July 2010 - BBClist - maillist.psb.ugent.be

PRIB 2010: poster abstracts deadline 1 August
by Elena Marchiori 31 Jul '10

31 Jul '10

Apologies for multiple postings - Please distribute within your lab - Dear Colleague, We are inviting submissions for short papers and poster abstracts at PRIB 2010. The deadline is 1 August. Best wishes, The PRIB 2010 Organizing Committee ---- *** PRIB 2010: Call for short papers and poster abstracts *** http://www.prib2010.org/ The Pattern Recognition in Bioinformatics conference aims to bring together top researchers, practitioners and students from around the world to discuss the applications of pattern recognition methods in the field of bioinformatics to tackle problems in the life sciences. Prospective authors are invited to submit papers in the research areas of interest to the conference. These include: •Bio-sequence analysis •Gene and protein expression analysis •Protein structure and interaction prediction •Motifs and signal detection •Metabolic modelling and analysis •Systems and synthetic biology •Pathway and network analysis •Immuno- and chemo-informatics •Evolution and phylogeny •Biological databases, integration and visualisation •Bio-imaging Pattern recognition techniques of interest include, but not limited to: •Static, syntactic and structural pattern recognition •Data mining, Data based modelling •Neural networks, Fuzzy systems •Evolutionary computation and swarm intelligence •Hidden Markov models, Graphical models We are inviting submissions of short papers (up to 6 pages in LNCS formats) and poster abstracts (up to 1 page) in all the areas of relevance to the conference. Accepted short papers will be published in the PRIB 2010 supplementary proceedings. Authors of both short papers and abstracts will be expected to present their work in the form of a poster at the conference. To submit short papers select the "Short Paper" category in the EasyChair submission system. Important Dates •Short Paper Submission: 1 August 2010 •Author Notification: 15 August 2010 •Early Bird Registration: 20 August 2010

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(no subject)
by Nicolaes G (BIOCH) 30 Jul '10

30 Jul '10

INVITATION The Netherlands Society on Biomolecular Modelling (NSBM) would like to invite you to its second one-day conference on protein structure and modelling related topics. Title: "Mutations in proteins: structure, function, dynamics, and disease" Date: September 20th, 2010 Venue: UMC St Radboud, NCMLS Building, Nijmegen Information about the programme can be found in the flyer attached (PDF-document) as well as on the NBIC website: http://www.nbic.nl/about-nbic/events/all-events/detail/article/mutations-in… Poster presentations: Abstracts can be submitted for poster presentations. Two master or PhD student poster presenters will be invited to discuss their poster in a 15 minute seminar. A poster prize will be awarded to the best poster presented at the conference. The abstract submission details can be found on the webpage mentioned above. Registration: Please use the following link to register: http://www.nbic.nl/about-nbic/events/registration-forms/nsbm-conference/. The registration will close on Friday September 10th, 2010. For questions about the conference please contact Barbara van Kampen (b.vankampen(a)cmbi.ru.nl<mailto:b.vankampen@cmbi.ru.nl>, tel. +31(0)24 3619390) or Gerry Nicolaes (g.nicolaes(a)bioch.unimaas.nl<mailto:g.nicolaes@bioch.unimaas.nl>, tel. +31(0)43 3881688). We are looking forward to welcome you on September 20th! Kind regards, On behalf of the Netherlands Society on Biomolecular Modelling [cid:image001.jpg@01CB2FE3.9E292790] Gerry Nicolaes, PhD Senior Researcher Cardiovascular Research Institute Maastricht Biochemistry Department g.nicolaes(a)bioch.unimaas.nl <mailto:g.nicolaes@bioch.unimaas.nl> www.maastrichtuniversity.nl <http://www.maastrichtuniversity.nl/> Universiteitssingel 50, 6229 ER Maastricht P.O. Box 616, 6200 MD Maastricht, The Netherlands T +31 43 3881688 F +31 43 3884159 http://www.unimaas.nl/3dstructure-function [cid:image002.jpg@01CB2FE3.9E292790]Please consider your environmental responsibility before printing this e-mail.

