April 2013 - BBClist - maillist.psb.ugent.be

Computational Cancer Biology Positions
by Lodewyk Wessels 12 Jul '13

12 Jul '13

COMPREHENSIVE COMPUTATIONAL MODELING FOR COMBINATION TREATMENT DESIGN PROJECT OUTLINE All cancers arise due to alterations in their genomes. Although insight into the genetic lesions in tumors by genome sequencing does already assist in selecting some drug regimens, it rarely results in disease eradication due to the emergence of drug-resistance. More sophisticated combination therapies in which several oncogenic pathways are targeted simultaneously could alleviate this problem. However, at present we are unable to extract and interpret the necessary information from tumors to predict which drug regimen will be most adequate. In this project we will collaborate with Welcome Trust Sanger Center and employ the 1000 cancer cell line data set to tackle this problem. This data set comprises large-scale molecular characterization and cancer drug screening of all cell lines for 400 anti-cancer drugs. The molecular data currently consists of gene expression, copy number (SNP-6), and whole exome sequencing data and is being expanded. The successful candidate will work closely with scientists at the Welcome Trust Sanger Center and the Netherlands Cancer Institute and employ computational approaches to mine this rich, valuable pre-clinical resource. Potential results include 1) new molecular biomarkers to identify sensitive populations 2) repositioning of existing drugs in other tumor types and 3) potential drug combinations aimed at overcoming resistance mechanisms. Hypotheses emerging from these analyses will be validated in model systems and where possible in clinical settings. CANDIDATE REQUIREMENTS – EDUCATION AND EXPERIENCE We are seeking highly motivated Postdoc or PhD candidates with a degree in bioinformatics, computer science, mathematics or physics and with a strong cancer biology interest. Preferably applicants should have a documented experience in analyzing high-throughput genomic data. The candidate needs to be proficient in common bioinformatics scripting and programming languages. Fluency in spoken and written English is a strong requirement. LOCATION The project involves groups at the Netherlands Cancer Institute, Amsterdam (Rene Bernards, Molecular Carcinogenesis, and Lodewyk Wessels, Computational Biology) and the Welcome Trust Sanger Institute (Mathew Garnet and Ultan McDermott, Cancer Genome Project). This position will be embedded in the Computational Biology Group lead by Lodewyk Wessels. CONTACT DETAILS Please contact Lodewyk Wessels, tel. +31 20 512 7987 or e-mail: l.wessels(a)nki.nl. When applying, please ensure you include a CV, list of publications and the names and addresses of at least two persons that can be approached as references. Also see bioinformatics.nki.nl for further information. CLOSING DATE 3 February 2013

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Reminder: Junior PI meeting: a satellite of ISMB-ECCB 2013
by Magali Michaut 25 May '13

25 May '13

Transitioning from Post-doc to (junior) PI is a major step in the scientific career ladder bringing new challenges to the scientist. Key among these challenges is moving from a single project-based responsibility to being responsible for the projects of students, technicians, and postdocs. On top of this, the researcher is expected to be a successful grant writer, a human resources manager, an engaging speaker, etc. In this meeting we aim to bring together scientists who have recently started or wish to start their own research group. This meeting will serve as a platform for building a community of junior PIs within the broader field of Computational Biology. To participate you have to submit a short summary of your scientific research interests and future plans which will be distributed before the event to all participants to facilitate the interactions. They will also be peer-reviewed as part of the participant selection process. One of the most important goals of this meeting is to stimulate peer-to-peer interactions, which requires time and effort. We will thus require all participants to commit to the entire program duration. The total number of delegates will be capped at 50, so don't wait to submit your abstract! ** Submission deadline: April 19 ** https://www.easychair.org/conferences/?jpi2013 Date of the meeting: 20 July 2013 http://www.iscb.org/ismbeccb2013-program/ismbeccb2013-jpi/about-jpi Organizers: Jeroen de Ridder, Delft University of Technology, The Netherlands Venkata P. Satagopam, University of Luxembourg, Luxembourg Manuel Corpas, The Genome Analysis Centre, UK Magali Michaut, Netherlands Cancer Institute, The Netherlands Yana Bromberg, Rutgers University, USA Nils Gehlenborg, Harvard Medical School, USA Geoff Macintyre, University of Melbourne, Australia

