- BBClist - maillist.psb.ugent.be

Fwd: Announcing postdoc positions in MIT Computational Biology group
by Stein Aerts 08 Nov '09

08 Nov '09

Hi all, Several very interesting postdoc positions are available at MIT, in Manolis Kellis' group. Best, Stein Aerts Begin forwarded message: > From: Manolis Kellis <manoli(a)MIT.EDU> > Date: Sun 8 Nov 2009 15:04:27 GMT+01:00 > To: Stein Aerts <Stein.Aerts(a)med.kuleuven.be> > Subject: Announcing postdoc positions in MIT Computational Biology > group > Reply-To: "manoli(a)MIT.EDU" <manoli(a)MIT.EDU> > > > -------- > > Subject: Postdoctoral positions available in MIT Computational > Biology group > > The MIT Computational Biology group (compbio.mit.edu) is seeking > highly motivated postdocs to undertake exciting new projects in > computational and regulatory genomics. We seek applicants with a > strong background in machine learning, algorithm development, > statistical methods, and their applications to computational > biology, gene regulation, epigenomics, and integration of large- > scale biological datasets. > > Our group is part of the MIT Computer Science and Artificial > Intelligence Lab, and of the Broad Institute of MIT and Harvard, > leading to a truly interdisciplinary environment. We have numerous > ongoing collaborations with experimental and biological groups, and > are part of the NIH ENCODE, modENCODE, and Epigenome Roadmap > collaborative projects where our group plays a leadership role in > data analysis and integration. > > For more information about the group, please visit: http://compbio.mit.edu/ > > Applicants are sought for the following ongoing projects: > > (1) Integrative analysis of genomic and epigenomic datasets in the > human genome, in the context of the NIH Epigenome Roadmap and ENCODE > projects. Goal is to use many chromatin marks in multiple cell types > in order to discover and interpret chromatin states, understand > their biological roles, and their dynamics in differentiation and > disease (NIH RC1-HG005334, NIH U54-HG004570). > > (2) Integrative analysis of the Drosophila modENCODE project. Goal > is to systematically understand the functional elements encoded in > the fly genome, and the regulatory logic defining transcription > factor binding and chromatin domains, and guiding developmental > programs (NIH RC2-HG005639, NIH U54-HG004555). > > (3) Regulatory genomics in human and fly genomes. Goal is to > discover regulatory motifs, enhancers, and cis-regulatory modules in > the human and fly genomes, and develop predictive models of gene > regulation using comparative genomics and large-scale experimental > datasets (NIH R01-HG004037). > > (4) Role of non-coding RNAs in chromatin. Goal is to understand the > role of small and large non-coding RNAs in directing, establishing, > and maintaining chromatin modifications in human embryonic stem > cells and during differentiation and cancer (Collaborative work with > Ron Hart at Rutgers and John Rinn at HMS). > > (5) Additional projects are available in comparative genomics, > genome interpretation, microRNA regulation, phylogenomics, image > analysis, RNA structure, and applicants are welcome to define their > own projects within the context of ongoing activities in the group > (NSF 0644282, NIH U01-HG004264, NSF 0936234). > > For more information about open positions, please visit: > http://compbio.mit.edu/positions.html > or contact Prof. Manolis Kellis directly at <manoli(a)mit.edu>. Prof. Dr. Stein Aerts Laboratory of Computational Biology Center for Human Genetics University of Leuven Herestraat 49, P.O. Box 602 3000 Leuven, Belgium Tel +32 16 330132 Mobile +32 486 659003 http://med.kuleuven.be/lcb/

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VIB User Group Meeting
by Torik Ayoubi 06 Nov '09

