- BBClist - maillist.psb.ugent.be

Comp. biology position: ANDROGEN RECEPTOR GENOMICS
by Lodewyk Wessels 07 Dec '12

07 Dec '12

INTEGRATIVE COMPUTATIONAL ANALYSIS OF ANDROGEN RECEPTOR GENOMICS TO PREDICT OUTCOME AND THERAPY RESPONSE PROJECT OUTLINE Prostate cancer is one of the most prevalent cancers in males. Currently, Gleason grade, TNM stage, surgical margin status and serum PSA levels are used as prognostic markers in prostate cancer. Although these markers may predict survival and recurrence after radical prostatectomy, they are not suitable for selecting patients for further therapeutic interventions. In this project, we aim to identify predictors of prostate cancer recurrence and response to Androgen Deprivation Therapy. We will generate the most comprehensive overview of primary prostate cancer genomics, including Androgen Receptor/chromatin binding patterns, histone modifications, gene expression and copy number data derived from primary prostate tumor samples, prostate tumor samples that have become resistant to treatment as well as and prostate cancer cell lines. The successful candidates will work closely with biologists and clinicians to develop computational approaches that integrate all these data streams to arrive at improved predictors of recurrence and therapy response. CANDIDATE REQUIREMENTS –EDUCATION AND EXPERIENCE We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science, mathematics or physics and with a strong cancer biology interest. Preferably applicants should have a strong documented experience in analyzing ChIP sequencing and gene expression data. In addition, we value experience in one or more of the following: sequence motif analysis, clinical data analysis, gene expression analysis, machine learning or applied statistics. The candidate needs to be proficient in programming languages such as Java, Perl or Python, and be comfortable with Linux systems. Fluency in spoken and written English is a strong requirement. LOCATION The project involves a consortium consisting of the NKI-AVL and the Erasmus MC and will mainly employ the complementary expertise and of the groups of Andre Bergman (Molecular Genetics and Internal Medicine), Wilbert Zwart (Molecular Pathology) and Lodewyk Wessels (Computational Biology) at the Netherlands Cancer Institute, Amsterdam. CONTACT DETAILS Please contact Prof Dr Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl., or Dr Wilbert Zwart, tel +31 512 7920 or e-mail: w.zwart(a)nki.nl When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached as references. Also see bioinformatics.nki.nl for further information. CLOSING DATE 3 February 2013 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)614413040 http://bioinformatics.nki.nl/

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NBIC PhD Course Pattern Recognition 21-25 January 2013, Amsterdam
by Celia van Gelder 05 Dec '12

05 Dec '12

With apologies for double posting , the mail from Oct 19 contained the wrong hyperlink to the course page! * * *NBIC PhD Course Pattern Recognition (3rd edition)* Date: 21-25 January 2013 Location: Amsterdam Course Coordinator: Perry Moerland (AMC)<http://www.nbic.nl/education/nbic-phd-school/course-schedule/optimisation-t…> Website:http://www.nbic.nl/education/nbic-phd-school/course-schedule/pattern-recognition/ Registration: http://www.nbic.nl/education/nbic-phd-school/enrolment/ On Jan 21-25, 2013 the NBIC PhD School organises the third edition of the PhD Course 'Pattern Recognition' in Amsterdam. The course aims at PhD students with a background in bioinformatics, computer science or a related field. The course introduces basic techniques from the fields of pattern recognition and machine learning to solve bioinformatics problems. After having followed this course, a student should have an overview of basic pattern recognition techniques and be able to recognize what method is most applicable to classification problems (s)he encounters in bioinformatics applications. This course is part of the Education Programme of the NBIC PhD School. The PhD School offers training and education for PhD students in bioinformatics. More information about the NBIC PhD School can also be found on the NBIC website (www.nbic.nl <http://www.nbic.nl> -> Education -> NBIC PhD School). For more information about the course you can contact Celia van Gelder (NBIC Education) at education(a)nbic.nl -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail:C.vanGelder@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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Personal Data Protection Manager at CNRS in Lyon (IMI eTRIKS Consortium)
by Johann Pellet 04 Dec '12

