August 2011 - BBClist - maillist.psb.ugent.be

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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Integrative Bioinformatics 2011: 2nd call for abstracts
by Jack Leunissen 16 Jul '12

16 Jul '12

Dear colleague, The 2011 International Symposium on Integrative Bioinformatics (IB2011) will take place on March 21-23, 2011 in Wageningen (the Netherlands). This seventh meeting on Integrative Bioinformatics will be of interest to bioinformaticians, computer scientists and all working in, or interested in the developing area of integrative bioinformatics. There will be opportunities to present and discuss methods, theoretical approaches, and their practical applications. We invite you to register for the conference, and to send in an abstract for a presentation at the conference. Accepted abstracts will be invited for a presentation at the conference, and will also be invited to send in a full manuscript, to be published (after peer reviewing) in the IB2011 Special Issue of the Journal of Integrative Bioinformatics. The deadline for sending in an extended abstract is January 15th; submissions should not exceed 4 pages. Authors will be informed of acceptance before February 1st. There are also opportunities for presenting posters and software demonstrations at the Symposium. The deadline for sending in abstracts for posters or a software demo is February 15th, 2011. The best poster will receive an award sponsored by IMBio e.v. The conference website is open for registration and abstract submission, and can be found at www.bioinformatics.nl/ib2011/ and www.imbio.de/ib2011/. We hope to meet you in March in Wageningen. On behalf of the organizing committee, Jack Leunissen Wageningen UR IB2011 is organized by Wageningen University, the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, and IMBio e.V. == Disclaimer: We have tried our best to remove duplicate e-mail addresses from our mailing list to reduce the amount of clutter in your mailbox. It may nevertheless still happen that you receive this mail via different channels. We apologize if you receive this mail more than once.

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CAMDA'11 Announcement
by Yves Moreau 12 Oct '11

12 Oct '11

On behalf of Simon Lin, chair of CAMDA'11 > > ------------------- > CAMDA'11 - ISMB Satellite Meeting, Vienna, 15-16 July 2011 -- > > www.camda.info > > Programme announcement & Call for Posters > > Dear colleague! > > We enthusiastically invite you to attend this year's conference on > > Critical Assessment of Massive Data Analysis (CAMDA) . > > which will be held 15-16 July 2011 in Vienna, Austria (www.camda.info) > > > The early registration discount for CAMDA/ISMB ends 3 June – book now if you want to join us! This year's exciting line up of keynote speakers includes Terry Speed (WEHI), John Storey (Princeton) and Stefano Volinia (Ferrera). See the full two-day programme for details on papers and events... > > CAMDA still accepts poster submissions (abstracts will be published in the conference proceedings). > > > CAMDA was founded in 2000 to provide a forum for the critical assessment of different techniques used in large-scale data analysis in the life-sciences, such as for high-dimensional gene expression profiling. It aims to establish state-of-the-art analysis methods, as well as identify progress and highlight promising directions for future efforts. To this end, CAMDA adopted the approach of a scientific community-wide contest, with everybody analysing the same data sets. Researchers worldwide are invited to take the CAMDA challenge, which has become a prominent fixture (cf. Nature Methods 5, 569). Accepted contributions are presented through talks and posters, and the results and methods of the different analyses are discussed and compared at the conference. > > As a special focus this year, we consider the integrated analysis of a particularly rich structured data set that includes gene and miRNA expression, DNA SNPs, copy number variation, and methylation for about 500 matched samples. With the fast ongoing development of novel genome-wide experimental techniques (such as next generation sequencing), an assessment of how we can gain better insight from an integration of heterogeneous large-scale data is particularly topical. > > CAMDA was founded by Simon Lin and Kimberly Johnson at Duke University (Nature 411, 885. Nature 424, 610). In 2006 CAMDA became a roving conference, with recent venues including Valencia and Chicago. This year, we will host CAMDA in Austria. For the first time, the conference is run as an official Satellite meeting of ISMB/ECCB, providing further opportunities for interaction with colleagues at the conference. > > We can still accept suitable posters for presentations of recent topical work in the dedicated poster session. Poster abstracts are published in the conference proceedings. > > Please also distribute this announcement to other colleagues who might be interested. > > We look forward to seeing you in Vienna! > > > David Kreil (Boku) > Joaquin Dopazo (CIPF) > Simon Lin (Northwestern) > (chairs) > > > Submission of poster abstracts: open (accepted in order of submission) > Early registration closes: 3 Jun 2011 > CAMDA 2011 Conference: 15-16 Jul 2011 > ISMB/ECCB 2011 Conference: 17-19 Jul 2011

