- BBClist - maillist.psb.ugent.be

Tenure Track Position - Personal Genomic Data Analysis
by Yves Moreau 01 Sep '09

01 Sep '09

Dear Colleagues, We have a full-time tenure-track position opening up at the University of Leuven for a candidate with an interest in bioinformatics and computational biology for next-generation sequencing, personal genomes, etc. Deadline for application is September 30. Through our collaboration with the University Hospitals and the Genomics Core, we offer a great environment for this kind of research. Best regards, Yves Moreau ================================== Tenure Track Position - Personal Genomic Data Analysis The Science, Engineering and Technology Group of K.U.Leuven invites applications for a full-time academic position in genomic data analysis at the Department of Electrical Engineering-ESAT. See http://www.kuleuven.be/personeel/jobsite/vacatures/ engineering.html for more information DUTIES Research The tenure track positions are intended to foster high quality research in strategically selected domains. The successful candidate will be expected to develop a research programme that delivers excellent, international level research results and to support and enhance national and international research collaboration in genomic data analysis for personalized medicine. This research will concentrate on integrative data mining methodologies that leverage complex genomic data towards emerging strategies for personalized medicine. Specifically, array and next- generation sequencing technologies deliver unprecedented amounts of data that need to be translated into both fundamental and practical insights towards human health and disease, including congenital disease, complex disorders, and cancer. In particular, the research will focus on how genetic variation causes or modulates disease in different individuals, and how such knowledge can be translated into improved diagnosis, understanding of the disease pathways, or better drug treatments. While a specific therapeutic area could be targeted, the analysis strategies should be broadly applicable and part of the work will be dedicated towards setting up an infrastructure that can deploy such strategies in a broad range of collaborations across the university. Research will be conducted within the framework of the research centre BioSCENTer and the centre of excellence SymBioSys, and in close collaboration with several of the genomic facilities of the university. Teaching The successful candidate will take on teaching responsibilities in the Master of Bioinformatics and/or in other faculties. He or she is expected to meet the reigning K.U.Leuven standards regarding academic program level and orientation and to adhere to the K.U.Leuven’s concept of education. Commitment to quality of education as a whole is a matter of course. QUALIFICATIONS Candidates should hold a PhD or doctoral degree in Engineering, Computer Science or related fields. They are expected to be excellent researchers who show independence and originality. They are dedicated to high-quality teaching and will contribute to the quality of both research and teaching at the Faculty and the Department. The candidate's research ability of the candidate should be evidenced by publications in international peer-reviewed journals. International research experience is most important. In their application, candidates should include a description of objectives they wish to realise/methods they plan to use during the five-year period of the position. At K.U.Leuven the main language of instruction is Dutch. Successful applicants, who are not proficient in Dutch, will be provided language training in order to be able to also instruct in the Dutch language within three years time. Near-native proficiency in the English language is expected of all applicants. The full-time position will be offered for a period of five years starting on March 15, 2010 at the level of assistant professor (docent). A positive evaluation at the end of the five-year appointment will result in a tenured appointment as associate professor (hoofddocent). The K.U.Leuven pursues a policy of equal opportunity and diversity. Contact person: Prof. Yves Moreau, yves.moreau(a)esat.kuleuven.be If you experience any technical difficulties while completing your online application, please contact Katoe Buyle, katoe.buyle(a)pers.kuleuven.be tel.: +32 (0)16 328 324. DEADLINE September 30, 2007 Yves Moreau, K.U.Leuven ESAT-SCD & SymBioSys tel: +32 16 32 17 09 www.kuleuven.be/symbiosys fax: +32 16 32 19 70 www.kuleuven.be/bioinformatics If it is important, call my mobile +32 478 32 40 11 --- do not rely on email. *** ECCB10 *** www.eccb10.org *** ECCB10 *** *** Join us @ ECCB10, Belgium, Sept. 26-29, 2010 *** European Conference on Computational Biology

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Group coordinator position for Proteomics Identifications Database (PRIDE)
by Henning Hermjakob 10 Aug '09

10 Aug '09

http://www.embl.de/aboutus/jobs/jobs_embl_ebi_hinxton/2009/w_09_063_ebi/ind… -- Best regards, Henning

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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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progress report
by fred opperdoes 18 Jul '09

18 Jul '09

Dear All, We got almost at 350 signatures in 4 days for our petition "Keep BEN Alive" http://bit.ly/fJ5Ep . Not bad at all:-). We got also strong support from users of many EMBNet Nodes in the other European countries . Don't stop now!. Maybe we will get 400 signatures this WE? Thank you all! Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf

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GMOD Community Meeting, 6-7 August, 2009, Oxford UK
by Dave Clements 18 Jul '09

