June 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

1 2

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.

3 3

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

3 5

postdoc bioinformatics at PSB-VIB/UGent
by Stefanie De Bodt 30 Jun '11

30 Jun '11

Dear all, We have a job opening for a postdoctoral scientist in Bioinformatics who will be involved in the integrative analysis of RNA-seq data and growth phenotype data. More detailed information can be found in attach. Please forward to any interested colleagues. Kind regards, Stefanie De Bodt (our apologies for multiple posting) -- ================================================================== Stefanie De Bodt, PhD VIB Department of Plant Systems Biology, UGent Technologiepark 927 B-9052 Gent Belgium Tel: 32 (0)9 3313692 Website: http://www.psb.ugent.be ==================================================================

1 0

2 Ph.D. student positions in Systems Biology for Tissue Engineering
by Liesbet Geris 30 Jun '11

30 Jun '11

Two PhD student positions in Systems Biology for Tissue Engineering (4 years, fully funded by ERC starting grant) are available immediately in the group of Prof. Liesbet Geris at the University of Liège, Belgium. Work in our group focuses computational modeling for bone tissue engineering. The PhD students will work on the development and evaluation of computation models of the in vitro bone formation process in order to enhance robustness and predictability of the in vitro culture process and the resulting in vivo bone formation. The models range from mechanistic (differential equations) to more phenomenological (Boolean networks, empirical modeling). Dedicated experimental work will be executed at the University of Leuven (Belgium). Candidates should have a strong background in biomedical engineering, systems biology and/or computational modeling. The work will be carried out in a interdisciplinary research environment. Strong communication skills (English) and an open attitude towards other scientific disciplines are necessary. Applications (including a CV and contact details of 3 referees) should be sent by e-mail to: Prof. Dr. Lies Geris Biomechanics Research Unit, U.Liège Chemin des Chevreuils 1 - BAT 52/3|4000 Liège 1|Belgium tel.: +32 4 3669587 | fax : +32 4 3669505 e-mail (1): liesbet.geris(a)ulg.ac.be e-mail (2): liesbet.geris(a)mech.kuleuven.be Additional information : http://www.ltas.ulg.ac.be/cmsms/uploads/File/RESEARCH%20biomedical_GERIS.pdf <http://www.kuleuven.be/prometheus> http://www.kuleuven.be/prometheus http://orbi.ulg.ac.be/browse?type=author <http://orbi.ulg.ac.be/browse?type=author&value=Geris%2C+Liesbet+p084700> &value=Geris%2C+Liesbet+p084700 _______________________________________________ Prof. Liesbet Geris, PhD Biomechanics Research Unit, U.Liège Chemin des Chevreuils 1 - BAT 52/3|4000 Liège 1|Belgium tel.: +32 4 3669587 fax : +32 4 3669505 e-mail (1): liesbet.geris(a)ulg.ac.be e-mail (2): liesbet.geris(a)mech.kuleuven.be <http://www.kuleuven.be/prometheus> http://www.kuleuven.be/prometheus _______________________________________________

1 0

job opening
by Tobias Verbeke 27 Jun '11

27 Jun '11

L.S. OpenAnalytics is an international company based in Belgium that provides data analysis services and products across geographies and industrial sectors. We currently have an open position for a molecular or computational biologist with strong experience in R / BioConductor. More detailed information on the position is available from http://www.openanalytics.eu/jobs Kind regards, Tobias Verbeke -- Tobias Verbeke Manager OpenAnalytics BVBA Kortestraat 30A 2220 Heist-op-den-Berg Belgium E tobias.verbeke(a)openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

1 0

Postdoc or Ph.D. student in Computational Systems Biology (Network analysis of diseases)
by Antony Le Béchec 24 Jun '11

24 Jun '11

Dear all, The Computational Biology Research Unit of the Luxembourg Centre for Systems Biomedicine in collaboration with the Systems Biology Institute (Tokyo, Japan) has the following vacancy Postdoc or Ph.D. student in Computational Systems Biology (Network analysis of diseases) • Fixed-term contract 1 year, 40h/week, may be extended up to 5 years. • Employee status (start date: as soon as possible) • Research will be carried out in Luxembourg and Tokyo Area: Multidisciplinary project in systems biology approaches to model diseases. Tasks/Mission: • Modeling and analysis of biological networks (e.g. gene regulatory networks, metabolic networks, protein-protein interaction networks) will be used to elucidate disease mechanism and development. The goal of this project is the study of different aspects of these networks, including topology, dynamics, and perturbations by combining concepts from different areas of mathematics, such as graph, information and game theories, which then allows a better prediction of how some of major diseases (in particular neurodegenerative diseases, such as Parkinson’s and Alzheimer’s diseases) can be prevented or treated. Collaboration with different medical and clinical research groups will be essential. Profile: • A Ph.D. or Master in Bioinformatics, Computer Science, Biology or a related discipline • Strong computational skills • High interest in researchers with prior experience in mathematical modelling of biological systems especially in network construction and statistical analysis • Excellent working knowledge in English. . Offer: • Opportunity to participate in the development of a newly created LCSB in collaboration with SBI Japan • An exciting international environment • A competitive salary For further information, please contact: Prof. Dr. Antonio del Sol E-mail: antonio.delsol(a)uni.lu Prof. Dr. Hiroaki Kitano E-mail: kitano(a)sbi.jp Applications should contain the following documents: • A detailed curriculum vitae • cover letter mentioning the reference number • list of publications • description of past research experience and future interests • name and addresses of three referees All applications should be sent preferably in electronic version until August 1st , 2011 to the following address: Luxembourg Centre for Systems Biomedicine Universite' du Luxembourg Campus Limpertsberg 162a Rue de la Faiencerie L-1511 Luxembourg Tel: +352-466644-6982 Email: antonio.delsol(a)uni.lu Best regards, Antony Le Béchec -- Dr. Antony Le Béchec University of Luxembourg FSTC - Faculty of Sciences, Technology and communication Campus Limpertsberg 162a, avenue de la Faïencerie L-1511 Luxembourg Tel: (+352) 46 66 44 6581 Email: antony.lebechec(a)uni.lu<mailto:antony.lebechec@uni.lu> www.uni.lu