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[ECCB10] Early registration deadline - August 20 - European Conference on Computational Biology 2010
by Yves Moreau 29 Jul '10

29 Jul '10

[[[ APOLOGIES FOR MULTIPLE POSTINGS ]]] Dear Colleagues, We would like to kindly remind you of the early registration deadline for ECCB10: August 20, 2010. Don't miss it, so that you get the best registration rate. As you probably know, this year's European Conference on Computational Biology will act as the yearly Benelux Bioinformatics Conference. It is a unique opportunity to show internationally how active our bioinformatics community is, and for all research teams to put their work in the spotlight. The Benelux Bioinformatics Conference has always attracted numerous researchers from our bioinformatics community. We have had 215 paper submissions - the largest number so far for ECCB. From those submissions, 36 contributions have been selected for oral presentation, which guarantees a high-quality scientific program. We have also been able to accept 392 abstracts for poster presentation, with more than 100 of them from Benelux participants. ECCB10 will be a major scientific event happening "next door" - a not-to-be-missed opportunity! A call for late-breaking posters will open up in the next few days, so that there will be one last chance to present your work. Looking forward to meeting you in September, Yves Moreau - ECCB10 Conference Chair for the ECCB10 Local Organizing Committee === Apologies for multiple postings - Please distribute widely within your lab === Dear Colleague, This is a friendly reminder that the early registration deadline for ECCB10 is quickly approaching: Friday, August 20, 2010. Register before the deadline to benefit from the best registration rate. This year, we had a record number of 216 manuscript submissions, 36 of which were accepted for oral presentation, and we could also accept 392 abstracts for poster presentation, so that we look forward to an exciting scientific meeting. For more details and registration: www.eccb10.org www.eccb10.org/index.php/registration * Do not forget to register also for the workshops and tutorials that will take place on Sunday, September 26. This is a unique opportunity to focus on one of several key emerging topics under the guidance of scientific leaders in the field. You will find the list of workshops and tutorials below. * For students, the ISCB European Student Council Symposium will also take place on Sunday, September 26 and offer a unique opportunity for students to present their work to an international audience. * We also encourage you to participate to the conference banquet, which will take place in the magnificent city of Bruges, at the historic site of Old Saint John (originally a medieval hospital) - http://www.eccb10.org/index.php/eccb10info/social-event Finally, we recommend that you book your accommodation as early as possible. (The multiple international events related to Belgium's presidency of the European Union means that accommodation could become tight.) Best wishes, The ECCB10 Organizing Committee ============================ TUTORIALS * TUTORIAL 1: WORKING WITH NEXT-GENERATION SEQUENCING DATA In recent years, there has been a revolution in the area of DNA sequencing with the arrival of next-generation sequencing technologies. The type and volume of the data produced by next-generation sequencing machines presents many previously unseen informatics challenges. This tutorial will help people who are getting started on next-gen sequencing get an idea of the tools, flows, and procedures that they may need to set up to handle this data. In this short course, we will introduce the participants to the different next-generation sequencing technologies, show how to do some basic quality checking of the data, how to run the various next-generation alignment tools, create de novo sequence assemblies, and call variants (such as SNPs, short indels, and structural variants) from a reference sequence. * TUTORIAL 2: USE OF SEMANTIC WEB RESOURCES IN COMPUTATIONAL BIOLOGY AND BIOINFORMATICS The Semantic Web is a set of technologies, or a framework, which is designed to make data integration possible via the web, with the addition of a precise semantic characterization of entities and relations (ontologies). As data integration is a pre-requisite for systems biology and translational research, the Semantic Web can bring relevant benefits in these areas. The aim of this tutorial is to briefly introduce the key basic principles needed to understand what it means to represent information on the Semantic Web, and then to provide the attendees with basic hands on competences to start using biomedical information resources which are now available on this framework. * TUTORIAL 3: CURRENT METHODS AND APPLICATIONS FOR REGULATORY SEQUENCE ANALYSIS The annotation of the non-coding genome with gene regulatory function is lagging far behind the annotation of protein-coding genes and improved annotation will depend both on deeper biological insight into cis-regulatory logic and on more efficient computational prediction algorithms. Recent data obtained by high-throughput experiments accelerate the genome-wide identification of regulatory elements but also provide additional bioinformatics challenges. In the light of these