September 2014 - BBClist - maillist.psb.ugent.be

FW: SEMINAR on 18/9 by Vanessa Didelez on Causal Models for Optimal Dynamic Treatments with Survival Outcomes
by Katrijn Vannerum 16 Sep '14

16 Sep '14

-----Original Message----- From: Stijn Vansteelandt [mailto:stijn.vansteelandt@ugent.be] Sent: dinsdag 16 september 2014 13:33 To: Olivier Thas Cc: Ann Vanreusel; Beatrijs Moerkerke; Carlos De Wagter; Dirk De Bacquer; Dirk Van den Poel; Els Goetghebeur; Georges Van Maele; Georges De Moor; Gino Verleye; Hubert De Saedeleer; Jean-Pierre Ottoy; Jo Demeester; Luc Duchateau; Marc Van Meirvenne; Maria.Ysebaert Ysebaert; Nele De Belie; René Boel; Ronan Van Rossem; Stefan Van Aelst; Thierry Marchant; Yves Rosseel; Tom Loeys; Lieven Clement; Lieven Clement; Karel Vermeulen; Machteld Varewyck; Bart Jacobs; Johan Steen; Bart Van Rompaye; Tim De Craecker; Kristof De Beuf; Holger Cevallos Valdiviezo; Kristof Vansteelandt; Ludger Goeminne; Sjouke Vandenberghe; Arnout Van Messem; Dominik Sznajder; Joris Meys; Dries Benoit; Gerdie Everaert; Dieter Fiems; Herman Van Oyen; An Vandebosch; Peter Dawyndt; Veronique Storme; Jan De Neve Subject: SEMINAR on 18/9 by Vanessa Didelez on Causal Models for Optimal Dynamic Treatments with Survival Outcomes Dear all, You are cordially invited to the following seminar, which will take place on Thursday September 18 at 12h in Room A3 (De Sterre, S9). Vanessa Didelez, University of Bristol, U.K. Causal Models for Optimal Dynamic Treatments with Survival Outcomes A dynamic treatment is a set of rules that assigns for each time point when a treatment decision needs to be made what this should be, given the patient's history so far. An example in the context of HIV studies is "start treatment when CD4 count first drops below 600". An optimal dynamic treatment is such a set of rules that optimises a criterion reflecting better health for the patient. I will give an overview of the main methods in this context (based on structural models), with particular attention to the case of survival outcomes. For instance we may use the g-computation approach or dynamic marginal structural models - the latter are becoming popular for HIV studies as mentioned above. The particular difficulty with survival outcomes is that marginal and conditional models are typically not compatible. I will discuss and compare approaches, as well as the issue of simulating from structural models; this (hopefully) leads to additional insight and understanding of the models used in this context. Best wishes, Stijn.

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Computational microbiome postdoc positions at Broad Institute
by Katrijn Vannerum 16 Sep '14

16 Sep '14

The microbiome field is at an important and exciting crossroad: numerous associations have been made that connect the microbes living in and on our bodies with diseases such as inflammatory bowel disease, type 1 diabetes, obesity, and many others, but how these organisms impact the host in health and disease remains largely unknown. We are expanding our team that is broadly engaged in multiple collaborative studies of the roles of the human microbiome in health and disease. The focus of these position(s) is on computational methods to characterize biomolecular functions within these microbial communities and their interactions with host immunity and genetics. We are part of the vibrant research community at the Broad Institute, the Harvard Medical School, Massachusetts General Hospital, and Harvard School of Public Health, and the broader Boston biomedical and life sciences communities, resulting in a rich environment for quantitative, computational, and laboratory collaborations. The successful candidate will perform computational analysis of population-scale metagenomic data, the largest datasets of its kind in the world. Specifically, we seek to determine A) links between microbial membership and metabolic function in the gut microbiota; B) causal or correlative changes in the human microbiota during disease onset and treatment; and C) potential biomolecular interactors between the gut microbial community and the host immune system. The candidate will be responsible for computational methods development and/or applications, should be conversant with bioinformatic techniques for genomic data analysis, and will collaborate closely with experimental laboratories in order to validate computational results and their translation to the clinic. The position will be located within the Broad Institute, and work closely with the Xavier and Huttenhower labs. The Broad Institute is a new kind of deeply collaborative research institution that is transforming medicine and human health by performing experimental research and analyzing scientific data on an unprecedented scale. We will consider candidates with a doctoral degree in Computer Science, Bioinformatics, Biostatistics, Biology, or a related field; familiarity with functional genomic and/or metagenomic data, as indicated by publication record; proficiency in one or more scripting languages appropriate for scalable data analysis; ability to communicate scientific material; Candidates should be resourceful, self-motivated, and possess a proven record of scientific advances leading to high quality publications. Must be capable of working in a collaborative and fast-paced team environment and working on self-directed research projects within broader goals set by group. If you are interested in applying, please send a cover letter and your CV to Dirk Gevers (dgevers(a)broadinstitute.org) If you would like more information about the microbiome program at Broad Institute, visit http://www.broadinstitute.org/blog/new-phase-microbiome Dirk Gevers Via Dr. Katrijn Vannerum 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@01CFD197.A8E572B0]

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Fwd: Position open: Scientific programmer, Genome Variation, Algorithms Development, TGAC, UK
by Frederik Coppens 15 Sep '14