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NBIC PhD course on Managing Life Science Information: registration is open!
by Celia van Gelder 01 May '13

01 May '13

*NBIC PhD Course on Managing Life Science Information (2nd edition) *Course coordinators: Marco Roos, Scott Marshall _Date:_ 17-21 October 2011 (one week of tutorials) and a final workshop on Friday 28 October 2011 to discuss project results _Location:_ Science Park, Amsterdam _Registration:_ http://www.nbic.nl/education/nbic-phd-school/enrolment/ _Website: _http://www.nbic.nl/education/nbic-phd-school/course-schedule/managing-life-science-information/ Did you ever suspect that the data that you need is somewhere but neither discoverable nor accessible? Have you ever produced valuable data that nobody can use anymore, including yourself? Have you ever wondered how to create a federation of distributed data sources? If you do not want your data to end up in a data graveyard, and for many other information management issues, we have organised a course for you. In this course we will teach you methods to make data shareable and self-describing. You will learn how: 1. the 'Linked Data' principle works and how it can be applied for 'meaningful' data integration 2. to expose your local data (including relational databases) for use in other systems. 3. Web Services can be used to analyse data from anywhere. 4. text mining can be applied to link resources such as biobanks. 5. human knowledge can be made computable and associated with data. 6. to make your data publishable artifacts for which you can get scientific credit. 7. to use tools such as MolGenis <http://www.molgenis.org/>, Taverna <http://www.taverna.org.uk/>, SPARQL <http://www.w3.org/TR/sparql11-query/>, D2RQ <http://www4.wiwiss.fu-berlin.de/bizer/d2rq/>, SWObjects <http://tinyurl.com/swobjects-swat4ls>, NCBO's BioPortal <http://bioportal.bioontology.org/>, Anni <http://www.biosemantics.org/index.php?page=anni-2-0>, LarKC <http://larkc.org/>(Large Knowledge Collider). 8. to collaboratively solve an information management problem _Program_ (tentative) Monday: Introduction by leading Semantic Web expert Prof. Dr. Frank van Harmelen; Hands-on with RDF and SPARQL (Scott Marshall) Tuesday: XML, RDF, Minimal information models, and exposing data from local databases (Scott Marshall); hands-on with MolGenis (Erik Roos) Wednesday: Data integration with Web Services (Katy Wolstencroft); hands-on with Taverna (Katherine Wolstencroft) Thursday: Knowledge management and nano-publication (Andrew Gibson); hands-on federated queries with SWObjects (Scott Marshall) Friday: Text mining for linking biobanks and hands-on with Anni (Marco Roos, Kristina Hettne); Hands-on with LarKC (Spyros Kotoulas); DRINKS!!! -- Dr. Celia W.G. van Gelder Coordinator Education CMBI Projectleader Education NBIC tel. +31-(0)24-3666120 e-mail: C.vanGelder(a)cmbi.ru.nl websites: www.cmbi.ru.nl, www.nbic.nl Postal address: CMBI 260 Radboud University Nijmegen-Medical Centre /NCMLS PO Box 9101, 6500 HB Nijmegen The Netherlands

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Project leader positions at IECB – Bordeaux 2013
by Macha Nikolski 29 Apr '13

29 Apr '13

Project leader positions at IECB – Bordeaux 2013 The European Institute of Chemistry and Biology, Institut Européen de Chimie et Biologie (IECB, www.iecb.u-bordeaux.fr) is a research team incubator placed under the joint authority of the University of Bordeaux, CNRS and INSERM. It benefits from the strong scientific environment of the Bordeaux campus in the Southwest of France. The Institute hosts 16 research groups working at the interface of chemistry and biology in a recent building (6000 sq meters) with state-of-the-art equipment and facilities. The scientific policy of the institute is under the responsibility of an International Scientific Advisory Board, in charge of the selection of new group leaders. IECB is looking for outstanding candidates who will complement the existing strength of the Institute in: • SYNTHETIC BIOLOGY We are interested in projects aiming at re-programming, re-constructing life through the use of microbiology, molecular biology, molecular engineering or mathematical modelling. Projects related to cell cycle or development will be considered with particular interest • CHEMICAL BIOLOGY We are looking for chemical biologists interested in the development of novel molecular approaches towards the understanding and modulation of biological functions, and the upstream development of innovative therapeutic or diagnostic tools. • BIO-INSPIRED NANOTECHNOLOGY and MOLECULAR BIOPHYSICS We seek biochemists/biophysicists developing protein/nucleic acid scaffolds, techniques for single molecule analysis, or devices of potential interest in the field of technologies for health, in particular biomaterials or imaging. Applicants are expected to run independent and creative projects. They should be open to interdisciplinary collaborations with other groups of the institute. Successful candidates will have access to IECB’s facilities in structural biology, chemistry, molecular and cellular biology. The candidates will be asked to apply for start-up funding such as ATIP-Avenir Inserm-CNRS programme, FRM "amorçage", ANR support or ERC funding. The applicants should be fluent in English. Knowledge of French is not mandatory. Applicants are invited to submit - prior to July 4, 2013 - a detailed biography and publication record together with a 5 page summary of research achievements and projects as well a list of potential referees to: Dr Jean-Jacques Toulmé, Director of IECB 2 rue Robert Escarpit 33607 Pessac Cedex, France e-mail: assist-dir(a)iecb.u-bordeaux.fr