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DSM03260 (Associate) Scientist Bioinformatics
by Roubos, Hans 25 Aug '11

25 Aug '11

DSM03260 (Associate) Scientist Bioinformatics DSM is looking for professionals with a PhD degree in Bioinformatics, Metabolic engineering or Bioprocess modeling. Preferably, you have experience in metabolic pathway modeling / engineering with applications to microbial strain development or fermentation processes. Furthermore, you are a multidisciplinary team player, who takes initiative with good communication skills. Personal skills like problem analysis, judgment, creativity, leadership, adaptability characterize your identity. Behaviors like engaging people, drive for results, customer focus, improve, innovate and change are essential to make this job a success. Hans Roubos Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 [cid:565123209@25082011-2FC6] ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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DSM03232 Scientist Biostatistics
by Roubos, Hans 25 Aug '11

25 Aug '11

DSM03232 Scientist Biostatistics DSM is looking for professionals with a PhD degree in (Bio)Statistics or Chemometrics. Preferably, you have experience in statistical processing of biological relevant data from high throughput screening campaigns or metabolomics research. Furthermore, you are able to translate a biological question to a statistical approach and are well capable to communicate even complex statistical results to novices in statistics using visualization techniques. You are a multidisciplinary team player, who takes initiative with excellent communication skills. Behaviors like engaging people, drive for results, customer focus, improve, innovate and change are essential to make this job a success. Hans Roubos Senior Scientist Bioinformatics DSM Biotechnology Center | Alexander Fleminglaan 1 | 2613 AX Delft | The Netherlands | T +31 15 2792147 | F +31 15 2793771 | hans.roubos(a)dsm.com | www.dsm.com | Trade Registration number 27235314 [cid:953443309@25082011-2FBF] ________________________________ DISCLAIMER : This e-mail is for the intended recipient only If you have received it by mistake please let us know by reply and then delete it from your system; access, disclosure, copying, distribution or reliance on any of it by anyone else is prohibited. If you as intended recipient have received this e-mail incorrectly, please notify the sender (via e-mail) immediately.

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Vacature Biostatistician Pronota - Zwijnaarde
by Vicky Aerts 24 Aug '11

24 Aug '11

Biostatistician Pronota is looking for a biostatistician to join its team working on biomarker validation studies. The ideal candidate is highly motivated and enjoys a challenging environment. He will be involved in Pronota's key programs and have the opportunity to contribute to cutting-edge projects. Profile: * You are driven by data analysis and have pride in delivery. * You like to work in a structured and evolving environment within a dynamic team. * You are familiar with modern statistical methods. Responsibilities: * QC/QA of high-throughput proteomics data. * Analysis of clinical and protein expression data for biomarker validation studies. Qualifications: * Master or equivalent degree in statistics. * Working knowledge of R. * An experience in life sciences would be an asset, but is not essential. To apply Please send your CV and motivation (with a reference to the position applied for) to info(a)pronota.com<mailto:info@pronota.com> tel: +32 (0)9 241 11 64 fax: +32 (0)9 241 11 69 Website: www.pronota.com<http://www.pronota.com> Vicky Aerts ________________________________ Pronota nv Management Assistant Technologiepark 4 9052 Zwijnaarde - BELGIUM- T +32 9 241 11 47 F +32 9 241 11 69 www.pronota.com<http://www.pronota.com/> ________________________________ Confidential Notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at info(a)pronota.com<mailto:info@pronota.com>