04 Dec '12

On behalf of Charles Auffray: We are seeking an experienced individual to lead the Biomedical Personal Data Protection & Ethics activities of the newly formed eTRIKS Consortium of the Innovative Medicines Initiative (IMI). eTRIKS is dedicated to delivering European Translational Information and Knowledge Management Services initially for all IMI projects, then for other European translational research projects. Candidates should have a proven track record of research, management and implementation of the ethical and legal (i.e. personal data protection) frameworks of biomedical research and their interaction with information and communication technology. The required proven skills and experience include: - At least five years of experience in data protection and/or ethics in Europe - Experience in biomedical and clinical research in academy and/or industry - Proven distributed project management and communication skills in English - Experience in information security (technical knowledge would be a plus) The selected candidate should be able to proactively lead complex workstreams on data security and privacy monitoring and compliance, and engage multiple academic and industrial partners in a pre-competitive collaborative innovation effort. The objective is to reach international harmonization of personal data protection rules in the context of the fast evolving area of translational research and systems medicine. She/he will be based in Lyon-Gerland within the CNRS-EISBM team led by Charles Auffray, hosted by Claude Bernard University and the Lyonbiopole competitive cluster on the Charles Mérieux campus. She/he will be working closely with academic partners at Imperial College in London and the Luxembourg Center for Systems Biomedicine, with Sanofi and the 9 other pharmaceutical partners of eTRIKS. The initial contract will be for 2 years with a possible extension up to 5 years. Send application with CV and names of two referees by e-mail to Charles Auffray: jobs(a)eisbm.org More information at: http://job.eisbm.org/personal-data-protection-manager/ Regards, The EISBM team

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Open position for Bioinformatician to develop software for Next Generation Sequencing
by W. Mulder 04 Dec '12

04 Dec '12

l.s., We have an open position (full time) for a Software Developer at GenDx, Utrecht Can you send the attached information to the members of the BeNeLux bioinformaticians forum? Thank you in advance. Wietse W. Mulder PhD | Managing Director GenDx | Yalelaan 48 | 3584 CM Utrecht | The Netherlands Phone: +31 (0)30 252 3799 | Fax: +31 (0)30 254 2611 | w.mulder(a)gendx.com | www.GenDx.com | Skype: wietse-gendx- (+31 30 320 0762) <http://www.gendx.com> SBTengine(r) GPS: Navigate the shortest route to high resolution <http://www.gendx.com/SBTengine/Help/hs510.htm> Please note: This communication is intended for use by the addressee. It may contain confidential or privileged information. If you receive this communication unintentionally, please immediately notify the sender and delete the original, copies and enclosures.-----Original Message-----

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Postdoc position: Regulatory Genomics and cis-Regulatory Variation
by Stein Aerts 03 Dec '12

03 Dec '12

Postdoc position: Regulatory Genomics and cis-Regulatory Variation The Laboratory of Computational Biology, within the Center for Human Genetics - University of Leuven, is seeking a highly motivated and experienced postdoctoral researcher to apply integrative genomics, computational models, and next-generation sequencing to further our understanding of genome regulation and chromatin conformation. You will develop computational approaches and work in close collaboration with the wet-lab, performing high-throughput experiments using RNA-Seq, ChIP-Seq, damID-Seq, DHS-Seq, FAIRE-Seq, and 4C-Seq/HiC. You will apply these methods to various systems, including eye development across Drosophila species, and different tumor types (melanoma, leukemia). The challenge is to integrate these data with computational predictions of cis-regulatory modules, and with publicly available data from (mod)ENCODE and TCGA, to ultimately characterize cis-regulatory changes that underlie morphological changes (Drosophila data) or that drive oncogenesis (cancer data). Qualifications: PhD degree in Life sciences or computational field Proven track record of high-impact publications in the field of computational biology, analysis of high-throughput data sets, data integration Solid experience with bioinformatics programming and statistics for bioinformatics, including scripting (e.g., Python), R (incl. Bioconductor), UCSC Genome Browser, Ensembl API, etc. Experience with pathway analysis and cis-regulatory sequence analysis is a plus. Thorough understanding of molecular and developmental biology, expertise on cancer biology is a plus. Experience with software development and object-oriented programming (e.g., Java) is a plus. Experience with data mining and machine learning is a plus. Experience with the analysis of next-generation sequence data is a plus: whole exome re-sequencing, whole-genome re-sequencing, SNP/indel calling, CNV, Structural variation; RNA-Seq, ChIP-Seq Links: The Laboratory of Computational Biology Center for Human Genetics University of Leuven Highly motivated candidates can apply by sending a motivation letter, names and contact information for at least two references, publication list, and CV to stein.aerts(a)med.kuleuven.be.

