- BBClist - maillist.psb.ugent.be

Associate Bioinformatics at TGX,Maastricht University
by Theunissen Daniël (TGX) 12 Sep '14

12 Sep '14

Dear colleagues, The Department of Toxicogenomics at Maastricht University is looking for an associate Bioinformatics. Your aim as an associate bioinformatics will be to implement, manage and maintain bioinformatics tools for the analysis of omics and NGS data. These omics and NGS data are to be analyzed in order to improve the understanding of our ongoing genomics and toxicology research. Another essential task that you will perform is maintaining/updating the several application- and storage-servers that have been set up in our department. Subsequently, desired bioinformatics tools are to be frequently updated and additional ones to be installed. The development of analysis pipelines will be part of your work. Profile A BSc in (Bio)informatics with experience in database and software design, development, implementation, management and maintenance. Programming skills in R, Perl or other relevant language is required. Knowledge of genomics and UNIX system administration is highly desirable. More information can be found at https://www.academictransfer.com/employer/UM/vacancy/24400/lang/en/ For inquiries: Dr. D.G.J. Jennen (+31 (0)43-3883983, danyel.jennen(a)maastrichtuniversity.nl<mailto:danyel.jennen@maastrichtuniversity.nl>) Department of Toxicogenomics, Maastricht University, PO Box 616, 6200 MD Maastricht Best regards, Daniel Theunissen

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CSCDA 2014
by CSCDA2014＠montefiore.ulg.ac.be 11 Sep '14

11 Sep '14

Dear Friends and Colleagues, On behalf of the entire organizing committee, we are glad to invite you to the third edition of CAPITA SELECTA IN COMPLEX DISEASE ANALYSIS (CSCDA2014). This year's meeting aims to create a broad platform to discuss issues in complex disease analysis, in particular in uncovering population and patient heterogeneity, as well as in data fusion and integration to improve mechanistic insights in rare diseases. Our target audience has a background in life sciences, biomedical sciences, statistics, bioinformatics, statistical genetics and medicine, or related disciplines. The mini-conference will exist of two parts: tutorial sessions in the forenoon of November 24, and keynote speaker sessions, followed by contributed oral and poster presentations on November 24 - 26. The ABSTRACT SUBMISSION DEADLINE IS 1 OCTOBER 2014. More information about abstract submission and registration details are available on the conference website: http://www.statgen.ulg.ac.be/CSCDA2014/cscda2014.html We have already an impressive list of confirmed speakers and hope to see you in Liège during the fall! Please feel free to forward this email correspondence to others. With best regards, on behalf of the CSCDA2014 Organizing committee, Kristel Van Steen and Kristel Sleegers

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Announcing R2 workshop 22/9/14
by P. Molenaar 10 Sep '14

10 Sep '14

Dear Investigator, R2 is a publicly accessible web-based program ( http://r2.amc.nl) allowing biomedical researchers, without bioinformatics training, to integrate clinical and genomics data. Over the past years, the versatile platform has been cited in more than 160 peer reviewed publications including high impact journals such as Cell and Nature. To help researchers get started, the department of Oncogenomics is organizing a 1 day introduction workshop in the AMC (Amsterdam, the Netherlands) with hands-on training on Monday Sept 22nd (09:30-17:00 CET). The workshop will cover the essentials of working with mRNA data in R2 and will be an excellent opportunity to learn how to use this versatile tool. If you are: Studying a specific pathway in disease Trying to find biomarkers in specific tissue Investigating the function of a specific protein Involved in any kind of molecular biology Then this workshop may be of interest to you. If you are interested in participating in the workshop then please visit the R2 website for more information and registration (http://hgserver1.amc.nl/cgi-bin/r2/main.cgi?option=about_intro_workshop ). Participants are requested to register before Sept 16th. Registration is at a first come, first serve basis. This workshop is provided free of charge and includes lunch, coffee and a printed R2 tutorial book. It would be appreciated it if you could distribute this message to anyone who may be interested. A PDF flyer for the workshop can be found http://hgserver1.amc.nl/r2/help/r2_tutorials.pdf Best regards, R2-support r2-support(a)amc.nl Department of Oncogenomics, M1-132 Academic Medical Center University of Amsterdam Meibergdreef 9 1105 AZ Amsterdam the Netherlands ________________________________ AMC Disclaimer : http://www.amc.nl/disclaimer ________________________________