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Job opening: Senior Scientist Systems Biology
by karen.lemmens＠cropdesign.com 23 Aug '11

23 Aug '11

Job opening: Senior Scientist Systems Biology, BASF Plant Science Location: Ghent Job description: You will be responsible for defining and executing systems biology data analyses leading to the identification of genes that potentially improve target crop traits or the elucidation of the molecular mechanisms governing such traits. You will organize, analyze and interpret the obtained data, in collaboration with biometricians, and plant physiologists. You will be member of a group of systems biology experts. More information on the job opening can be found here: http://www.cropdesign.com/jobs.php?jid=69 Karen Lemmens, PhD Bioinformatics research scientist Phone: +32 9 242 3-464, Fax: +32 9 242 3-489, E-Mail: karen.lemmens(a)cropdesign.com Postal Address: CropDesign N.V., 1190 - CD2, 9052 Gent (Zwijnaarde), Belgium CropDesign N.V. - A BASF Plant Science Company Technologiepark 3 - B-9052 Gent - Belgium - General Telephone: +32-9-242 34 00 - Fax: +32-9-242 34 89 Confidentiality notice: The information contained in this e-mail is confidential and may be the subject of legal professional privilege. It is intended for the authorized use of the individual or entity addressed. If the receiver or reader of this message is not the intended recipient, you are hereby notified that any disclosure, copying, distribution or use of the contents of this message is prohibited. If this email is received in error, please accept our apologies, delete all copies from your system, and notify us at info(a)cropdesign.com.

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Call for participation PRIB 2011
by Thomas Abeel 18 Aug '11

18 Aug '11

6th IAPR Conference on Pattern Recognition in Bioinformatics November 2-4 2011, Delft, The Netherlands Website: http://prib2011.tudelft.nl/ Early Bird Registration August 24, 2011 Registration October 12, 2011 We invite you all to join the Pattern Recognition in Bioinformatics conference series. It aims to bring together researchers, practitioners and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology and systems biology. For the 2011 program we carefully selected an interesting mix of topics, with 5 great keynote speakers and (almost) 30 presenters from the community. The preliminary program and the registration can be found on the webpage: http://prib2011.tudelft.nl

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Mini-symposium Ghent - September 28: Bioinformatics: tools in research
by Maté Ongenaert 01 Aug '11

01 Aug '11

Bioinformatics: tools in research WOUD, a research group of the Ghent University Association organises a mini-symposium: Bioinformatics: tools in research. During this meeting, researchers not trained in bioinformatics should get an idea how bioinformatics can be a tool for their research. More details and registration on http://mellfire.ugent.be/public/woud The program is included below. September 28th 2011, Congress Center Het Pand, Gent, Belgium Program 13:30 Welcome reception 14:00 Introduction: WOUD and bioinformatics (prof. dr. Bruno Verhasselt, prof. dr. Jo Vandesompele) 14:05 Investigating the human gut flora using metagenomics (prof. dr. Jeroen Raes, VUB) 14:25 The post-genomic era: epigenetic sequencing applications and data integration (dr. ir. Maté Ongenaert, CMGG - UGent) 14:45 Visualisation of large datasets (drs. Geert Trooskens, BIOBIX - UGent) 15:00 Race against the sequencing machine: processing of raw DNA sequence data at the Genomics Core (dr. Luc Dehaspe, Genomics Core - UZLeuven) 15:20 Coffee break 15:45 Integrative transcriptomics to study non-coding RNA functions (dr. ir. Pieter Mestdagh, CMGG - UGent) 16:05 Large scale machine learning challenges for systems biology (dr. Yvan Saeys, VIB - UGent) 16:25 Pathway analysis: example from the bench (drs. Jolien Vermeire, HIVlab, Department of Clinical Chemistry, Microbiology and Immunology - UGent) 16:40 Proteomics and cross-omics integration (prof. dr. Lennart Maertens (VIB - UGent) 17:00 Closure

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