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vacancy bioinformatician metabolomics Singapore/Ireland
by Kris Laukens 24 Apr '13

24 Apr '13

Dear colleague, feel free to distribute the attached vacancy for a bioinformatician (metabolomics) to potentially interested candidates. Kind regards, Kris Laukens -- Advanced Database Research and Modelling (ADReM - adrem.ua.ac.be) Biomedical Informatics research center Antwerpen (biomina - www.biomina.be) University of Antwerp, Belgium

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RECOMB-CG 2013 - Call for papers
by macha＠labri.fr 20 Apr '13

20 Apr '13

Eleventh Annual RECOMB Satellite Workshop on Comparative Genomics October 17-19, 2013, Lyon, France Website: rcg2013.sciencesconf.org Contributions to the workshop are welcomed on any theoretical and/or empirical approach to genome-wide comparison. This includes genome evolution, algorithms for genome rearrangement, comparative tools for assembly, gene identification or annotation, comparison of functional networks, genomic variation in humans and model organisms, cancer genomics, duplication patterns of genes, segments and whole genomes, and comparative epigenetics. We encourage paper submissions that offer new biological findings or otherwise highlight their relevance to biology. Refereed papers will be published as open-access manuscripts in the journal BMC Bioinformatics. -------- KEY DATES Paper submission deadline June 21, 2013 Acceptance notification July 19, 2013 Workshop October 17-19, 2013 - Lyon, France -------- CONFIRMED KEYNOTE SPEAKERS - Tal Dagan, Heinrich Heine Universität, Dusseldorf - Ludovic Orlando, Centre for GeoGenetics, natural History Museum of Denmark -------- THEME AND SCOPE The continuing advance of DNA sequencing technology has produced an avalanche of genome sequence and genome structural information across the evolutionary spectrum. Transforming that information into biological knowledge requires creative and innovative new computational and statistical methods for comparative genomics. The RECOMB Satellite Workshop on Comparative Genomics aims to provide the premier forum for new computational developments applied to all aspects of comparative genomics. We solicit contributions on topics including comparison of genome structure and organization, genome function, and evolution. We particularly encourage contributions that use new computational methods to acquire new insight into biological processes. Advances in computational theory are welcome, though all submissions should include genome-scale analyses informed by comparative data. All peer-reviewed and accepted RECOMB-CG manuscripts will be published in a supplement to BMC Bioinformatics as open-access, author-subsidized, articles. Specific topics of interest include but are not limited to: . Gene and genome duplication . Gene family evolution . Genome structural variation . Algorithms for comparative genomics . Genome rearrangements . Ancestral genome reconstruction . Multiple genome alignment . Genome sequence comparison . Modeling genome evolution . Comparative genomics for genome annotation . Gene tree reconciliation . Species and gene tree inference . Comparative metagenomics . Comparative genomics linked to proteomics, metabolomics, and other ~omic data . Comparative genomics and gene expression and regulation . Applications of comparative genomic methods . Paleogenomics -------- CALL FOR PAPERS Papers should be submitted via the EasyChair system: https://www.easychair.org/conferences/?conf=recombcg13. Submissions must be received in electronic form by 11:59pm (Samoa time), June 21th, 2013. Papers submitted for review should represent original, previously unpublished work. At the time the paper is submitted to the conference, and for the entire review period, the paper should not be under review by any other conference or scientific journal. At least one author per each successful submission is required to register and present the paper at the workshop. The paper will be included in the conference proceedings, which will be published in BMC Bioinformatics as open-access author-subsidized articles. Authors are encouraged to use the BMC document templates when preparing manuscripts. Templates are available in Microsoft and LaTeX formats. Otherwise, submissions should be typeset as double-spaced A4 pages with at least 1-inch margins all around in a minimum of 10 point font. Submissions should be limited to 16 pages, everything included (title, authors, addresses, abstract, references, figures, tables). Exceptions to this limit may be granted by consultation with the Program Committee Chairs. Submissions must include the corresponding author’s email address. When preparing your submission please follow the instructions for authors of BMC supplements: http://www.uff.br/recombcg/docs/Instructions-for-authors-BMC-Appendix-B.pdf. Submitted manuscripts must be rendered to PDF format prior to upload into EasyChair at the review stage. Address any questions to the program committee chairs: Macha Nikolski macha (at) labri (dot) fr and Yves Van de Peer yves (dot) vandepeer (at) psb (dot) vib (dash) ugent (dot) be -------- PROGRAM COMMITTEE Chairs: Macha Nikolski (LaBRI & CBiB, Université Bordeaux, France) Yves Van de Peer (VIB / Ghent University, Belgium) PROGRAM COMMITTEE (preliminary) Lars Arvestad Sweden Anne Bergeron Canada Mathieu Blanchette Canada Guillaume Blin France Guillaume Bourque Singapore Titus Brown United States Frederic Brunet France Marilia Braga Brasil Cedric Chauve Canada Aaron Darling Australia Alexei Drummond New Zealand Niklas Eriksen Sweden Martin Frith Japan Gerton Lunter United Kingdom Vsevolod Makeev Russia Kateryna Makova United States Guilherme Oliveira Brasil Francis Ouellette Canada Benedict Paten United States Ian Paulsen Australia Teresa Przytycka United States Ben Raphael United States Matt Rasmussen United States Hugues Roest-Crollius France Fredrik Ronquist Sweden Marie-France Sagot France Cathal Seoighe Ireland Joao Setubal Brasil Hayssam Soueidan Netherlands Jens Stoye Germany Krister Swenson Canada Eric Tannier France Glenn Tesler United States Raluca Uricaru France Miguel Vazquez Spain Christopher Workman Denmark Sophia Yancopoulos United States Louxin Zhang Singapore STEERING COMMITTEE Jens Lagergren (KTH Royal Institute of Technology and SciLifeLab Stockholm, Sweden) Aoife McLysaght (University of Dublin, Ireland) David Sankoff (University of Ottawa, Canada)

