February 2009 - BBClist - maillist.psb.ugent.be

Bioinformatics Postdoc, Amsterdam, NL
by Lodewyk Wessels 05 Aug '09

05 Aug '09

BIOINFORMATICS POSTDOC Topic: Pathway-based tumour characterisation by alignment against cell panels along multiple molecular dimensions. Research: Astra Zeneca Oncology has constructed large cell panels to serve as in vitro models for drug response. These cell panels have been extensively characterized by mutation analysis, mRNA expression, aCGH, response to a wide variety of drugs, micro-RNA expression and phosphoprotein characterization. In parallel, the same measurements are being performed on a collection of colorectal samples. In this project two aims are pursued. First, a comparative analysis will be performed between the cell line data and the tumor data to determine the multi-dimensional molecular states spanned by the cell lines and whether these states faithfully recapitulate the space spanned by a representative and clinically relevant selection of tumor samples. Guided by this mapping and by following a pathway-based approach, integrative modeling will be applied on the cell line panel data to construct models predictive of resistance. Job description: The successful candidate will be responsible for the bioinformatics analysis of the cell line and tissue data. More specifically, these tasks include 1) constructing a comprehensive gene list of the PI3K and ERK network; 2) Molecular characterisation of the colorectal cell panel and tumour samples through integrative analysis of the various data sources within the space spanned by the identified network genes and 3) Pathway-based alignment of cell panel to tumours to determine the extent to which the cell panel recapitulates the heterogeneity in the tissue set. Location: The position is embedded within the Bioinformatics and statistics group lead by Dr Lodewyk Wessels (http://bioinformatics.nki.nl) at the Netherlands Cancer Institute, Amsterdam and the Oncology Informatics group, Discovery Medicine, Astra Zeneca, Alderley Park, UK lead by Dr Tim French. We plan to have regular meetings, and the postdoc will also spend time at both locations. Requirements: Candidates should fulfill the following criteria. - MSc or PhD in one of the following areas: bioinformatics, engineering, computer science, statistics, physics, biotechnology, or biology. - Knowledge of fundamental aspects of cancer biology, especially signalling pathways. - Knowledge of fundamental aspects of computer science (algorithms and data structures, programming languages). - Knowledge or experience of informatics. - Knowledge of statistics, artificial intelligence or bioinformatics is highly desirable. Conditions of Employment: The successful candidate will be employed by the Netherlands Cancer Institute. The employment conditions follow general employment rules as laid down in the 'CAO' for hospitals. The salary will be determined depending on education and experience. Contact and Applications: Dr. Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl or Dr Tim French Discovery Medicine, Cancer Bioscience, tel. +44 1625-519922 or e-mail: Tim.French(a)AstraZeneca.com. Applicants should send a CV, list of publications and the names and addresses of at least two persons that can be approached to obtain further information. Website: http://bioinformatics.nki.nl Closing date: 30 January 2009 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)634485714 http://bioinformatics.nki.nl/ 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)634485714 http://bioinformatics.nki.nl/

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Postdoc Plant Genome Assembly, Reference number: DPW 09-10
by Ham, Roeland van 25 Feb '09