06 Nov '09

Dear Listers, The VIB MicroArray Facility (MAF) is organizing a User Group Meeting, this time focusing on miRNA expression analysis. Other topics covered are: AGRONOMICS1, a new tiling array for Arabidopsis, DamID, an alternative for ChIP-chip, Breast cancer gene expression profiling, Toxicogenomics, nCounterR analysis system, and many more. Attendance is completely free but as space is limited you are required to register and attendance will be acknowledged on a "first come first served" principle. Check out the preliminary program below and at: www.microarrays.be You may register at: torik.ayoubi(a)vib.be, do not forget to state "registration" in the subject header. In the body of the email please give your - -Name -Affiliation Torik Ayoubi (PhD) Research Manager VIB MicroArray Facility, K.U. Leuven Herestraat 49 O&N 1, Post Box 816 3000 Leuven, Belgium email: <mailto:torik.ayoubi@vib.be> torik.ayoubi(a)vib.be tel: 0032-16347939 web site: http://www.microarrays.be/ <https://vibportal.vib.be/f5-w-68747470733a2f2f7765626d61696c2e6d61617374726 9636874756e69766572736974792e6e6c$$/owa/redir.aspx?C=79d0788ad2864e59b7182fa dcb4db57e&URL=http%3a%2f%2fwww.microarrays.be%2f> , http://www.vib.be/ <https://vibportal.vib.be/f5-w-68747470733a2f2f7765626d61696c2e6d61617374726 9636874756e69766572736974792e6e6c$$/owa/redir.aspx?C=79d0788ad2864e59b7182fa dcb4db57e&URL=http%3a%2f%2fwww.vib.be%2f> personal web site: http://www.biomedicalgenomics.org <https://vibportal.vib.be/f5-w-68747470733a2f2f7765626d61696c2e6d61617374726 9636874756e69766572736974792e6e6c$$/owa/redir.aspx?C=79d0788ad2864e59b7182fa dcb4db57e&URL=http%3a%2f%2fwww.biomedicalgenomics.org> 9.30-10.00 Registration 10.00-10.30 New developments at VIB MicroArray Facility; More, Better, Faster, Cheaper, Torik Ayoubi, VIB MAF 10.30-11.00 MicroRNAs: A comparison of different platforms, Hinrich Goehlmann, Johnson & Johnson, Beerse 11.00-11.15 MicroRNA data analysis, Rudy van Eijsden, VIB MAF 11.15-11.30 Microarray analysis of microRNA profiles in a mouse model of left ventricular hypertrophy, Peter Pokreisz, Department of Cardiovascular Diseases, KU Leuven and Vesalius Research Center, VIB. 11.30-11.45 MicroRNAs in heart progenitor cells, Stefania Crippa, Maurilio Sampaolesi, Stem cell Institute, K.U.Leuven 11.45-12.15 MicroRNA profiling and targets genes in normal and malignant B cells, Anke Van den Berg, Pathology & Medical Biology, University Medical Center Groningen 12.15-13.20 Lunch 13.20-13.40 Extracting knowledge from your microarray experiment, Joke Allemeersch, VIB MAF 13.40-14.00 AGRONOMICS1, a new tiling array for Arabidopsis transcriptome profiling, Pierre Hilson, Functional Genomics, VIB Department of Plant Systems Biology, Ghent University 14.00-14.20 High resolution profiling of the LEDGF/p75 chromatin interaction in the ENCODE region, Jan De Rijck, Moleculaire Virologie en Gentherapie, K.U.Leuven 14.20-14.40 Prediction of lymph node involvement in breast cancer from primary tumor tissue using gene expression profiling, Ann Smeets, Multidisciplinary Breast Centre Leuven 14.40-15.10 Coffee 15.10-15.30 Toxicogenomics in an in vitro estrogenic screening context: added value to classical single endpoint estrogenicity screens , Caroline Vanparys, Laboratory of Ecophysiology, Biochemistry and Toxicology, University of Antwerp 15.30-15.50 Mapping gene regulatory networks in Drosophila, Stein Aerts, Laboratory of Computational Biology, Center for Human Genetics, KULeuven 15.50-16.10 nCounterR, multiplex transcript quantification using a molecular barcoding detection system, Frederik Coppens, VIB Department of Plant Systems Biology, Ghent University 16.10-16.25 End Remarks