18 Jul '09

There will be a GMOD Community Meeting, 6-7 August, 2009 at the University of Oxford, in Oxford, UK. GMOD (http://gmod.org) is a collection of interoperable, open-source software components for managing, visualizing, annotating, and sharing biological data. GMOD is also a community of users and developers addressing common challenges with their biological data. The popularity of next generation sequencing and other high-throughput methods has made this GMOD meeting particularly timely. GMOD meetings are an excellent opportunity to learn best practices from other researchers, to meet GMOD users and developers, and to learn and affect what is coming in the project. As with previous meetings, there will be a mixture of project talks, component-focused talks, and user talks. Registration for the meeting is now open and space is available on a first come, first served basis. Attendance is limited to the first 55 people to register. The meeting cost is £50. See http://gmod.org/wiki/August_2009_GMOD_Meeting to register for more. Please join us in Oxford this August. Cheers, Dave Clements GMOD Help Desk -- Register now for the August GMOD Meeting: http://gmod.org/wiki/August_2009_GMOD_Meeting

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Benelux Bioinformatics Conference 2009 in Liège, first announcement
by Pierre Geurts 17 Jul '09

17 Jul '09

Dear Colleagues, This email to announce you that the next Benelux Bioinformatics Conference (BBC'09) will be organised in Liège, Belgium. The key dates are as follows: - Conference: December 14-15, 2009 - Deadline for abstract submission: October 11, 2009 Please mark these dates in your agenda! Further information will be sent in August. Best regards, Pierre Geurts

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Two open positions at BITS, VIB's Bioinformatics Training and Service Facility
by Mark Veugelers 14 Jul '09

14 Jul '09

[cid:image001.jpg@01CA0473.359D93B0] VIB (http://www.vib.be) is looking to expand its Institute-wide bioinformatics platform, BITS (Bioinformatics Training and Services; http://www.bits.vib.be) with two positions: 1. Next-Generation Sequencing Bioinformatics Analyst 2. Bioinformatics Trainer Job descriptions: 1. Next-Generation Sequencing Bioinformatics Analyst You will play a key role in the processing, analysis, visualization and dissemination of genomics datasets to support research groups with the analysis of genome-wide next-generation sequencing experiments. Responsibilities include the analysis of next-generation DNA sequence data from multiple platforms, including alignment, genome assembly and annotation, genome re-sequencing, microRNA deep-sequencing, Chip-seq, gene expression analysis, SNP-analysis etc....for multiple species, including human. In this position, you will also meet with researchers and group leaders to discuss study design and sequence analysis strategies. You will assist in the analysis of the generated data and disseminate information through comprehensive research reports and presentations. Additionally, you will evaluate new and existing algorithms, software (commercial and open source) and computer infrastructure requirements to efficiently set up data analysis pipelines. You will have close interactions with other VIB facilities such as the VIB Microarray Facility and the VIB Genetic Service Facility. Profile We are seeking an experienced bioinformatics scientist for this position. Ideally, you will have a Master's or PhD Degree in Biology, Biomedical Sciences, Bioinformatics or a related degree. Strong experience with bioinformatics methods, databases, software (especially sequence analysis tools), statistics and managing large data sets is required. A good working knowledge of Linux/Unix and programming languages such as Perl, SQL, R, Java, Python or C would be desirable. Excellent collaboration, communication and reporting skills are also a requisite. Familiarity with next generation DNA sequencing technologies is a plus. Contact Marijke Lein (HR Director VIB) - Marijke.Lein(a)vib.be<mailto:Marijke.Lein@vib.be> 2. Bioinformatics Trainer As Bioinformatics Trainer, you will be responsible for training/teaching of VIB-scientists in the efficient use of the latest bioinformatics software and database tools. This will include organizing, hosting and teaching workshops/tutorials/seminars on how to efficiently access and use life sciences data and how to use bioinformatics software and databases, both at the beginner and advanced level. You will provide bioinformatics user support, including updating the BITS website, troubleshooting and helping in the analysis of genome, transcriptome, proteome, imaging data etc... You will also provide support to individual scientists to solve bioinformatics bottlenecks and problems. You will review and decide on the acquisition of new software tools/databases at the institutional level. We offer: Access to a broad platform of science and technology in a stimulating environment. Interactions and collaborations with top level scientists and bioinformaticians. A unique opportunity to expand your experience and knowledge of science and bioinformatics and to build a network of scientists and bioinformaticians. Profile * You have a university degree in Sciences (Biology/Biochemistry/Biotechnology/Bioinformatics) with several years of Bioinformatics experience * You are familiar with the latest bioinformatics tools and databases (Ensembl, TAIR, ...), sequence analysis, and have at least basic knowledge of computational programming in common scripting languages, such as (Bio)-perl or (Bio)-python. * You have demonstrated capabilities in data analysis using commercial and freeware software. Excellent knowledge of data/literature mining is a plus. * Knowledge of microarray data analysis and statistics is a plus. * Excellent knowledge of English, communication and teaching skills and the ability to interact proactively with research scientists are essential requirements. * Organizational talent. Contact Marijke Lein (HR Director VIB) - Marijke.Lein(a)vib.be<mailto:Marijke.Lein@vib.be>

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1st Symposium on Systems Genetics; October 1-2, 2009 in Groningen
by Morris Swertz 14 Jul '09

14 Jul '09

FYI: ------------------------------------------------------------------------ Appologies for multiple postings.

