December 2008 - 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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January 12: CINBIOS
by Marianne Rooman 29 Dec '08

29 Dec '08

Dear all, Please have a look at the program (attached) of the CINBIOS meeting (centre de BioInformatique et BioModélisation, ULB), which will take place on Monday January 12 at the ULB. Everybody is wellcome ! All the best, Marianne Rooman ------------------------------------------------------------------------- Marianne Rooman Unité de BioInformatique génomique et structurale Service de BioSystèmes, BioModélisation & BioProcédés (3BIO) Université Libre de Bruxelles avenue Roosevelt 50, CP 165/61, 1050 Bruxelles, Belgium Tél: +32-2-650 2067 Email: <mailto:mrooman@ulb.ac.be> mrooman(a)ulb.ac.be -------------------------------------------------------------------------

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BioSapiens School of Bioinformatics in Brussels
by Jacques van Helden 16 Dec '08

16 Dec '08

The Laboratoire de Bioinformatique des Génomes et des Réseaux (BiGRe) from the Université Libre de Bruxelles is organizing the 9th Biosapiens European School of Bioinformatics The course will run from January 26th to 30th 2009, at ULB (Brussels , Belgium). The goal of the school is to initiate biologists to the utilization of bioinformatics software tools. The course will cover the following topics: Biological databases Sequence analysis Protein structures Analysis of regulatory sequences Biomolecular networks and pathways Systems biology More information and registration form are available from the Web site: http://www.bigre.ulb.ac.be/9esb/ Registrations are restricted to a maximum of 40 participants. The deadline for applications is January 15th 2009. Contact: Olivier Sand <oly(a)bigre.ulb.ac.be> Myriam Loubriat <mloubria(a)ulb.ac.be> Please spread this information around.

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JOBIM 2009
by Jacques van Helden 10 Dec '08

10 Dec '08

--------------------------------------------------------------------------------------------- JOBIM - Journées Ouvertes en Biologie Informatique Mathématiques Nantes, du 9 juin au 11 juin 2009 --------------------------------------------------------------------------------------------- [english version below] La dixième édition de JOBIM se tiendra du 9 juin au 11 juin 2009 à Nantes, au Palais des Congrès. Toutes les informations sont disponibles à l'adresse http://www.jobim2009.fr Vous pouvez également contacter le comité d'organisation jobim09(a)univ-nantes.fr ---------------------------------------------------------------------------------------------- Appel à communication ---------------------------------------------------------------------------------------------- Les thèmes abordés par JOBIM couvrent le spectre de la bio-informatique dans ses multiples composantes. Cela comprend à la fois des aspects méthodologiques en amont (modélisation mathématique, informatique, statistique, physique) et des contributions applicatives allant jusqu'à l'établissement de nouveaux résultats en biologie. Sans être exhaustif, on peut citer les domaines suivants : * génomique, génomique comparative et métagénomique * réseaux biologiques * modélisation des systèmes dynamiques et biologie des systèmes * analyse de séquences, comparaison de génomes, et recherche de motifs * structures des macromolécules * protéomique et interactions * ARN non-codants * évolution et phylogénie * expression des gènes * haplotypes et polymorphismes (SNP) * ontologies, bases de données, intégration de données * algorithmique et statistiques appliquées à la bio-informatique * épigénétique, épigénomique * algorithmique pour le traitement de données de séquençage haut-débit * inférence de motifs, domaines, prédiction fonctionnelle Deux types de contribution sont possibles: résumé étendu (4 à 6 pages) ou poster (1 à 2 pages), en français ou en anglais. Les instructions sont disponibles sur le site de la conférence. Dates importantes : -------------------------------------- - date limite de soumission : 29 janvier 2009 - notification aux auteurs : 20 mars 2009 - conférence : 9-11 juin 2009 Journées Satellites ----------------------------------- Si vous souhaitez proposer une journée satellite, veuillez prendre contact avec les coordinateurs : - Dominique Tessier <tessier(a)nantes.inra.fr> - Jin Kao Hao <hao(a)info.univ-angers.fr> --------------------------------------------------------------------------------------------------- JOBIM - Open days in biology, computer sciences and mathematics --------------------------------------------------------------------------------------------------- The tenth JOBIM conference will be held in Nantes, from June 9th to 11th, 2009. JOBIM is the major annual event in bioinformatics in France. It brings together researchers working in this multidisciplinary field in an informal setting that encourages fruitful exchanges. More information is available at the website: http://www.jobim2009.fr For information, please contact jobim09(a)univ-nantes.fr ---------------------------------------------------------------------- Call for communication ---------------------------------------------------------------------- Topics of interest include, but are not limited to * Genomics, comparative genomics and metagenomics * Biological networks * Dynamic system modelling and systems biology * Sequence analysis, genome comparison, pattern matching * Molecular structures * Proteomics and macromolecular interactions * Non coding RNAs * Evolution, phylogeny * Gene expression * Haplotypes, polymorphisms * Ontology, knowledge representation, data bases * Algorithmics and statistics for bioinformatics * Epigenetics, epigenomics * Algorithmics for the processing of high throughput sequencing data * Motif inference, domains, function prediction You are invited to submit an extended abstract (from 4 to 6 pages) or a poster (1 or 2 pages). Formatting instructions are available at the conference website. The official languages of the conference are English and French. key dates ------------------------------ - submission deadline: January 29, 2009 - acceptance notification: March 20, 2009 - conference : June 9-11, 2009 Satellite meetings ----------------------------- If you wish to propose a satellite meeting, please contact the organizers : - Dominique Tessier <tessier(a)nantes.inra.fr> - Jin Kao Hao <hao(a)info.univ-angers.fr