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Invitation: Seminar Extreme Desktop Virtualization with VirtualStorm
by Axio Systems 05 Nov '09

05 Nov '09

Open this mail in your browser: http://tools.emailgarage.com/Pub/42gpCwAAAAA~/RadYa0BQJ0m2gT1mw5EFrA~~/Text… http://tools.emailgarage.com/Pub/42gpCwAAAAA~/SCcehdPcTEm_0KNcLramFA~~/Text… Invitation: Seminar Extreme Desktop Virtualization with VirtualStorm Dear , Axio Systems and partners DinamiQs and VMware invite you to a seminar about VirtualStorm: Extreme Desktop Virtualization! VirtualStorm is all about reducing management tasks to the absolute minimum. VirtualStorm is software you add to your dekstop virtualization software in order to: - reduce your entire IT environment requirements to an absolute minimum - reduce storage needs by 80 to 90% - save on all levels: hardware, licenses, bandwith, power, administration, support, maintenance... - lower desktop management costs Compared to a classic PC, the end user experience is the same with VirtualStorm. The end user can customize his own Windows desktop and all applications are fully installed and integrated. Ready to use with an improved user productivity! Agenda: 09h00: Welcome & registration 09h30: Our view on the future of VDI - Mr Gert Van der Jeugt - Axio Systems 09h45: Announcing VMware View 4 and the new PC over IP protocol - Mr Jan Tiri - VMware 10h15: View 4 & PCoIP demo - Mr Jan Tiri - VMware & Mr Wouter Coppens - Axio Systems 10h45: Coffee Break 11h00: Extreme Desktop Virtualization with VirtualStorm - Mr Mike Jansen - DinamiQs & Mr Wouter Coppens - Axio Systems 12h00: VirtualStorm reference case: SAP - Mr Jean Paul Beerens - SAP IT Infrastructure Services EMEA 12h15: Q&A 12h30: Networking lunch Date: November 24, 2009, 09h00 - 12h30 Location: Van der Valk hotel Brussels Airport, Culliganlaan 4b, B-1831 Diegem Don't miss this unique event and register now http://tools.emailgarage.com/Pub/42gpCwAAAAA~/k2xvl7lM7kq8qiiCx4JZzQ~~/Text… We are looking forward to meeting you there! If you do not want to receive any emails on the products and services of Axio Systems, you can unsubscribe here http://tools.emailgarage.com/Pub/42gpCwAAAAA~/7PmMiv80eke5Vp5YtMHSzA~~/Unsu…

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Post-doc / PhD position at Netherlands Metabolomics Center
by Alkema, W.B.L. (Wynand) 03 Nov '09

03 Nov '09

Dear colleagues, A 3-years post-doc position or 4-years PhD student position is available within the Netherlands Metabolomics Center, in a joint project between Schering-Plough, Leiden/Amsterdam Center for Drug Research (LACDR), TNO Zeist and Radboud University Medical Center Nijmegen. Please see the attachment for more details. Regards, Wynand Alkema <<project_description_NMC.pdf>> This message and any attachments are solely for the intended recipient. If you are not the intended recipient, disclosure, copying, use or distribution of the information included in this message is prohibited --- Please immediately and permanently delete.