1 0

PhD studentship or postdoctoral research assistant in Luxembourg
by Antony Le Béchec 23 Jun '11

23 Jun '11

Dear all, Luxembourg Centre for Systems Biomedicine in collaboration with Center for Neurogenomics in Amsterdam is currently seeking a postdoctoral research assistant or PhD student to work in the group of prof. Antonio del Sol. The aim of the project is to investigate novel statistical and data mining techniques to analyze high-throughput high-content functional image data of neuronal proteins implicated in Parkinson’s disease (PD). Human SH-SY5Y neuroblastoma cells are used as an in vitro cell model to study the effects of candidate PD susceptibility genes on dopamine neuron differentiation and viability. Successful candidate will be responsible for the development of scientific methodologies and computational solutions for the interpretation of high-throughput imaging data. Experience in network analysis will be an important asset. QUALIFICATIONS • PhD (or Msc) in bioinformatics, computational biology, computer sciences, statistics or molecular biology; • Excellent verbal and written communication skills; • Experience in the large-scale data analysis and software programming skills; • Experience with machine-learning, feature-selection techniques and network analysis is a definite asset; • Good background in statistics; • Experience with Unix/Linux environment The position is for 3 years for postdoc or 4 years for PhD student and is funded by an FNR Luxembourg grant. The successful candidate will actively participate in grant preparation process. For further information, please contact: prof. dr. Antonio del Sol E-mail: antonio.delsol(a)uni.lu Best regards, Antony Le Béchec -- Dr. Antony Le Béchec University of Luxembourg FSTC - Faculty of Sciences, Technology and communication Campus Limpertsberg 162a, avenue de la Faïencerie L-1511 Luxembourg Tel: (+352) 46 66 44 6581 Email: antony.lebechec(a)uni.lu<mailto:antony.lebechec@uni.lu> www.uni.lu

1 0

Postdoc or Ph.D. position for a position in Computational Systems Biology
by Antony Le Béchec 23 Jun '11

23 Jun '11

Dear all, The Computational Biology Research Unit of the Luxembourg Centre for Systems Biomedicine in collaboration with the Institute for Systems Biology (Seattle, United States) is looking for a postdoc or a Ph.D. candidate in the field of in Computational Systems Biology. The goal is to model and analyze various types of biological networks (e.g. gene regulatory networks, metabolic networks, protein-protein interaction networks) in order to explain mechanisms involved in metastasis of cancer. For this purpose the candidate will explore different aspects of these networks, including topology, dynamics, and perturbations by combining concepts from areas of mathematics including graph theory, information theory and game theory. Collaboration with experimental research group in ISB, Seattle, is essential and the candidate will be given a unique possibility to complement the computational skills with biological knowledge and wet lab practice. Therefore candidates with strong commitment for exploring a fascinating research area and obtaining valuable experience are especially encouraged to contact us for further details. Profile: • Ph.D. or Master in Bioinformatics, Computer Science, Biology or a related discipline • Strong computational skills • Excellent working knowledge in English. For further information, please contact: prof. dr. Antonio del Sol E-mail: antonio.delsol(a)uni.lu Best regards, Antony Le Béchec -- Dr. Antony Le Béchec University of Luxembourg FSTC - Faculty of Sciences, Technology and communication Campus Limpertsberg 162a, avenue de la Faïencerie L-1511 Luxembourg Tel: (+352) 46 66 44 6581 Email: antony.lebechec(a)uni.lu<mailto:antony.lebechec@uni.lu> www.uni.lu

1 0

Vacancy bioinformatician @ PSB
by Thomas Van Parys 22 Jun '11

22 Jun '11

Dear all, In order to strengthen the synergy between wet- and dry-labs within PSB, and to support the use of bioinformatics approaches by wet-lab scientists, PSB is looking for an *Experienced Bioinformatician* May we ask you to spread the vacancy attached to your colleagues in the field? -- ================================================================== Thomas Van Parys Tel:+32 (0)9 331 36 95 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM thomas.vanparys(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be ==================================================================

1 0