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Bioinformatics Postdoc
by Lodewyk Wessels 02 Dec '12

02 Dec '12

POST DOCTORAL BIOINFORMATICIAN IDENTIFICATION AND VALIDATION OF NEW TARGETS FOR COLORECTAL CANCER OVERALL OBJECTIVES The aim of this project is to redefine colorectal cancer (CRC) at the molecular level, by identifying and validating new activated pathways and specific drug targets for defined CRC patient populations. The project will employ the complementary expertise and tools at Astra Zeneca, two academic laboratories (those of Lodewyk Wessels and Rene Bernards at the Netherlands Cancer Institute, Amsterdam) and a leading diagnostics company with an established presence in oncology (Agendia BV, Amsterdam). PROJECT OUTLINE AND STRATEGY We will first use computational approaches to perform a ‘pathway’ or ‘module’ level integration of molecular profiling (gene expression and next generation sequencing data) and extensive clinical annotation data from a collection of 400 CRC tumours to identify and prioritise pathways that are deregulated in each CRC sub-disease. Next, we will define for each pathway, targets that are amenable to drug discovery efforts, and that can be validated in cell culture models. To enable target validation, we will develop approaches to identify, based on molecular profiling data, CRC cell lines in the AZ collection that represent each molecular sub-disease. Once these are in place, target validation experiments will be conducted, using established RNAi methodology. Targets whose functions are shown to be essential for cell viability in the appropriate cell line models will then be recommended for new drug discovery projects. These results will be fed back to refine the target section procedure based on the tumor data. EMPLOYER INFORMATION The Netherlands Cancer Institute is a dedicated cancer center conducting research in all major areas of cancer, with a strong emphasis on translational research. The Bioinformatics and Statistics group (Wessels lab.) provides leadership on the collection and analysis of data for the research programs of the institute, by developing novel compuational approaches and performing state of the art analyses of a wide array of data types, including laboratory and animal experiments, clinical trials, and epidemiologic studies. REQUIREMENTS The ideal candidate is a highly motivated postdoc with a strong background in bioinformatics or computational biology. The vacancy is a research position within the field of bioinformatics/computational biology and the research will be carried out in close collaboration with the involved partners: Bernards lab, Astra Zeneca and Agendia. The ideal candidate has a background in the analysis of high throughput molecular data, computational diagnostics, bioinformatics, computer science, statistics or physics with strong analytical and algorithmic skills. EMPLOYMENT CONDITIONS The temporary employment will be for a period of three years. The gross monthly salary for a Postdoc will range from €3140,- to €3.495,- and depends on previous experience. We can help you find housing. The NKI-AVL has been listed in the top 25 of ‘Best Employers’ in 2009 offering a specialized cancer research institute and hospital with good working conditions and an excellent atmosphere. INTERESTED? Please contact Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr George Orphanides, Director of Discovery Medicine, tel. +44 1625 232312 or e-mail George.Orphanides(a)astrazeneca.com. When applying please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. http://bioinformatics.nki.nl CLOSING DATE 1 May 2011

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NBIC advanced NGS course: "de novo assembly from NGS data"
by Patrick Koks 30 Nov '12

30 Nov '12

De novo assembly from NGS data This advanced NGS course is part of the NBIC PhD-school On January 8-9th, NBIC, WUR and LUMC will organise the PhD advanced NGS course: "De novo assembly from NGS data". Course Coordinators: Gabino Sanchez-Perez (WUR), Jan van Haarst (WUR), Johan den Dunnen (LUMC), Leon Mei (NBIC) Venue: Wageningen UR, The Netherlands De novo assembly from (short read) NGS data is challenging and may require tailored approaches for different complex genomes like those of polyploid plants. After a quick introduction into NGS techniques and platforms, this course will cover topics like: Sequencing strategies using short– or long-read sequences, paired-end and mate-pairs and having a (remotely related) reference genome or not. Elementary steps like Quality assurance and read filtering are essential and much of your results depend on the wise choice of the right algorithm and assembler with your specific type of data, data coverage and genome. Closing the gaps and finishing strategies, functional annotation and comparative genomics will conclude this course. This hands-on course is targeted at PhD's and researchers with experience in genomics or NGS data analysis. For more information, check: http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsdenovo/ The course programme and additional information for travelling and staying will be published here soon. For registration and information about course fees, you can also directly go to: http://www.nbic.nl/education/nbic-phd-school/enrolment/ Here, you can also go to the pre-registration page where you can express your interest in our other courses that are planned but not scheduled yet. 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 and life sciences. All NBIC courses are co-developed and co-organised by experts in the field and in close collaboration with leading research groups throughout the Netherlands. All NBIC courses are taught in English and are open to PhD students and researchers worldwide. 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). For more information, you can send e-mail to Patrick Koks (education(a)NBIC.NL<mailto:education@NBIC.NL>) Regards, The NBIC BioWise team Patrick Koks, NBIC BioWise – Education Tuesday – Wednesday - Thursday phone: #31-(0)24-3615210 e-mail: Patrick.koks(a)nbic.nl<mailto:Patrick.koks@nbic.nl> web: www.nbic.nl<http://www.nbic.nl/>, www.ebiomics.org<http://www.ebiomics.org/> Postal Address: CMBI 260 Radboud University / UMC / NCMLS PO Box 9101, 6500 HB Nijmegen, The Netherlands