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PhD sholarship: bioinformatics pipelines for genotype-to-phenotype experiments - 4 years
by Morris Swertz 02 Nov '09

02 Nov '09

Dear colleages, I have a PhD position available in genotype-to-phenotype bioinformatics pipelines that might be of interest to members of our Taverna community. Could you please circulate within your respective institutions? Thank you, Morris ---------- 4year PhD scholarship Flexible bioinformatics pipelines for the integration of genotype-to-phenotype experiments Where: Genetics department & Groningen Bioinformatics Center, University Medical Center Groningen, Netherlands Apply: To m.a.swertz(a)rug.nl before November 6st, 2009 Start: Before December 31st, 2009 Summary: Most (disease) phenotypes have a complex inheritance. Integrated analyses of (i) high-throughput sequencing, genotype, transcript, protein, metabolic and phenotypic/clinical profiling data, (ii) use of model organisms such as mouse and worm, and (iii) integration of background information from literature and public database show much potential to unravel these genome-to-phenotype trajectories. This exciting project will (i) define minimal parameters, models, algorithms and tools for the efficient generation of (ii) flexible “cyber infrastructures” to pipeline far greater volumes of experimental, functional and network data on human and mouse than can be achieved using manual analysis (iii) to pinpoint genes and molecular networks underlying complex phenotypes at significantly increased accuracy and reduced effort. You will build on novel "model-driven strategies" to generate the necessary software efficiently (Swertz, Nature Reviews Genetics, 2007), minimal models and ontologies for integrated representation of all these types of data (e.g. http://www.xgap.org, http://www.ebi.ac.uk/EFO) and a suite of open source software for the integration of data and tools (e.g. http://www.molgenis.org) The ideal candidate has an MSc in bioinformatics, computer science, molecular biology, computational biology, artificial intelligence or a related field, proven interest in biology and bioinformatics, a strong programming background and excellent English communication skills. This bursary grant is guaranteed for 4 years at approximate € 1500 euro/month with an evaluation after one year. Find the complete vacancy at http://www.rug.nl/biologie/onderzoek/onderzoekGroepen/bioinformatics/Intern… Organisation: http://www.rug.nl/umcg/faculteit/disciplinegroepen/medischegenetica/ http://www.rug.nl/gbic **

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Fwd: Recrutement bioinfo, suite... avec description du poste !
by Jacques van Helden 30 Oct '09

30 Oct '09

Dear colleagues Jean-Louis Ruelle asked me to forward this announcement for a job opening at GSK. Best regards Jacques van Helden ============================================ Begin forwarded message: From: jean-louis.ruelle(a)gskbio.com Date: 30 October 2009 09:37:43 CET To: Jacques van Helden <jacques.van.helden(a)ulb.ac.be> Subject: Fw: Recrutement bioinfo, suite... avec description du poste ! Job Purpose =========== The Bioinformatics group within the R&D of GSK Biologicals is currently seeking a highly motivated scientist-bioinformatician to be involved in cutting-edge research comprising data analysis and interpretation of microarray data, as well as investigating systems biology approaches relevant to the field of vaccines. The ideal candidate will have an interdisciplinary background in biology and bioinformatics/computational biology, particularly in the analysis and interpretation of microarray and/or proteomics data, working knowledge of statistical and machine learning data analysis methods, the reconstruction of signaling networks, computational network inference from experimental expression data, and the integration of public data sources/biological ontology to enable systems biology research. Responsibilities ================ The job involves: - Performing data analysis of µarray experiments, and collaborating with molecular and cellular biology and immunology for their biological interpretation - Using available methods, or developing new ones, to make sense of gene expression data in terms of signaling pathways, expression regulatory networks and modules, transcription factors activation. - Technology watch to stay up-to-date in this rapidly moving field - Sharing expertise and know-how - Driving contacts with external colleagues and academic research. - Reporting on progress and results to the research project teams. Profile ======= - A PhD in Life Sciences or Computer Sciences or equivalent; familiarity with immunology would be a plus. - Expertise in data analysis and statistics, especially machine learning methods, more generally computational biology. - Expertise in using genome wide approaches to study transcriptional regulation and signaling pathways; experience in computational network inference and modeling would be a plus. - Familiarity with processing of gene expression microarray data (QC, normalization, etc ), preferably with R+Bioconductor - You are willing to learn everyday, you are open, creative, you can work autonomously. - You have excellent communication and organizational skills. - You are fluent in English (oral and written). Contact and information: ======================= Please apply via the GSK Biologicals website : http://www.gsk-bio.com/english/html/online/apply.html and quote the following requisition number : 27260 Jean-Louis Ruelle <jean-louis.ruelle(a)gskbio.com> R&D GSKBiologicals Rix B62-J406 +32 2 656 8451