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FW: Group Leader position with start-up package in Bioinformatics at Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership - PLS DISTRIBUTE
by Vera van Noort 09 Sep '14

09 Sep '14

Call for a group leader Bioinformatics with start-up in Norway. Please forward to illegible candidates. Bw vera -- Vera van Noort Professor Computational Systems Biology KU Leuven - Faculty of Bioscience Engineering Kasteelpark Arenberg 22 box 2460 3001 Leuven Belgium URL: www.biw.kuleuven.be/m2s/cmpg/research/CSB From: Kjetil Tasken <kjetil.tasken(a)ncmm.uio.no> RE: Group Leader position with start-up package in Bioinformatics at Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership - PLS DISTRIBUTE Dear all, Good if you can all circulate this in your network nationally and internationally and particularly send to relevant candidates: Group Leader position with start-up package in Bioinformatics NCMM is seeking new outstanding international candidates for the position of group leader with a start-up package in bioinformatics. We expect to hire one new principal investigator through this call and particularly encourage international applicants. The successful candidate is expected to initiate a new independent research program integrating bioinformatics and experimental science with a clear relevance to molecular medicine and disease mechanisms. The bioinformatics research should be closely linked to biological research in the same disease areas. NCMM provides attractive sustainable support packages for new group leaders of more than 2.0 million EUR over the first five-year period. This includes salaries of the group leader, a postdoctoral fellow, a doctoral student as well as a programmer / technician, consumables and modern laboratory facilities.The candidate is expected to complement this budget through other national or international grants and/or through industrial collaborations. Application deadline: 15 October, 2014 See: http://www.ncmm.uio.no/open-positions/group-leader-position-with-start-up-pa ckage-in-bio.html and follow link to full add and web-based application portal. Best regards, Kjetil Kjetil Taskén, Professor of Medicine, M.D., Ph.D.; Director, Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership; Director, The Biotechnology Centre of Oslo; University of Oslo P.O. Box 1125, Blindern N-0317 Oslo NORWAY Phone: +47-22840505 Fax: +47-22840506 Cellular phone: +47-90860759 email: kjetil.tasken(a)ncmm.uio.no or kjetil.tasken(a)biotek.uio.no Web: www.ncmm.uio.no <http://www.ncmm.uio.no/> or www.biotek.uio.no <http://www.biotek.uio.no/>

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new N2N bioinformatics website
by Katrijn Vannerum 05 Sep '14

05 Sep '14

Dear, Please visit the new Nucleotides2Networks website http://www.nucleotides2networks.be/ , a portal to bioinformatics news, events, tools, databases, vacancies and much more. Contributions are welcome. With kind regards, Katrijn Project manager N2N (From Nucleotides to Networks) Multidisciplinary Research Partnership Bioinformatics and Systems Biology Ghent University http://www.nucleotides2networks.be/ twitter: @N2N_UGent Katrijn.Vannerum(a)UGent.be<mailto:Katrijn.Vannerum@UGent.be> Technologiepark 927 9052 Gent, Belgium +32 (0)9 331 36 85 [cid:image001.png@01CFC936.D9BB4720]

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[Gtpb] TA-AFADM14 - Bioinformatics Training Course - Announcement
by Pedro Fernandes 05 Sep '14

05 Sep '14

ANNOUNCEMENT IMPORTANT DATES for TA-AFADM14 Deadline for applications: September 26th 2014 Notification of acceptance dates: EARLY: Sept 19th 2014 (on special request, see Application) NORMAL: September 26th 2014 Course date: October 6th - October 9th 2014 The Gulbenkian Training Programme in Bioinformatics is pleased to announce that the applications for the hands-on Bioinformatics training course TA-AFADM14 Transcriptome Assembly, Automatic Annotation and Data Mining are now OPEN. Please have a look at our website here: http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM14/ Course duration: 4 days Course fee: Euro 320.00 We will have Stefan Goetz and Riccardo Alese Cigliano as instructors. This course has already been run here several times with a great deal of success, as revealed by very positive feedback reports and subsequent recruitment by word of mouth by satisfied attendees. Course description: This is a combined course in RNA-seq and functional annotation aimed at scientists working in next generation sequencing transcriptomics who want to extract the best possible information from their data. The course covers all aspects of RNA-seq analysis, from quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNA-seq data both in the presence and absence of a reference genome. The second part of the course is a practical workshop on Blast2GO, the most popular framework for functional annotation of sequence data. Participants will learn how to generate de novo functional labels, such as GO terms and KEGG pathways, for their sequence data and how to extract relevant information from these annotations, i.e. visualisation and enrichment analysis using the Gene Ontology. This part will be based on the use of the Blast2GO application and will mainly comprise exercises and practical cases. Participants may bring their own data. Who should attend? Experimentalists and bioinformaticians working on EST, NextGeneration Sequencing and microarray design projects, specially (but not exclusively) of non-model species. No programming knowledge is required. Thank you for your continued interest P.Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt

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Bioinformatics Post-doctoral position @ INRA, France
by emmanuelle morin 04 Sep '14

04 Sep '14

*post-doctoral CONTRACT IN bioinformatiCs* GEnomiCs and mEtagEnomiCs of FOREST SYMBIOTIC interactions ** *TITLE* Exploration of forest symbiotic fungi genomes and functional analysis of metatranscriptome data. *RESEARCH CONTexT* Under its researches in biology and ecology of the forest interactions, the UMR IaM contribute to the functional annotation of fungi and tree (meta)genomic sequences. A series of research programs are developed within it based (1) on comparative analysis of fungal genomes and transcriptomes and (2) on the study of metagenomes and metatranscriptomes of forest soils (JGI projects: CSP #305 ‘/Exploring the Genome Diversity of Mycorrhizal Fungi to Understand the Evolution and Functioning of Symbiosis in Woody Shrubs and Trees/’, CSP#978 ‘/Mycorrhizal Genomics Initiative: Exploring the Symbiotic Transcriptomes/’ et CSP#570 ‘/Metatranscriptomics of Forest Soil Ecosystems’/). ** *RESEARCH PROJECT* The research project is part of the comparative genomics and metagenomics programs developed in the UMR IaM Ecogenomics of interactions team. Its aim is to identify and characterize genetic determinants involved in symbiotic interactions between the mycorrhizal fungi and the forest trees using comparative analysis of genome, transcriptome and metatranscriptome data. Over the last few years, UMR IaM and JGI (Joint Genome Institute) joint efforts have allowed the assembly and the annotation of about thirty symbiotic fungi genomes. Bioinformatics analysis, carried in this project, will be focused particularly on lignocellulose degradation enzymes (CAZymes and FOLymes) of the fungal genomes to build a reference database and to better understand their regulation. These data will also help in the annotation and joint analysis of environmental eukaryotic metatranscripts sequences. The /in silico/ analysis of metatranscriptomic expression data will require the development of informatics processes dedicated to massive datasets, and the transposition of transcriptome analysis tools and programs to metatranscriptome data. ** *methodological approaches * - Comparative (meta)genomics of genes repertoires. - /In silico/ analysis of 454 and Illumina (HiSeq et MiSeq) sequencing data. - Quantification of fungal genes expression (trimming, mapping, normalization) - Differential gene expression and gene co-expression network - Graphical visualization of data and basic statistical analysis. ** *PROFILE* - PhD in Biology, Informatics or equivalent - Experience in Perl and Python programing, object oriented development, database management (MySQL, PostgreSQL) - Good knowledge of UNIX environment - Fundamentals in biology and biostatistics for data valorization. - Good interpersonal skills, team spirit and autonomy. ** *POSITION* - Short-term contract of 15 months (renewable one year) - The position is at INRA in Champenoux (France). *contacts*** UMR 1136, Interactions Arbres/Microorganismes (IaM). Annegret KOHLER, kohler(a)nancy.inra.fr <mailto:kohler@nancy.inra.fr>-Marc BUEE, buee(a)nancy.inra.fr <mailto:buee@nancy.inra.fr>-Tél : +33 (0)3 83 39 40 72. Francis MARTIN, fmartin(a)nancy.inra.fr <mailto:fmartin@nancy.inra.fr>. Emmanuelle MORIN, emmanuelle.morin(a)nancy.inra.fr <mailto:emmanuelle.morin@nancy.inra.fr>- Tél : +33 (0)3 83 39 41 33 If you wish to apply for this position, email your CV (no longer than 2 pages) and a 1-page cover letter. Deadline for receiving applications: 1 October 2014. -- Emmanuelle MORIN UMR 1136 INRA/Université de Lorraine F-54280 Champenoux Tel : + 33 3 83 39 41 33 http://mycor.nancy.inra.fr