25 Feb '09

Postdoc Plant Genome Assembly Laboratory of Bioinformatics of Wageningen University and Researchcentre Wageningen (The Netherlands), 38 hours per week Reference number: DPW 09-10 Background: Wageningen University and Research Centre (WUR) is involved in the international efforts to sequence the genomes of the Solanceous crops tomato and potato. To support these efforts, WUR has recently extended its sequencing capacity with the acquisition of a next generation sequencing platform. Our activities in plant genome sequencing are supported by a strong team of bioinformaticians involved in (comparative) genome analysis and responsible for the development and application of genome assembly and annotation strategies. The tomato genome is being sequenced by the SOL Consortium, a collaboration of 10 countries and in which the dutch effort is financed through the Centre of BioSystems Genomics and the EU-SOL project. Recently, the consortium has begun whole genome shotgun sequencing using novel technologies as a complementary approach to the ongoing BAC-by-BAC sequencing strategy. This initiative is led by the CBSG and EU-SOL from the Netherlands and covers coordination of the whole genome shotgun assembly effort. Job description: A postdoc position is immediately available in the Laboratory of Bioinformatics of WUR to work on the whole genome shotgun assembly of the tomato genome. This will involve very intensive (inter)national collaboration. Datasets will include sequence data from the Roche/454, SOLiD, Solexa and Sanger-ABI platforms. The candidate will participate in a team involved in the development of a bioinformatics platform for next generation sequencing technologies, which will be based on an advanced ICT infrastructure (Grid computing), webservices and workflow management technology. This development is linked to the BioAssist <http://www.nbic.nl/support/bioassist/> initiative of the Netherlands Bioinformatics Centre (NBIC). Profile: We are looking for a communicative team player with: * A PhD in bioinformatics or related area and a strong publication record * Strong background in sequence analysis and genome assembly * Advanced programming and database development skills (Java, SQL, Python, C++ or Perl) * Knowledge of next generation sequencing technologies and the data produced by these platforms * Experience with Grid computing, workflow management technology and creating and implementing webservices * The drive, ambition and skills to make a frontier sequencing project to a success; for this a cooperative spirit and good communication skills are a must. Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with laboratory experts in genomics and sequencing. The position is available for one year, full time, with a possible extension. Maximum gross salary will be EUR 4374,- (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> . Application: Send your letter with CV, list of publications and the names of two references before March 16th, 2009 to Mrs. Dorien Wissink, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number DPW 09-10

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Vacancy: scientific programmer, Delft
by Dick de Ridder 06 Feb '09

06 Feb '09

Delft University of Technology has a vacancy for a scientific programmer (m/f) in the Delft Bioinformatics group. Please feel free to bring this vacancy to the attention of any suitable candidate. The organisation: The faculty of Electrical Engineering, Mathematics and Computer Science of Delft University of Technology is known world wide for its high academic quality and social relevance of its research programs. The faculty’s excellent facilities accentuate its international position in teaching and research. The faculty offers an interdisciplinary setting for its 500 employees, 350 PhD students and 1700 undergraduates. Together they work on a broad range of technical innovations in the fields of sustainable energy, telecommunications, microelectronics, embedded systems, computer and software engineering, interactive multimedia and applied mathematics. Within the faculty, the Computer Science Department of Mediamatics focuses on media and knowledge processing. Four important application domains are telecommunications, consumer electronics, industrial automation, and life/health sciences. The department consists of three groups: Computer Graphics, Human Computer Interaction and Information and Communication Theory. The latter group focuses on processing, analysis, and interpretation of multimedia, biological and biomedical data with knowledge-based signal processing techniques, and is home to the Delft Bioinformatics group. The Delft Bioinformatics group has a strong background in pattern recognition/machine learning, and we apply this expertise to design (predictive) models that contribute to novel biological insights. Recent examples of our contributions include the discovery of 250 novel cancer genes by analyzing and modelling insertional mutagenesis data; proposing (combinatorial) cultivation dependent transcription factor activities based on a decomposition of transcriptomics data; assessing gene therapy protocols by integrating viral insertions with gene expression data; and modelling the mechanisms that underlie chromosomal arrangement in the nucleus. This is accomplished by closely co-operating with (among others) biotechnologists at Delft University of Technology and molecular biologists at the Netherlands Cancer Institute in Amsterdam, university medical centres in Rotterdam and Leiden, and companies such as DSM and Organon. Job description: The Delft Bioinformatics group is part of the Netherlands Bioinformatics Center (NBIC, www.nbic.nl) which coordinates bioinformatics research, tool development, service and education in the Netherlands. For the NBIC tool development and service program, we are looking for a scientific programmer that can take up a wide a variety of short-term bioinformatics problems arising within the different Genomic Centers in the Netherlands (www.ngi.nl) and in particular within the Kluyver Center for Genomics of Industrial Fermentation (www.kluyvercentre.nl) The candidate should be able to independently perform routine data analyses using existing tools, and to assist researchers in the different Genomic Centers in practical issues in the application of bioinformatics, e.g. through setting up databases, developing (web-based) applications, etc. Furthermore, (s)he should aid in the implementation, delivery and support of novel data analysis algorithms developed by researchers in the Netherlands Bioinformatics Centre. Finally, the candidate should act as an interpreter between the biologists and bioinformaticians, by signalling opportunities for the development and application of novel data analysis tools and setting up collaborations to this end. Job requirements: The candidate should have a well-founded basis in statistics, computer science and molecular biology, have excellent programming skills and should hold a BSc or higher in Bioinformatics or Computational Biology (or Computer Science, with a strong affinity to molecular biology and genomics). The candidate should have experience with working in multidisciplinary teams. (S)he should have good communication and organization skills, have a service-oriented attitude and be an enthusiastic team player. Conditions of employment: This is a full-time, fixed-term position for a period of four years. The starting salary, depending on age and experience, varies from scale 8 to 9 (€ 2.267-3.422 gross per month). TU Delft offers an attractive benefits package, including a flexible work week, free high-speed Internet access from home, and the option of assembling a customized compensation and benefits package (the 'IKA'). Salary and benefits are in accordance with the Collective Labour Agreement for Dutch Universities. Application and information: For more information about this position, please contact Marcel Reinders, phone: +31 (0)15-2786424, e-mail: M.J.T.Reinders(a)tudelft.nl; or Dick de Ridder, phone: +31 (0)15-2785114, e-mail: D.deRidder(a)tudelft.nl. To apply, please send a CV together with a letter of application and two references, before March 1, 2009 to: Dick de Ridder, Information & Communication Theory Group, Faculty of EEMCS, Delft University of Technology, Mekelweg 4, 2628 CD Delft, The Netherlands; or by e-mail to D.deRidder(a)tudelft.nl.