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BBC12 - Extended registration deadline: November 28!
by Femke Francissen 26 Nov '12

26 Nov '12

*BeNeLux Bioinformatics Conference (BBC12) - extended registration deadline - November 28!* Two more days to register for the BBC12! Register now via: http://www.nbic.nl/about-nbic/events/bbc2012/registration/ The 7th edition of the BBC12 will be organized in Nijmegen, the Netherlands on 10-11 December 2012. Key theme: "Bioinformatics at the interface". Conference website: http://www.nbic.nl/bbc2012 Contact: Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>), Centre for Molecular and Biomolecular Informatics, UMC St Radboud Nijmegen Femke Francissen (femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>), Netherlands Bioinformatics Centre

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Invitation of Plant Genomics Minisymposium
by Yao-Cheng Lin 22 Nov '12

22 Nov '12

Reminder: It's an open seminar. No need for registration. sorry for cross-posting Dear Colleagues: We would like to invite you to the "Plant Genomics Minisymposium" organized by Prof. Yves Van de Peer (PSB, VIB-UGent). This minisymposium is in conjunction with the ESF sponsored workshop "Generation and Analysis of Next Generation (NGS) Data". You can find the up-to-date progresses and the future perspective in the field of plant genomics during this minisymposium. Plant Genomics Minisymposium Date: 27th of November (Tuesday), 2012 Location: Jozef Schell seminar room, VIB FVMS building, Technologiepark 927 Zwijnaarde Program: 9:00 – 9:45 Sequencing complex plant genomes : the impact of New Sequencing Technologies. Prof. Patrick Wincker (Genoscope, France) 9:45 – 10:30 The past, present, and future of RNA sequencing and expression quantification. Prof. Manfred Grabherr (Uppsala University, Sweden) 10:30 - 11:00 Coffee break 11:00 – 11:45 Journey through the past: 200 million years of plant evolution Prof. Yves Van de Peer (Ghent University, Belgium) Contact: More information of this minisymposium please contact Dr. Yao-Cheng Lin (yalin(a)psb.vib-ugent.be)

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Fwd: Vacant position bioinformatics SESVanderHave
by Olivier Delgrange 20 Nov '12

20 Nov '12

-------- Message original -------- Sujet: vacant position bioinformatics SESVanderHave Date : Mon, 19 Nov 2012 11:14:28 +0000 De : Willems, Glenda <Glenda.Willems(a)sesvanderhave.com> Pour : olivier.delgrange(a)umons.ac.be <olivier.delgrange(a)umons.ac.be> Cher Dr. Delgrange, Je suis employée en tant que bioinformaticienne à la société SESVanderHave, située à Tirlemont. Nous produisons des semences de betteraves qui sont vendues mondialement. Nous sommes actuellement à la recherche d'un(e) bioinformaticien(ne) pour renforces notre équipe a Tirlemont. L'annonce de ce poste est attachée à cet email. Est-ce que vous pourriez faire circuler cette offre au sein de votre département, et/ou laboratoire, ou encore la transférer à des personnes qui pourraient être intéressés par ce job ? S'il est possible de publier cette annonce sur internet, sur le site des offres d'emplois pour les anciens étudiants par exemple, n'hésitez pas à le faire, ou à transférer cette email aux personnes compétentes. Merci d'avance de votre aide. Sincères salutations, Glenda Willems *Glenda**Willems* Bioinformatician Description: spacer *SESVANDERHAVE N.V./S.A.** *Phone: +32 16808392 www.sesvanderhave.com Description: S:\Workdata\SESV\SESVanderHave Email Template (83002-SESV)\ontwerp\Signature\Signature HTML - before install\img\logo.gif Description: environmentalwarning Please consider the environment before printing this e-mail

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