developments, this tutorial will focus on bioinformatics methods to predict cis-regulatory elements and to aid the process of regulatory annotation. Participants will be provided with an overview of existing resources (databases, tools) and methods for detecting cis-regulatory elements in genome sequences, and generate testable hypotheses about the binding specificity of transcription factors (motifs discovery), their precise binding locations (binding site prediction), and their target genes (target identification), and go towards regulatory networks. * TUTORIAL 4: PROTEIN STRUCTURE VALIDATION Recent advances in homology modelling and drug design have made clear that the quality of protein structures is really imnportant for good results. Today's software and CPU time availability on clusters, super computers, and the grid allow for easy improvement of old files. It is therefore important for all protein structure bioinformaticians to be able to evaluate the quality of the structures used in their studies and to know when it might be beneficial to ask an NMR spectroscopist or X-ray crystallographer to help bring an old file up to today's standards. This workshop will teach the participants how to use a series of protein structure validation tools and how to interpret the results. The origins of problems are discussed as well as their importance for follow up studies. SYMPOSIUM AND WORKSHOPS * ISCB EUROPEAN STUDENT COUNCIL SYMPOSIUM The ISCB Student Council and its European Regional Student Groups are organizing the first European Student Council Symposium to be held on Sunday, September 26th, the Tutorials/Workshop Day of ECCB 2010 in Ghent, Belgium. The European Student Council Symposium is a forum for students and young researchers in the fields of Computational Biology and Bioinformatics. Participants will have the opportunity to present their work to an international audience, build a network within the computational biology community and develop important soft skills in an environment that fosters exchange of ideas and knowledge. * WORKSHOP 1: LEARNING FROM PERTURBATION EFFECTS Reverse engineering of biological networks is a key for the understanding of biological systems and for identifying new drug targets. Perturbation techniques, like target specific inhibitors and RNA interference, open tremendous possibilities to detect so far unknown interdependencies from, possibly multidimensional, effects. At the same time computational methods being able to derive network hypotheses from such complex data play a crucial role. This workshop aims to bring together computational scientists working with various approaches for this challenging task. The goal is to give an overview over different computational methods in the field and to strengthen and initiate new cooperations. * WORKSHOP 2: ANNOTATION, INTERPRETATION, AND MANAGEMENT OF MUTATIONS (AIMM) This workshop will showcase the state of the art in extraction and reuse of genotype-phenotype information. Annotation of mutations with their impact on phenotypic expression is crucial to understanding genetic mechanisms involved in phenotypic processes and ultimately in complex diseases. Managing this knowledge is key to generating novel hypotheses. Despite the existence of literature and databases describing impacts of mutations, association studies fail to deliver linkage to phenotypes which is the most important contemporary research interest. Extraction of such information from scientific literature is a promising research field and existing solutions are ready to be deployed as services and as semantic web services. ============================ ABOUT ECCB10 The European Conference on Computational Biology (ECCB10) will be held on September 26-29, 2010 in Ghent, Belgium. www.eccb10.org ECCB10 is the key European computational biology event in 2010 uniting scientists working in a broad range of disciplines, including bioinformatics, computational biology, medicine, biology, and systems biology. This year we had a record number of 216 manuscript submissions, of which 36 were accepted for oral presentation. We have been able to accept 392 posters for presentation during the two poster sessions of Monday, September 27 and Tuesday, September 28. We are looking forward to a fruitful scientific meeting. Ghent is centrally located in Western Europe and is reachable by car within a day of travel from most cities in The Netherlands, Germany, Switzerland, France, and the UK. It is also easily reachable by high-speed train since Belgium is a hub of the European high-speed rail networks (Thalys, Eurostar, TGV, and ICE). Ghent is one of Europe's most exciting medieval settings, a glorious eclectic city with spectacular buildings and a vivid cultural experience (National Geographic Traveler recently ranked it 3rd best historic place to visit internationally). Ghent is directly accessible by train from Brussels airport. The conference venue is highly convenient and located in a beautiful park within the city center. We kindly request that you forward this announcement to the members of your team. We look forward to welcoming you to Ghent. The ECCB10 Organizing Committee www.eccb10.org UNSUBSCRIBE - If you do not wish to receive further announcements for ECCB10, please reply to info(a)eccb10.org with UNSUBSCRIBE in the subject heading.

