February 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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Vacancy Researcher Bioinformatics for Metabolomics
by Ham, Roeland van 24 Feb '11

24 Feb '11

Please find below a vacancy for Researcher Bioinformatics for Metabolomics Wageningen University & Research Centre, Plant Research International Wageningen (The Netherlands), 36 hours per week Reference number: PSG-BIOS-0002 Background: Metabolomics is a functional genomics technology that enables comprehensive characterization of the biochemical composition of a biological sample. With the increasing sophistication and throughput of current high-resolution mass spectrometry platforms, metabolomics datasets are becoming ever larger and more complex. Software is needed to enable the data to be processed and managed prior to their statistical analysis and biological interpretation.A dedicated workflow management system needs to be in place with which reusable computational pipelines can be built and exchanged between researchers. Furthermore, metabolite information scattered over distributed databases needs to be organized and integrated in order to accelerate metabolite annotation. We are addressing these needs through development of a metabolomics data support platform via internal and national / international collaborations. Job description: A position for an enthusiastic researcher is available within the Business Unit Bioscience at Plant Research International (PRI) to participate in the development of our in-house metabolomics support platform. This development is central to all projects related to bioinformatics for metabolomics. It is therefore essential that the candidate has the ability to take a proactive and coordinating role in this area. Specific tasks will further include implementation or, where necessary, development of databases and tools for automated metabolite annotation, mass-spectral processing, metabolic pathway visualization, and integration of these tools in a metabolomics workflow management environment. In addition the candidate will support biologists with data analysis in various ongoing projects. Profile: We are looking for a communicative team player with: * A recent PhD from a project focusing on chemoinformatics, chemometrics, bioinformatics or on metabolomics involving extensive data management / mining approaches. * Advanced programming and database development skills (fluent in Java, SQL, and preferably in C++, Perl, or Python) * Knowledge of workflow management and webservice technology. Experience in GUI development and data visualization is a plus * Knowledge of mass spectrometry and metabolomics technology is a requirement. Experience in LCMS and/or GCMS-based metabolic profiling and metabolomics data processing is a pre * Ability to work both independently and in close collaboration with bioinformaticians, analytical chemists and biologists in an internationally oriented research group * The drive, ambition and skills to acquire a leading role in the development of a metabolomics data analysis platform within PRI and to initiate new projects in this field Remuneration: We offer a place in an enthusiastic, dynamic and dedicated metabolomics team. Our metabolomics facilities and computational infrastructure are state-of-the-art; You will be situated in one of the world’s leading labs in plant metabolomics. The position is available for one year, with a possible extension of two years, full time. Maximum gross salary will be € 4438,- (scale 11) per month, depending on qualifications and experience. Information: dr. Roeland van Ham, +31-317-481053, roeland.vanham(a)wur.nl<mailto:roeland.vanham@wur.nl>, Dr. Robert Hall, +31-317-480441, robert.hall(a)wur.nl<mailto:robert.hall@wur.nl>, or Dr. Ric de Vos, +31-610960374, ric.devos(a)uwr.nl<mailto:ric.devos@uwr.nl>. Application: Send your letter with CV, list of publications and the names of two references before March 18, 2011 to Mrs. Lydia Bikker, Plant Research International, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl<mailto:vacaturemeldingen.psg@wur.nl> When applying for this job always mention the vacancy number PSG-BIOS-0002.

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Postdoc positions in Computational Biophysics, CWI, Netherlands
by Roeland Merks 17 Feb '11

