherlands Website: http://biosb.nl/education/course-portfolio/bioinformatics-portfolio/course-… Registration: http://biosb.nl/education/enrollment-algorithms-for-biological-networks-cou… More information: education(a)biosb.nl<mailto:education@biosb.nl> Target audience PhD students with a background in bioinformatics, computer science or a related field; a working knowledge of basic statistics and linear algebra is assumed. Course Description In the third edition of 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 networks from observed measurement data and of integrating various data sources and databases to refine networks. Once networks are derived they often serve as the cornerstone in the visualization, analysis and interpretation of high-throughput data; we will discuss a number of methods in this area. As an alternative to static networks, a number of alternative dynamic network models more suited for high-level simulation of cellular behaviour for will be introduced. Finally, we will give some examples of algorithms exploiting the networks found to learn about biology, specifically for inspecting protein interaction networks and for finding active sub networks. Course programme The course website, including full course programme, can be found at http://helix.ewi.tudelft.nl/nbic/abn/. BioSB Course Programme The course portfolios of NBIC (bioinformatics) and NCSB (systems biology) will be integrated and continued in the Netherlands Bioinformatics and Systems Biology Research School (BioSB). The Education Portfolio of BioSB can be found at http://biosb.nl/education/course-portfolio/. More information For more information about the course you can contact Celia van Gelder at education(a)biosb.nl<mailto:education@biosb.nl>. Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC/BioSB tel. +31-(0)24-3666120 e-mail: Celia.vanGelder(a)radboudumc.nl<mailto:C.vanGelder@umcn.nl> websites: www.cmbi.ru.nl<http://www.cmbi.ru.nl/>, www.nbic.nl<http://www.nbic.nl/>, www.biosb.nl<http://www.biosb.nl> Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands Het Radboudumc staat geregistreerd bij de Kamer van Koophandel in het handelsregister onder nummer 41055629. The Radboud university medical center is listed in the Commercial Register of the Chamber of Commerce under file number 41055629.

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