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post-doc position in structural bioinformatics
by Dimitri Gilis 29 Jul '10

29 Jul '10

Please find hereby a vacancy (8 months) for a post-doc in Structural Bioinformatics in Brussels. ---------------------------------------------------------------------------------------- Dimitri Gilis Genomic and Structural Bioinformatics 3BIO - Service de Biosystèmes, Biomodélisation et Bioprocédés (Biosystems, Biomodelling and Bioprocess Department) Université Libre de Bruxelles Av. F. Roosevelt, 50 CP 165/61 1050 Brussels Belgium Tel: +32 2 650 36 15 Fax: +32 2 650 35 75 e-mail: dgilis(a)ulb.ac.be

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CALL FOR ABSTRACTS: first European Student Council Symposium, Ghent, Sept 26
by Thomas Abeel 26 Jul '10

26 Jul '10

Dear Colleagues, The abstract submission deadline has been extended to accommodate late breaking research! The first European Student Council Symposium (ESCS1) will be held on September 26, 2010 in Ghent, Belgium, as a satellite meeting of the European Conference on Computational Biology (ECCB). === ABSTRACT SUBMISSION DEADLINE: July 26, 2010 === http://escs.iscbsc.org/submission/ The program is available on our website and includes: - a keynote presentation by Yves Van de Peer about Generating hypotheses for molecular biology through (top-down) systems biology - a soft skill workshop on the use of theatre skills for presenting - student presentations from abstract submissions - a poster session See http://escs.iscbsc.org/program We invite you to submit an abstract. This is your chance to present your work! We accept abstracts covering both scientific studies as well as novel tools and applications in the fields of computational biology and bioinformatics. A few abstracts will be selected for oral presentations. Other interesting contributions will be accepted for poster presentations. Looking forward to receiving your abstract! Magali Michaut ESCS1 chair Thomas Abeel ESCS1 co-chair

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job opening computational biologist
by Tobias Verbeke 20 Jul '10

20 Jul '10

L.S. OpenAnalytics 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 can be found at http://www.openanalytics.eu/careers.html 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

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Postdoctoral Fellow in Cancer Systems Biology
by Filip Pattyn 20 Jul '10

20 Jul '10

Postdoctoral Fellow in Cancer Systems Biology A 3-year FP7-funded postdoctoral position is available from November 1, 2010 in the Oncogenomics Laboratory at the Center for Medical Genetics, Ghent University. Job description: The candidate will perform gene expression network analysis and systems biology research aiming to gain insights into the perturbed signaling in the pediatric peripheral nervous tumor neuroblastoma. The project is part of a broader ongoing research effort at the Oncogenomics Laboratory in collaboration with various other research groups in Europe and worldwide. The candidate will be expected to develop and utilize bioinformatics algorithms to interpret and integrate various comprehensive genomic datasets including mRNA and miRNA expression data (Affymetrix, RNA-seq) of large unique pediatric tumor series and similar datasets, ChIP-seq and proteome data from in vitro model systems with emphasis on protein coding genes and miRNAs implicated in developmental pathways. Integrated gene regulatory network building will form the basis for further search for molecular targets for targeted therapies. This position offers many opportunities for collaboration in a diversity of methodologically and biologically challenging areas of cancer research and links fundamental cancer research to translational research with direct potential towards development of new therapeutic strategies. Requirements: 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. The ideal candidate has a PhD degree or equivalent in bioinformatics, computer science, statistics, physics, or biology and has preferably a strong background in algorithm development and/or machine learning, and experience with analyzing high-throughput data. Employer information: The laboratory of Prof. F. Speleman (http://medgen.ugent.be/CMGG/) has a proven track record both in the study of the genetic basis of neuroblastoma and bioinformatic algorithm development (see selected publications below). The past years, our laboratory has received substantial funding including grants from EU and the Belgian Federal government. We have a young, dynamic and highly interactive research team. The new postdoctoral fellow will be integrated in this team and will in particular work very closely and interact with a rapidly growing group of researchers with bioinformatics skills. The work is supported by in-house developed bioinformatic tools and a high level informatics environment. We support possibilities for further training through participation in workshops, meetings etc.. Ghent is a beautiful medieval city and one of the biggest student cities in Belgium with a vivid social and cultural life (www.visitgent.be<http://www.visitgent.be/>). Salary: The salary will be in accordance with university regulations for academic personnel at postdoc level depending on the level of experience (43,022 – 47,989 €). How to apply: Applicants should submit a CV, letters of recommendation of two orevious employers, pdf files of your best papers to Prof. Frank Speleman (franki.speleman(a)ugent.be) with email subject “Postdoctoral application”. The Oncogenomics Laboratory Center for Medical Genetics Ghent (CMGG) Ghent University Hospital Medical Research Building (MRB), 2nd floor, room 120.029 De Pintelaan 185, B-9000 Ghent, Belgium +32 9 332 2451 (phone) | +32 9 332 6549 (fax)

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Postdoc UMCG
by Patrick Deelen 20 Jul '10