17 Feb '11

Centrum Wiskunde & Informatica (CWI; www.cwi.nl) in Amsterdam, The Netherlands, has two full time vacancies for a Postdoc position: - One position for a two year period on Computational Biology of Tumour Development. See: http://www.cwi.nl/jobs/postdoc-0 - A three year position on Computational biomechanics of extracellular matrix materials and cell-matrix interactions during blood vessel growth. See: http://www.cwi.nl/jobs/postdoc The openings are research positions within the field of computational biology. The work will be embedded in the Biomodeling and Biosystems Analysis group of the Netherlands Consortium for Systems Biology (www.ncsb.nl) at the CWI in Amsterdam. As the “core modeling group” of the NCSB, the group carries out biomodeling research in collaboration with systems biology groups in partner institutes. Requirements: - The post-doc on Tumour Development modeling is required to have a completed PhD in computational biology or a related discipline. This is not a vacancy in bioinformatics: a background in modeling and simulation is required. The candidate is expected to have affinity with interdisciplinary applications, able to communicate with scientists in biology and bioinformatics, and have excellent programming skills. - The postdoc on extracellular matrix materials modeling is required to have a completed PhD in computational science, numerical mathematics, or a related discipline. The candidate is expected to have affinity with interdisciplinary applications, able to communicate with scientists in (theoretical) biology and mathematics, have excellent programming skills and a background in computational (fluid) mechanics. Both candidates are expected to have a demonstrated record of excellent research, have strong organizational and guidance skills, be able to carry out his/her own research agenda, and to be able to collaborate with colleagues at CWI and other institutions. Candidates are required to have an excellent spoken and written command of English. More Information: - For the postdoc on tumor modeling: http://www.cwi.nl/jobs/postdoc-0 - For the postdoc on extracellular matrix materials: http://www.cwi.nl/jobs/postdoc For general information about working at CWI, see our movies at: http://www.cwi.nl/general/movies-about-cwi Additional information can be obtained from dr. Roeland Merks, email Roeland.Merks(a)cwi.nl (NOT for sending applications), telephone +31(0)20 592 4117, website: www.cwi.nl/~merks Application: Please send your application before 31 March 2011 to: pd(a)cwi.nl. Applications should include a detailed CV, a motivation letter, and a list of publications. ----- Roeland M. H. Merks Netherlands Institute for Systems Biology (NISB) and Centrum Wiskunde & Informatica (CWI) Science Park 123, 1098 XG Amsterdam, The Netherlands Mailing address: P.O. Box 94079, 1090 GB Amsterdam CWI Office Room M246 Roeland.Merks(a)sysbio.nl / Roeland.Merks(a)cwi.nl http://www.cwi.nl/~merks Phone +31 20 592 4117 Fax +31 20 592 4199

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Fwd: [Enfin] CONFERENCE Enabling Systems Biology - April 11-14, 2011 - London - Registration deadline: March 1, 2011
by Anton Feenstra 09 Feb '11