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post-doc position: Bioinformatics for the melon project (Melonomics)
by Stephane Rombauts 05 Dec '08

05 Dec '08

---------- Forwarded message ---------- From: *Roderic Guigo Serra* <roderic.guigo(a)crg.cat> Date: Thu, Dec 4, 2008 at 5:46 PM Subject: melon /*Post Doctoral position BGG-1*/: Bioinformatics for the melon project (Melonomics) The BGG is part of the Melonomics project, a project sponsored by Genoma España to sequence the melon genome. Sequencing will be performed using a combination of the traditional BAC based approach, and the new sequencing technologies (454 and solexa). The main task of the candidate will be to use available tools, as well as to develop appropriate tools for genome assembly and gene annotation. The candidate should have a very strong background in comparative genomics, and should be familiar with the most common tools for genome assembly and gene finding and annotation. The candidate should also be very skilled with scripting languages. A background in Plant Genomics is a plus. -- ******************************************************************************* 10 La Caixa-CRG fellowships available to carry our PhD studies in the CRG International PhD program Deadline for applications: January 18, 2009 Information and application forms available at http://pasteur.crg.es ******************************************************************************* (1) Centre de Regulacio Genomica (2) Grup de Recerca en Informatica Biomedica (IMIM and UPF) Dr. Aiguader, 88 +34 93 3160168 ph +34 93 3160110 ph secretary E-08003 Barcelona +34 93 3969983 fax email: roderic.guigo(a)crg.cat http://genome.imim.es -- ================================================================== Stephane Rombauts scientific staff Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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post-doc position: Bioinformatics for the melon project (Melonomics)
by Stephane Rombauts 05 Dec '08

