December 2012 - BBClist - maillist.psb.ugent.be

Computational Cancer Biology Positions
by Lodewyk Wessels 12 Jul '13

12 Jul '13

COMPREHENSIVE COMPUTATIONAL MODELING FOR COMBINATION TREATMENT DESIGN PROJECT OUTLINE All cancers arise due to alterations in their genomes. Although insight into the genetic lesions in tumors by genome sequencing does already assist in selecting some drug regimens, it rarely results in disease eradication due to the emergence of drug-resistance. More sophisticated combination therapies in which several oncogenic pathways are targeted simultaneously could alleviate this problem. However, at present we are unable to extract and interpret the necessary information from tumors to predict which drug regimen will be most adequate. In this project we will collaborate with Welcome Trust Sanger Center and employ the 1000 cancer cell line data set to tackle this problem. This data set comprises large-scale molecular characterization and cancer drug screening of all cell lines for 400 anti-cancer drugs. The molecular data currently consists of gene expression, copy number (SNP-6), and whole exome sequencing data and is being expanded. The successful candidate will work closely with scientists at the Welcome Trust Sanger Center and the Netherlands Cancer Institute and employ computational approaches to mine this rich, valuable pre-clinical resource. Potential results include 1) new molecular biomarkers to identify sensitive populations 2) repositioning of existing drugs in other tumor types and 3) potential drug combinations aimed at overcoming resistance mechanisms. Hypotheses emerging from these analyses will be validated in model systems and where possible in clinical settings. 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 documented experience in analyzing high-throughput genomic data. The candidate needs to be proficient in common bioinformatics scripting and programming languages. Fluency in spoken and written English is a strong requirement. LOCATION The project involves groups at the Netherlands Cancer Institute, Amsterdam (Rene Bernards, Molecular Carcinogenesis, and Lodewyk Wessels, Computational Biology) and the Welcome Trust Sanger Institute (Mathew Garnet and Ultan McDermott, Cancer Genome Project). This position will be embedded in the Computational Biology Group lead by Lodewyk Wessels. CONTACT DETAILS Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(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

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NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- 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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Bioinformatics position at Hanze University of Applied Sciences Groningen
by Warris S, Sven 14 Dec '12

14 Dec '12

Dear all, At the ALIFE research center at the Hanze University of Applied Sciences, The Netherlands, we have an opening for a bioinformatics researcher/lecturer. The attached PDF contains the relevant information (in Dutch). Best, Sven Warris

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NBIC advanced NGS courses: "Metagenomics Approaches and data analysis" & "De novo assembly from NGS data"
by Patrick Koks 13 Dec '12

13 Dec '12

Metagenomics Approaches and data analysis This advanced NGS course is part of the NBIC PhD-school On February 6-8th, NBIC & CMBI will organise the PhD advanced NGS course: " Metagenomics Approaches and data analysis". Coordinators: Sacha van Hijum (NIZO food research) & Bas Dutilh (CMBI) Location: Leiden, The Netherlands Metagenomics, also called environmental genomics is the process of direct sequencing the DNA of an environmental sample, i.e. of a whole microbial community as it exists in nature, bypassing the need for culturing techniques. The Metagenomics course will cover Metagenomics and metatranscriptomics of prokaryotes, eukaryotes and viruses. Topics are Metagenomics-specific issues like calling taxa, functional annotation, metagenome assembly and comparative Metagenomics. This advanced course is targeted at PhD students and researchers. Participants will be invited to introduce their own research questions. Repeated announcement: De novo assembly from NGS data 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) & Hendrik-Jan Megens (WUR) Venue: Wageningen UR, The Netherlands For more information, check: http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsmetagenomic… http://www.nbic.nl/education/nbic-phd-school/course-schedule/ngsdenovo/ The course programmes 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 __________ Information from ESET NOD32 Antivirus, version of virus signature database 7795 (20121213) __________ The message was checked by ESET NOD32 Antivirus. http://www.eset.com

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vacature bio-informatician CardioGenx
by Barbara van Kampen 13 Dec '12

13 Dec '12

Vacature bij CardioGenx

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Job opportunity
by R. Kraaij 11 Dec '12

11 Dec '12

Dear reader, We are looking for a PhD student, preferably a bioinformatician, for our project : "DNA profiling of the human gut microbiome". Details can be found at: http://www.erasmusmc.nl/vacature/6789/PhD_student Please feel free to forward to anyone interested. With kind regards, Robert Kraaij R. Kraaij, Ph.D. Genetic Laboratory Department of Internal Medicine Erasmus MC, Rotterdam The Netherlands

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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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