09 Feb '11

Dear colleagues, On behalf of the organising committee, I am pleased to announce that the registrations to the Conference Enabling Systems Biology - April 11-14, 2011 - UCL, London (UK) are now open. ---------- Conference website: http://www.enfin.org/esb ---------- Registration deadline: March 1, 2011 Scope: The conference will gather the current expertise in systems biology approaches used to tackle 4 domains of research: cell cycle, cellular signaling, metabolism and stem cells. The conference will be followed by a workshop where bioinformatics tools developed for predicting discrete protein function, reconstructing networks, and model molecular systems will be demonstrated. The conference is organized by the European Network of Excellence ENFIN, which develops infrastructure for data integration, bioinformatics tools and assessment to enhance Systems Biology in Europe. Venue: University College London, Gower Street , London, United Kingdom Speakers: James ADJAYE, Max-Planck-Institute for Molecular Genetics, Berlin (Germany) Geoffrey BARTON, University of Dundee (UK) Ewan BIRNEY, European Bioinformatics Institute, Hinxton (UK) Michael BOUTROS, Deutsches Krebsforschungszentrum, Heidelberg (Germany) Søren BRUNAK, Centre for Biological Sequence Analysis, Lyngby (Denmark) Martha BULYK, Harvard Medical School (USA) Gianni CESARENI, University Tor Vergata - Rome (Italy) Bertie GÖTTGENS, Cambridge Institute for Medical Research (UK) John HANCOCK, Medical Research Council, Harwell (UK) Jean-Karim HERICHE, European Molecular Biology Laboratory, Heidelberg (Germany) Jaap HERINGA, Centre for Integrative Bioinformatics VU, Amsterdam (The Netherlands) Henning HERMJAKOB, European Bioinformatics Institute, Hinxton (UK) Edda KLIPP, Humboldt University Berlin (Germany) Xuedong LIU, University of Colorado-Boulder (USA) Tomi MAKELA, University of Helsinki (Finland) Aristidis MOUSTAKAS, Ludwig Institute for Cancer Research, Uppsala (Sweden) Stuart NEWFELD, Tempe (USA) Erich NIGG, BioZentrum, Basel (Switzerland) Christine ORENGO, University College London (UK) Christos OUZOUNIS, Institute of Agrobiotechnology, Thessaloniki (Greece) Bernhard PALSSON, University of California at San Diego, (USA) Kerstin SCHREIBER, Technical University Braunschweig (Germany) Eran SEGAL, Weizmann Institute of Science (Israel) Peter SORGER, Harvard Medical School (USA) Giulio SUPERTI-FURGA, Austrian Academy of Sciences, Vienna (Austria) Alfonso VALENCIA, Spanish National Cancer Research Centre, Madrid (Spain) Jaak VILO, QURETEC, Tartu (Estonia) Hans WESTERHOFF, Manchester Centre for Integrative Systems Biology (UK) Ioannis XENARIOS, Swiss Institute for Bioinformatics, Lausanne (Switzerland) Organising Committee: Ewan Birney (European bioinformatics Institute, Hinxton, UK) Chrstine Orengo (University Collage London, UK) Jonathan Lees (University Collage London, UK) James Adjaye (Max-Planck Institute Berlin, Germany) Tomi Mäkelä (Univ. Helsinki, Finland) Marino Zerial (Max Planck Institute Dresden, Germany) Giulio Superti-Furga (Center for Molecular Medicine, Vienna, Austria) Pascal Kahlem (European bioinformatics Institute (EMBL), Hinxton, UK) Best regards, Pascal Kahlem _________________________________________________________________________ Dr. Pascal KAHLEM Project Manager EMBL - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD United Kingdom Line +44(0)1223492588 / Fax +44(0)1223494468 Email: pkahlem(a)ebi.ac.uk Skype: pascalkahlem _________________________________________________________________________ >> European Network of Excellence ENFIN on Systems Biology - www.enfin.org >> European Collaborative Project SYBARIS on Finding biomarkers of anti-microbial drug resistance - www.sybaris-fp7.eu >> European Collaborative Project MICROME - A Knowledge-Based Bioinformatics Framework for Microbial Pathway Genomics - www.microme.eu _______________________________________________ Enfin mailing list Enfin(a)ebi.ac.uk http://listserver.ebi.ac.uk/mailman/listinfo/enfin -- Groetjes, Anton _____________ _______________________________________________________ | | | | _ _ ___,| K. Anton Feenstra | | / \ / \'| | | IBIVU/Bioinformatics - Free University Amsterdam | |( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands | | \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P136 | | | Feenstra(a)few.vu.nl - www.few.vu.nl/~feenstra/ | | | "We Can Dance Like Iggy Pop" (Red Hot Chili Peppers) | |_____________|_______________________________________________________|

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NBIC Conference 2011: April 19 & 20, 2011, Lunteren, the Netherlands
by Femke Francissen 08 Feb '11

08 Feb '11

6th NBIC Conference, April 19 & 20 2011, Lunteren, the Netherlands We are proud to announce the 6th edition of the annual NBIC Conference organized by the Netherlands Bioinformatics Centre (http://www.nbic.nl) - Conference website: http://conference.nbic.nl - Abstract submission deadline: February 18, 2011 - Registration is open! Conference programme: - 4 keynote speakers: o Bas van Steensel - NKI; o Phil Bourne - University of California; o Dorus Gadella - SILS/UvA; o Ewan Birney - EBI, UK. - Parallel sessions with contributed lectures (by abstract selection) - Poster presentations and an application showcase, parallel workshops - Social activities: conference diner and drinks/event on the evening of April 19 - Awards for: best poster, best lecture, best application showcase The day before the conference (Monday, April 18) other meetings are planned, such as a PhD retreat organized by RSG Netherlands: http://www.nbic.nl/about-nbic/nbic-conferences/nbic-conference-2011/rsg-ret… For more information visit the conference website: http://conference.nbic.nl Contact person at the NBIC Office: Femke Francissen, femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>, tel. 024-3619500

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2011 Galaxy Community Conference, May 25-26, Lunteren, the Netherlands
by Femke Francissen 07 Feb '11