05 Dec '08

---------- Forwarded message ---------- From: *Roderic Guigo Serra* <roderic.guigo(a)crg.cat> Date: Thu, Dec 4, 2008 at 5:46 PM Subject: melon /*Post Doctoral position BGG-1*/: Bioinformatics for the melon project (Melonomics) The BGG is part of the Melonomics project, a project sponsored by Genoma España to sequence the melon genome. Sequencing will be performed using a combination of the traditional BAC based approach, and the new sequencing technologies (454 and solexa). The main task of the candidate will be to use available tools, as well as to develop appropriate tools for genome assembly and gene annotation. The candidate should have a very strong background in comparative genomics, and should be familiar with the most common tools for genome assembly and gene finding and annotation. The candidate should also be very skilled with scripting languages. A background in Plant Genomics is a plus. -- ******************************************************************************* 10 La Caixa-CRG fellowships available to carry our PhD studies in the CRG International PhD program Deadline for applications: January 18, 2009 Information and application forms available at http://pasteur.crg.es ******************************************************************************* (1) Centre de Regulacio Genomica (2) Grup de Recerca en Informatica Biomedica (IMIM and UPF) Dr. Aiguader, 88 +34 93 3160168 ph +34 93 3160110 ph secretary E-08003 Barcelona +34 93 3969983 fax email: roderic.guigo(a)crg.cat http://genome.imim.es -- ================================================================== Stephane Rombauts scientific staff Tel:+32 (0)9 331 38 21 fax:+32 (0)9 3313809 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM strom(a)psb.ugent.be http://www.psb.ugent.be ==================================================================

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Speed dating at the Bioinformatics Event in Maastricht
by Andra Waagmeester 04 Dec '08

04 Dec '08

On behalf of Miranda stobbe of the RSG the netherlands: Dear PhD student, Have you already registered for the special bioinformatics event on Sunday 14th of December? Registration is still possible. The RSG Netherlands is organizing a social event specially for PhD Students who have registered for this program. Please see the flyer attached for more details. See you there, Jayne Hehir Chair of RSG Netherlands, the network of PhD-students in bioinformatics

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Position for a Scientific Programmer at NMC
by marijana radonjic 01 Dec '08

01 Dec '08

Vacancy ** *Scientific Programmer* * **Description * The scientific programmer will be part of a team of five programmers located at various institutes in the Netherlands, constructing a metabolomics data warehouse infrastructure and related applications, within the Netherlands Metabolomics Centre (NMC, http://www.metabolomicscentre.nl/) Within this team, the specific tasks of the scientific programmer are to adapt and expand bioinformatics tools for biological interpretation of nutritional and biomedical metabolomics data. These tools allow to link the metabolomics data, directly from the data warehouse, to intracellular and intra-organ activities, pathways and processes. This will provide a generic bioinformatics evaluation and visualization tool to be used in the area of life style associated diseases such as obesity, atherosclerosis and diabetes type II. It will help in the early diagnosis of disease and developing disease prevention strategies. All data warehouse and applications will be made exportable to controlled vocabularies and ontologies, to make easy exchange of data possible. The programmer will assist in providing web interfaces for the metabolomics database and web-enabling of applications. The data warehouse should be constructed in such a way that overview over the study design, the type of analysis used and the toolbox used for biological interpretation can be queried at once. *Background* The Netherlands Metabolomics Centre is a multicenter research program in which biologists, analytical chemists, database builders and statisticians work together. Therefore excellent networking capacities will be essential for this project. Metabolomics technologies measure a multitude of small chemical molecules in a sample, to get an accurate picture of the physiology of a cell, organ or system (such as human). The research projects within the NMC are mainly focused on human health care, nutrition and plant sciences. The scientific programmer will be appointed at the University of Leiden but work in the Physiological Genomics team of the Biosciences Busniness Unit of TNO, located in Zeist. Physiological Genomics is responsible for the biological and physiological interpretation of "omics" data in (human) health research. At the moment our team exists of 12 (young) researchers. *Requirements* - Experience with HTML, PHP, MySQL, Java and Javascript. - Master in (bio)informatics, ICT / automation or related background with a strong affinity for life sciences, - Knowledge of ontologies and pathway visualization will be of advantage. - Team worker, self-reliant, flexible, and innovative. * *Additional Information: Dr. B. van Ommen, tel : 030 6944438, e-mail: ben.vanommen(a)tno.nl

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