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PathVisio 2.0 pathway tool released
by Martijn van Iersel 20 Oct '09

20 Oct '09

The BiGCaT Bioinformatics group at Maastricht University is happy to announce the release of PathVisio 2.0. [1] What is PathVisio? PathVisio is a tool for creating and analysing biological pathway diagrams. Stay organized by using PathVisio as a notebook to collect the various bits of information related to a biological research subject. Create images suitable for presentation or publication. Draw pathways, export them to many image formats, annotate them with links to online biological databases such as Ensembl or Entrez gene, and add comments and literature references from pubmed. PathVisio is fully compatible with WikiPathways [2], a wiki where researchers can contribute pathway knowledge. What is new? New in PathVisio 2.0 is the ability to import experimental datasets and visualize them on top of pathways. Explore large datasets in a way that is more interesting and understandable than just a huge spreadsheet. Import microarray, proteomics or metabolomics data. Microarray reporters will be automatically converted to gene or protein identifiers. You can customize the visualization, using gradients, boolean color rules, or colored icons. Perform over-representation analysis to find the pathway that was most affected by experimental conditions. We prepared a Visual Tour [3] to get an overview of new and old features. For Developers: PathVisio has a plugin interface that lets users customize it to new analysis types, new visualization methods and new pathway formats. PathVisio is fully open source, and we're always looking for Java developers who are interested in contributing, either to new plugins or to the core of the program. Contact us on our mailinglist [4]. [1] http://www.pathvisio.org/ [2] http://www.wikipathways.org/ [3] http://www.pathvisio.org/wiki/VisualTour [4] http://www.pathvisio.org/wiki/MailingLists

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Benelux Bioinformatics Conference 2009: deadline extended
by Pierre Geurts 15 Oct '09

15 Oct '09

[apologies for multiple postings] Deadline for abstract submission has been extended to ** MONDAY, OCTOBER 26 ** **************** Second Call for Abstracts ************************* Fifth Benelux Bioinformatics Conference December 14-15, 2009, Liège, Belgium ********************************************************************** http://www.montefiore.ulg.ac.be/services/stochastic/bbc09 SCOPE The Benelux Bioinformatics Conference is a two-day international conference on bioinformatics. It is the primary community event for bioinformatics researchers in the Netherlands, Belgium, and Luxemburg with excellent networking opportunities. The conference is aimed at both academic and industry researchers. This year's edition, BBC 2009, will take place in Liège, Belgium on December 14-15, 2009. Check out the conference web site at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/. CALL FOR ABSTRACTS The BBC 2009 program will feature four invited talks together with oral presentations and poster sessions. Participants are cordially invited to submit an abstract (max. 500 words) for their conference contribution. Submissions can be done using the form at http://www.montefiore.ulg.ac.be/services/stochastic/bbc09/ submission.php. VENUE The conference will take place at the Academic Room of the University of Liège, place du 20-Août, 7, 4000 Liège, Belgium. The venue is located in the heart of Liège, near Christmas markets and other tourist interests. Liège is a thousand-year-old city with a historical centre and numerous monuments, churches, and museums. Liège is located one hundred kilometers east of Brussels. KEY DATES * Deadline for abstract submission October 26, 2009 * Notification of selection of oral contributions November 16, 2009 * Deadline for early registration November 23, 2009 * Conference December 14-15, 2009 LOCAL ORGANIZING COMMITEE Louis Wehenkel, Pierre Geurts, Kristel Van Steen, Eric Bullinger Department of EE and CS and GIGA-R, University of Liège, Belgium