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Keep BEN alive
by fred opperdoes 13 Jul '09

13 Jul '09

Dear colleagues, I have now created an on-line petition "Keep BEN alive" where you can support our initiative to try and reverse the unfortunate decision of the Belgian Science Policy makers to stop the funding of BEN, the Belgian bioinformatics server. Please visit http://www.petitionspot.com/petitions/belgianben/ to sign this petition. Thank you for your support, Fred R. Opperdoes, Secretary Belgian Society of Biochemistry and Molecular Biology Avenue Hippocrate 74-75, B-1200 Brussels, Belgium Tel: ++32-2-764.74.39 Fax: ++32-2-762.68.53 E-mail: info(a)biochemistry.be PGP key: 0x037DDD42 Web site: http://www.biochemistry.be Blog: http://www.biochemistry.be/bmb_blog/ Twitter: http://twitter.com/biochem_be Facebook: http://www.facebook.com/profile.php?id=100000004937038&ref=nf

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Ghent university is looking for a tech transfer manager and a PhD student in bioinformatics ...
by Yves Van de Peer 08 Jul '09

08 Jul '09

--------------------------------------------- The computational systems biology team in the Bioinformatics & Evolutionary Genomics group (http://bioinformatics.psb.ugent.be/) at the VIB Department of Plant Systems Biology studies the structure, function and evolution of biological networks in multiple organisms. As part of its research, the team continuously develops, in collaboration with other Flemish universities, novel software tools for the integration of large-scale data sets and the inference of regulatory networks. To strengthen the technology transfer mission of the department, we are currently looking for a Systems biology technology transfer manager As a member of VIB's technology transfer team, you will be responsible for the commercialization of our software tools and, in close collaboration with the research scientists, for the development of software usability improvements. Responsibilities include: * Developing and implementing software improvements and extensions, especially with regards to usability improvement (user interface, output visualization, etc.) and integration of multiple tools (often written in different programming environments). * Setting up collaborations and providing consultancy services for software testing and validation: definition of suitable test data sets, NDA, running software and analyzing output together with the company's bioinformatics team. * Writing project applications (e.g. IWT) for proof-of-concept studies. * Participating in meetings with bio, pharmaceutical, agbio and food companies to present our in-house systems biology software tools. Profile: * PhD in computational or biological sciences, with experience or strong interest in computational systems biology. * Fluent in English. * Excellent communication skills. * Strong interest in technology transfer and research commercialization. * Fluent in multiple programming languages (Java, Matlab, Perl, etc.). * Work experience in industry is a plus. Contact: If you have the necessary skills and would like to be considered, please send your resume by email to Yves Van de Peer ( yves.vandepeer(a)psb.ugent.be <mailto:yves.vandepeer@psb.ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ). Applications will be accepted until the position is filled. --------------------------------------------- The Laboratory of Protistology and Aquatic Ecology and the Bioinformatics Group of the VIB Department of Plant Systems Biology, University of Ghent, Belgium are seeking a PhD student in Bioinformatics Analysis of Diatom Life Cycle Regulation Job description: We are looking for a motivated and enthusiastic PhD student for the Laboratory of Protistology and Aquatic Ecology working on diatom biology and physiology. You will be involved in a project where transcriptomics and genomic investigations are used to understand key aspects of diatom life cycle regulation. Your work will be highly complementary to ongoing research in the group, where cDNA-AFLP, microarray, and interaction data related to diatom cell division, growth and sexual reproduction are generated. You will be responsible for the application and development of computational methods to analyze and integrate these data, to be performed in the Bioinformatics group of PSB/VIB, which has strong experience in genomics data analysis and large computer facilities (http://bioinformatics.psb.ugent.be/) You will collaborate with both experimental and computational biologists to obtain an understanding of diatom life cycle control. Profile: * You have a degree in Bioinformatics, Informatics, Biology, Biotechnology, Biochemistry or Bioengineering * You are motivated by Biology and the new opportunities given to enlarge knowledge through the analysis of Genome data * You read, write and speak English fluently * You have good communication skills. * You are a team player. You are independent and like to take initiative. You are flexible. We offer: Contract of 1 year, within Ghent University, with the possibility of prolongation. Start date: As soon as possible, the position remains vacant until a suitable candidate is found. Further information can be obtained by contacting Prof. Wim Vyverman ( Wim.Vyverman(a)ugent.be <mailto:Wim.Vyverman@ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) or Prof. Yves Van de Peer ( yves.vandepeer(a)psb.vib-ugent.be <mailto:yves.vandepeer@psb.vib-ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) Application: Send your letter of motivation, your CV and references to Prof. Wim Vyverman ( Wim.Vyverman(a)ugent.be <mailto:Wim.Vyverman@ugent.be> This e-mail address is being protected from spambots. You need JavaScript enabled to view it ) -- Yves Van de Peer, PhD. Professor in Bioinformatics and Genome Biology Group Leader Bioinformatics and Evolutionary Genomics VIB Department of Plant Systems Biology, UGent Ghent University Technologiepark 927 B-9052 Ghent Belgium Phone: +32 (0)9 331 3807 Cell Phone: +32 (0)476 560 091 Fax: +32 (0)9 331 3809 email: yves.vandepeer(a)psb.vib-ugent.be http://bioinformatics.psb.ugent.be/

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