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CSCDA 2014
by CSCDA2014＠montefiore.ulg.ac.be 26 Aug '14

26 Aug '14

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Reminder Invitation: Bioinformatics Symposium, Utrecht Bioinformatics Center
by Breukelen, B. van (Bas) 25 Aug '14

25 Aug '14

To remind those who were on holidays or have forgotten to register: The Utrecht Bioinformatics Center (UBC) will celebrate it’s kickoff with a mini symposium at september 15th 2014. Everyone who is interested in bioinformatics and would like to hear the plans of the UBC and of course hear a few great talks is welcome to attend. There is no fee at all, we only ask you to register yourself so that we can make sure that there are enough chairs to sit on, coffee at the start and drinks afterwards. Confirmed speakers: Gerrit van Meer, Dean of the Faculty of Science Utrecht University, Utrecht Harmen Bussemaker, Columbia University , USA Edwin Cuppen, UMC Utrecht & Hubrecht Institute, Utrecht Albert Heck, Utrecht University, Utrecht Alexander van Oudenaarden, Hubrecht Institute, Utrecht The program starts at 13:00 with tea and coffee and at 13:15 the symposium will begin. Around 16:30 we will finish the scientific program with drinks and some snacks till 18:00. Everyone is welcome, See you soon, Berend Snel, Patrick Kemmeren and Bas van Breukelen to register: http://ubc.uu.nl/events/4/kickoff-mini-symposium-ubc/ our home page: http://ubc.uu.nl Bas. van Breukelen, PhD Assistant Professor, Biomolecular Mass Spectrometry and Proteomics | http://www.hecklab.com | Utrecht University Coordinator Bioinformatics | Utrecht Bioinformatics Center (UBC) | http://ubc.uu.nl | Utrecht University Hugo R. Kruytbuilding | Room O605 | Padualaan 8 | 3584 CH Utrecht | T +31(0)30253 9761 | M +31(0)6 42222520 | b.vanbreukelen(a)uu.nl<mailto:b.vanbreukelen@uu.nl> | Skype b.vanbreukelen [cid:2CDF3FE1-6FA1-40F3-A816-1D933B578100@science.uu.nl]

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Multiscale Modeling of Biomolecular Systems - 28 November 2014
by Sanne Abeln 22 Aug '14

22 Aug '14

Dear All, You are cordially invited to the Multiscale Modeling of Biomolecular Systems symposium on Friday 28 November 2014. This meeting is jointly organized by the Amsterdam Center for Multiscale Modeling (ACMM) and the Netherlands Society for Biomolecular Modeling (NSBM). The meeting aims to bridge multiple levels of modeling, from structural bioinformatics to biomolecular simulation at various scales. Please pass on this information to anyone who might be interested. See also http://www.acmm.nl and http://www.nsbm.nl Scope: The meeting will focus on multi-scale and multi-level modeling of biomolecular systems including proteins, DNA or RNA. Topics will cover (but are not limited to): bioinformatics sequence analysis, structure analysis, structure prediction methods (including docking), coarse grained simulations, full atomistic classical force field simulations, combined QM/MM, ab initio and/or DFT calculations, and enhanced sampling methods. Keynote Speakers: Prof. David Jones (UCL, UK) Prof. Ursula Roethlisberger (EPFL, Switzerland) Date: 28 November 2014 - 11:00 - 18:00 Location: VU University, De Boelelaan 1081, Amsterdam, the Netherlands Registration & posters: details will follow soon Program Committee: Jocelyne Vreede (UvA), Paola Gori-Giorgi (VU) Daan Geerke (VU), Sanne Abeln (VU) Advisory board (NSBM+ACMM): Gerry Nicolaes (UM), Gert Vriend (UMCN) Peter Bolhuis (UvA), Evert Jan Meijer (UvA) Matthias Bickelhaupt (VU), Luuk Visscher (VU) Best regards, Jocelyne Vreede, Paola Gori-Giorgi, Daan Geerke, Sanne Abeln -- Sanne Abeln Assistant Professor Bioinformatics - VU University Amsterdam s.abeln(a)vu.nl +31 20 59 87816 www.few.vu.nl/~abeln

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