20 Jul '10

The Department of Genetics at the University Medical Center Groningen, the Netherlands, has a vacancy for a Postdoctoral Fellow in the field of functional genomics. The Wijmenga laboratory focuses on the genetics of immune-related diseases such as celiac disease and inflammatory bowel diseases (IBD). We have implicated some 40 genetic loci in celiac disease and shown that many of these are not unique for celiac disease but are in fact shared with other diseases, in particular with IBD, rheumatoid arthritis and type 1 diabetes. We want to investigate – systematically and on a genome-wide level – the biological processes in which the known disease-associated genes are involved. Our aim is to understand how these different genes together cause the disease phenotype. The work will be carried out in a highly dynamic team containing PhD students and postdocs with genetic, molecular biology, statistical genetic, epidemiology and bioinformatic backgrounds. We also collaborate widely with other groups, at a national as well as international level. The department is an energetic, dynamic, and international environment, with state-of-the-art technology. We are interested in recruiting self-motivated individuals with the drive to be competitive at the international level. Candidates will be strongly encouraged to develop new avenues like iPS technology or to set up cellular screens using shRNA. Candidates with good analytical skills and a strong background in genetics, molecular biology, or immunology are encouraged to apply. You should preferably have experience in high-throughput methods (SNP or gene expression microarrays, next generation sequencing) and an interest in working on large datasets with bioinformatics tools (such as PLINK, R/BioConductor). The successful candidate will be appointed at a level in accordance with his/her experience. For more advanced candidates, we can offer a tenure-track position at the assistant/associate professor level. Contact details Cisca Wijmenga, PhD Professor of Human Genetics University Medical Center Groningen Room E2.030 PO Box 30001 9700 RB Groningen The Netherlands phone: +31 50 361 7245 (Personal assistant) E-mail: c.wijmenga(a)medgen.umcg.nl www.geneticsgroningen.nl

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temporary position bioinformatics
by Van Vlijmen, Herman [TIBBE] 09 Jul '10

09 Jul '10

We have a temporary position in our bioinformatics group in Beerse. This position is open until the end of 2010. In this function you will be part of the bioinformatics team and be involved in: * Development of better analysis methodology of the results of next generation sequencing experiments in the fields of HIV, Hepatitis C, and Oncology. These experiments are done in support of the discovery and development of new drugs, and in the development of biomarkers for these drugs. We have a specific project that involves the optimization of an alignment algorithm. Qualifications * Master's or Ph.D. degree in Bioinformatics or a related field * Expertise in scientific programming and/or scripting, and algorithm development. * Outstanding communication and team work skills. Contact info: Herman van Vlijmen Director Integrative Chem-BioInformatics Tibotec-Virco BVBA Turnhoutseweg 30 2340 Beerse, Belgium hvvlijme at its.jnj.com

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Postdoc Bioinformatics: Gene Regulatory Networks in Development and Cancer
by Stein Aerts 09 Jul '10

09 Jul '10

Postdoc Bioinformatics: Gene Regulatory Networks in Development and Cancer Applications are invited for a postdoctoral position in the Laboratory of Computational Biology at the Center for Human Genetics, University of Leuven, Belgium. Your research will focus on developing algorithms for the integrated analysis of cis-regulatory and next-generation sequence data, both RNA- Seq and DNA-Seq, with the goal of identifying coding and non-coding variations underlying oncogenesis and developmental diversity. Particular focus will be on integrating genomic variation with transcriptional modules and gene regulatory networks and on the identification of genomic regulatory variations. Context: You have the opportunity to apply your methods both on patient samples and on mammalian and Drosophila model systems. You will work in collaboration with the MPL lab (Molecular Pathogenesis of Leukemia) for next-generation sequencing experiments and functional validations in leukemia cell lines. You will have contacts with the Genomics Core Facility, hosting an Illumina HiSEQ2000 and a Roche 454 sequencer. You will be part of the Leuven SymBioSys Center of Excellence for Computational Systems Biology, where you will be surrounded by several other postdocs and students in a stimulating environment consisting of four bioinformatics research groups and four genomics labs. Qualification: We are seeking a motivated and enthusiastic computational biologist, preferably with a proven track record in gene regulatory bioinformatics (e.g., prediction of enhancers, promoters, transcription factor binding sites, gene regulatory networks). Experience with transcriptomics and with the analysis of next- generation sequence data is a plus. PhD in bioinformatics; PhD in engineering or computer science provided substantial insight in genetics; PhD in biological sciences provided substantial programming experience. Skills: genome informatics, statistics, programming. Links: The Laboratory of Computational Biology: http://med.kuleuven.be/bioinformatics/ Center for Human Genetics: http://med.kuleuven.be/cme/ and http://organigram.kuleuven.be/ext/5/50000622e.htm University of Leuven: http://www.kuleuven.be/english/ Highly motivated candidates can apply by sending a motivation letter, names and contact information for three references, publication list, and CV to stein.aerts(a)med.kuleuven.be.

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