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vacancy: bioinformatics scientist sequence applications
by Antoine Janssen 12 Oct '09

12 Oct '09

Keygene n.v., internationally operating biotechnology company located in Wageningen is looking for a BIOINFORMATICS SCIENTIST sequence applications Vacancy number 09004 Position As a scientist you will be responsible for the analysis and method development for next generation sequencing applications. You will take the scientific lead for sequence analysis in the field of plant breeding application, with the use of novel methods for assembly, mapping and variation detection. You will be responsible for quality control and method implementation. You will work in a team of 5 professional Bioinformaticians and in close collaboration with researchers from other research domains. The team operates under the supervision of a team leader. Candidate Required: * A PhD degree in bioinformatics or comparable experience * Broad experience with sequence assembly, mapping and various analyses for marker discovery and genotyping * Good knowledge and preferably hands on experience with the available tools and methods in the field * Ambition to work in a pioneering research field * Keen on leveraging research results in a project centered environment * Leading personality Preferential: * Experience with the analyses of Roche GS (FLX) and Illumina GA (II) data * Experience with the use of cluster and grid infrastructure KeyGene offer KeyGene offers you a dynamic job with a competitive salary and benefits in a challenging, highly innovative and ambitious research company with an internationally recognized position in plant genetic research. You will be able to further build on the already existing modern facilities (Bioinformatics high performance computing power and high tech lab equipment such as robots and various next generation sequencing platforms). Furthermore, you will have full access to supporting services (IP and legal support, financing). More information Additional information can be obtained from Antoine Janssen, Keygene N.V., telephone +31 317 466866, email Antoine.Janssen(a)keygene.com<mailto:Antoine.Janssen@keygene.com>. If you are interested in this position you can send your letter of application and resume to: Keygene N.V. Attn. Ms A. Philipsen, HR manager, P.O. Box 216, 6700 AE Wageningen, The Netherlands or by email: Angelique.Philipsen(a)keygene.com<mailto:Angelique.Philipsen@keygene.com>. Please mention the vacancy number 09004 in your application. For more information on Keygene n.v., please visit www.keygene.com<http://www.keygene.com/>

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Reminder IUAP BioMaGNet Annual meeting 2009 :: Registration deadline October 16th 2009
by Klaas Vandepoele 07 Oct '09

07 Oct '09

Dear colleagues, The Bioinformatics and Evolutionary Genomics division of the Department of Plant Systems Biology (VIB -- Ghent University) is organizing *BioMaGNet's Annual Meeting* on *October 22nd 2009*. We invite all scientists working on bioinformatics, modelling or related disciplines to participate in this one-day symposium which will focus on research topics covered by the different national and international partners of the Interuniversity Attraction Pole BioMaGNet. Apart from the keynote talks and contributed BioMaGNet presentations (cfr. Program), abstracts can be submitted for the poster session. _Invited speakers: _ -Mark Veugelers, Integration Manager VIB 'Surfing the wave of emerging technologies in life sciences' -Stein Aerts, Laboratory of Computational Biology 'Mapping gene regulatory networks in Drosophila' -Florence d'Alché-Buc, Université d'Evry-Val d'Essonne 'Network inference : coupling graph and parameter estimation' The meeting will take place at the "Fiers-Schell-Van Montagu" FSVM research building at the Technologiepark 927 in Ghent, Belgium. For more information about registration, abstract submission and updates of the program, please visit http://bioinformatics.psb.ugent.be/biomagnet_2009 The registration deadline is *October 16th 2009*. We are looking forward to see you at the conference! The organization committee -- Klaas Vandepoele, PhD Tel. 32 (0)9 33 13822 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, Belgium E-mail: Klaas.Vandepoele(a)psb.vib-ugent.be Website: http://bioinformatics.psb.ugent.be/ ---------------------------------------------------------

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