15 Sep '14

Begin forwarded message: > From: "Bernardo Clavijo (TGAC)" <Bernardo.Clavijo(a)tgac.ac.uk> > Subject: Position open: Scientific programmer, Genome Variation, Algorithms Development, TGAC, UK > Date: 15 Sep 2014 11:27:30 GMT+2 > To: "Bernardo Clavijo (TGAC)" <Bernardo.Clavijo(a)tgac.ac.uk> > > Hi all, > I just wanted to ask you a favour. I have an opening in my Algorithms Development at TGAC for a scientific programmer/postdoc. Would you please spread the word among the people that could be interested? > Work area will be mainly variant analysis on genomes (challenging genomes, such as a variety of plants), with a focus going from tool evaluation and pipeline design to algorithm development, depending on the profile of the successful candidate. There is a couple of directions we want to expand our research into, so there will be freedom to choose among those and purse the candidate’s own research ideas. > The ideal candidate should have a good CS/math/stats background, and some experience on NGS, but the main thing I am looking for is someone with a lot of enthusiasm to learn and develop new techniques. > More details available on the website: http://jobs.tgac.ac.uk/Details.asp?vacancyID=8119 and obviously for any other questions, simply write me an e-mail. > > Thank you! > > Best, > > > Bernardo J. Clavijo > > Project Leader > Bioinformatics Algorithms Development > The Genome Analysis Centre, Norwich, UK ================================================================== Frederik Coppens, Ph.D. Project Leader Applied Bioinformatics & Biostatistics Tel: 32 (0)9 3313692 Fax:32 (0)9 3313809 VIB DEPARTMENT OF PLANT SYSTEMS BIOLOGY, UGent Technologiepark 927, 9052 Gent, BELGIUM frcop(a)psb.ugent.be http://www.psb.ugent.be/abb ==================================================================

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MG-RAST workshop (17-18 Sept 2014)
by Katrijn Vannerum 13 Sep '14

13 Sep '14

MG-RAST workshop (17-18 Sept 2014) MG-RAST (the Metagenomics RAST; http://metagenomics.anl.gov<http://www.google.com/url?q=http%3A%2F%2Fmetagenomics.anl.gov&sa=D&sntz=1&u…>) server is an automated analysis platform for metagenomes providing quantitative insights into microbial populations based on sequence data. The server primarily provides upload, quality control, automated annotation and analysis for prokaryotic metagenomic shotgun samples. This 2-day workshop will offer researchers opportunities to analyze shotgun metagenomics high-throughput sequencing datasets with MG-RAST, understand the user interface, provide metadata and perform analysis. Special attention will be paid to the API and the R interface, together with general tips and trick for data processing. Sample data will be provided for hands-on analysis. This workshop will acquaint researchers with MG-RAST sequence analysis tools, enable them to implement their research with MG-RAST, provide hands-on training with real sequence data and offer opportunities to discuss analysis strategies directly with the MG-RAST developers. Instructors Folker Meyer (Argonne National Laboratory and University of Chicago) Andreas Wilke (Argonne National Laboratory and University of Chicago) Schedule day1: Wednesday September 17, 2014, 9:00-17:30 1. MG-RAST overview and user interface * browse and search public data * understanding the pipeline and its limitations * understanding the overview page (a first glance at your data) * check primer/probe coverage in Probe Match 2. Analysis and comparison with the web interface * review concepts (abundance profile) * adjusting parameters * comparison of multiple samples * exporting data day2: Thursday September 18, 2014, 9:00-17:30 1. R Interface (matR) and the API * using R * the MG-RAST API * simple script examples using the API * exporting from MG-RAST to other software 2. Metadata GSC --- Standards and Data Submission * GSC genome standards * Entering metadata with MetaZen 3. Specialist topics * sequence pathology --- common problems with NGS and how to find them * to assemble or not to assemble? * details on the pipeline * scripting with MG-RAST Venue The course will be organised in the multimedia room of the Information and Communication Technology Department (DICT) at Ghent University, as this facilty has laptop computers for participants that cannot bring their own. Participants that work on their own laptop computer are invited to install a recent version of Firefox. This venue will be made freely available by DICT, with coffee and soda drinks free of charge for all participants. Organizing committee Prof. Dr. Peter Dawyndt (Ghent University) Prof. Dr. Anne Willems (Ghent University) ir. Bart Mesuere (Ghent University) ir. Caroline De Tender (Institute for Agricultural and Fisheries Research; ILVO) Contact Prof. Dr. Peter Dawyndt Department of Applied Mathematics, Computer Science and Statistics Ghent University phone: +32 9 264 4779 email: Peter.Dawyndt(a)UGent.be<mailto:Peter.Dawyndt@UGent.be> Please fill up this form<https://docs.google.com/forms/d/1_4awjkASXBa52s1ckdfEv4pcZMIO9MraHerFIlpxEr…> to register your participation to this workshop. -- ------------------------------------------------------------------------- Prof. Dr. Peter Dawyndt Ghent University Department of Applied Mathematics, Computer Science and Statistics (WE02) Krijgslaan 281 (S9) B-9000 Ghent Belgium Tel: (32)9.264.47.79 Fax: (32)9.264.49.95 Email: Peter.Dawyndt(a)UGent.be<mailto:Peter.Dawyndt@UGent.be> -------------------------------------------------------------------------

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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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