07 Feb '11

2011 Galaxy Community Conference, May 25-26, Lunteren, the Netherlands We are pleased to announce the 2011 Galaxy Community Conference, being held May 25-26 in Lunteren, The Netherlands. This year the conference is co-organized by the Netherlands Bioinformatics Centre (NBIC). The meeting will feature two full days of presentations and discussion on extending Galaxy to use new tools and data sources, deploying Galaxy at your organization, and best practices for using Galaxy to further your own and your community's research. Links: http://galaxy.psu.edu/gcc2011/Home.html and http://www.nbic.nl/about-nbic/events/all-events/detail/article/2011-galaxy-… Overview: This event aims to engage a broader community of developers, data producers, tool creators, and core facility and other research hub staff to become an active part of the Galaxy community. We'll cover defining resources in the Galaxy framework, increasing their visibility and making them easier to use and integrate with other resources, how to extend Galaxy to use custom data sources and custom tools, and best practices for using Galaxy in your organization. Additional topics include, but are not limited to: - Talks submitted by the Galaxy community - Integration of tools (including NGS analysis tools) and distributed job management - Deployment of Galaxy instances on local resources and on the Cloud - Management of large datasets with the Galaxy Library System - Using the Galaxy LIMS functionality at NGS sequencing facilities - Visualizing Data without leaving Galaxy - Performing reproducible research - Performing and sharing complex analyses with Workflows - An "Introduction to Galaxy" session, offered on May 24, for Galaxy newcomers Registration: The conference fee is €100 on or before April 24, and €120 after that. The meeting is being held at the Conference Centre De Werelt in Lunteren, The Netherlands, which is also the conference hotel. You are encouraged to register early, as space at the hotel (and at the "Intro to Galaxy" session) is limited and is likely to fill up before the conference itself does. Link: http://galaxy.psu.edu/gcc2011/Register.html Abstract submission: Abstracts are now being accepted for short oral presentations. Proposals on any topic of interest to the Galaxy community are welcome and encouraged. The abstract submission deadline is the end of February 28. Link: http://galaxy.psu.edu/gcc2011/Abstracts.html Sponsors: The 2011 Galaxy Community Conference is co-sponsored by the US National Science Foundation (NSF), and the Netherlands Bioinformatics Centre (NBIC). Links: http://www.nbic.nl/ and http://www.nsf.gov/ About Galaxy: Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biomedical research. - Accessibility: Galaxy enables users without programming experience to easily specify parameters and run tools and workflows. - Reproducibility: Galaxy captures all information necessary so that any user can repeat and understand a complete computational analysis. - Transparency: Galaxy enables users to share and publish analyses via the web and create Pages--interactive, web-based documents that describe a complete analysis. Galaxy is open source for all organizations. The public Galaxy service (http://usegalaxy.org) makes analysis tools, genomic data, tutorial demonstrations, persistent workspaces, and publication services available to any scientist that has access to the Internet. Local Galaxy servers can be set up by downloading the Galaxy application and customizing it to meet particular needs. We are looking forward to a great conference and hope to see you in Lunteren! The Galaxy and NBIC Teams

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Bioinformatics postdoc in Brussels
by Vincent Detours 01 Feb '11

01 Feb '11

A postdoc position in bioinformatics is immediately available at IRIBHM, Université Libre de Bruxelles, Belgium, for 2 years. IRIBHM is a leading European molecular biology lab with 130 researchers. The successful applicant will join an interdisciplinary team of molecular biologists and bioinformaticians passionate about cancer research. He/she will tackle the thyroid cancer transcriptome data sets generated using cutting edge microarray and next generation sequencing platforms. The project addresses fundamental problems related to thyroid cancer progression. Only applicants with demonstrated proficiency in programming, and statistics and/or machine learning will be considered. Experience with sequence data, genome-wide data sets and demonstrated interest in oncogenomics will be assets. We highly value creativity and autonomy. Please, e-mail PDFs of 1) a cover letter explaining why you are skilled and motivated for the job, 2) your CV with the contact of three qualified referees, and 3) a copy of your best (preferably first author) publication to Vincent Detours, vdetours(a)ulb.ac.be, with 'postdoc-w-2011' in the subject line.

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