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Vacancy PhD student
by Stefan Weckx 06 Feb '09

06 Feb '09

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Postdoc Plant Genome Assembly, Reference number: DPW 09-10
by Ham, Roeland van 05 Feb '09

05 Feb '09

Postdoc Plant Genome Assembly Laboratory of Bioinformatics of Wageningen University and Research Centre Wageningen (The Netherlands), 38 hours per week Reference number: DPW 09-10 Background: Wageningen University and Research Centre (WUR) is involved in the international efforts to sequence the genomes of the Solanceous crops tomato and potato. To support these efforts, WUR has recently extended its sequencing capacity with the acquisition of a next generation sequencing platform. Our activities in plant genome sequencing are supported by a strong team of bioinformaticians involved in (comparative) genome analysis and responsible for the development and application of genome assembly and annotation strategies. The tomato genome is being sequenced by the SOL Consortium, a collaboration of 10 countries and in which the dutch effort is financed through the Centre of BioSystems Genomics and the EU-SOL project. Recently, the consortium has begun whole genome shotgun sequencing using novel technologies as a complementary approach to the ongoing BAC-by-BAC sequencing strategy. This initiative is led by the CBSG and EU-SOL from the Netherlands and covers coordination of the whole genome shotgun assembly effort. Job description: A postdoc position is immediately available in the Laboratory of Bioinformatics of WUR to work on the whole genome shotgun assembly of the tomato genome. This will involve very intensive (inter)national collaboration. Datasets will include sequence data from the Roche/454, SOLiD, Solexa and Sanger-ABI platforms. The candidate will participate in a team involved in the development of a bioinformatics platform for next generation sequencing technologies, which will be based on an advanced ICT infrastructure (Grid computing), webservices and workflow management technology. This development is linked to the BioAssist <http://www.nbic.nl/support/bioassist/> initiative of the Netherlands Bioinformatics Centre (NBIC). Profile: We are looking for a communicative team player with: * A PhD in bioinformatics or related area and a strong publication record * Strong background in sequence analysis and genome assembly * Advanced programming and database development skills (Java, SQL, Python, C++ or Perl) * Knowledge of next generation sequencing technologies and the data produced by these platforms * Experience with Grid computing, workflow management technology and creating and implementing webservices * The drive, ambition and skills to make a frontier sequencing project to a success; for this a cooperative spirit and good communication skills are a must. Remuneration: a young, dynamic and driven bioinformatics group, focusing on computational challenges in a range of comparative and functional genomics related topics; a state-of-the art computational infrastructure; close collaboration with laboratory experts in genomics and sequencing. The position is available for one year, full time, with a possible extension. Maximum gross salary will be EUR 4374,- (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> . Application: Send your letter with CV, list of publications and the names of two references before February 23, 2008 to Mrs. Dorien Wissink, Department Personnel & Organisation, P.O. Box 16, 6700 AA Wageningen, The Netherlands. E-mail: vacaturemeldingen.psg(a)wur.nl <mailto:lydia.bikker@wur.nl> . When applying for this job always mention the vacancy number DPW 09-10

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