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Postdoc position in bioinformatics at Oslo University Hospital, Norway
by Maté Ongenaert 19 Apr '13

19 Apr '13

A one-year postdoc position is available at Institute for Cancer Research at Oslo University Hospital. Applications are invited from students holding a PhD in bioinformatics or molecular biology with experience in analysis of high throughput data. The post.doc will participate in the development of a gene based diagnostic test for detection of aggressive cervical cancer. A gene signature underlying the test has been identified, and validation and optimization of the signature in a new patient cohort will be major tasks. Extension of the post.doc period with two more years will be possible in case of a decision towards commercialization of the test. For more information: project leader Heidi Lyng, heidi.lyng(a)rr-research.no<mailto:heidi.lyng@rr-research.no> Web site: http://ous-research.no/lyng/ Application with CV to Heidi Lyng, heidi.lyng(a)rr-research.no<mailto:heidi.lyng@rr-research.no> Deadline: 29th of April 2013

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Marie-Curie Post-Doc Fellowship in Systems Biology - GSK Vaccines : Rixensart, Belgium
by Robert Van den Berg 19 Apr '13

19 Apr '13

Dear all, We are currently looking for a postdoc interested in writing a joint application for a Marie-Curie grant. The topic will be: Development of systems biology approaches to better understand the longitudinal development of the immune response after vaccination, and the relation of this development to vaccine efficacy. For more information please check: http://www.nature.com/naturejobs/science/jobs/318215-Marie-Curie-Post-Doc-F…. Feel free to share this further. Kind regards, Robert Robert van den Berg PhD Expert scientist Bioinformatics GlaxoSmithKline Vaccines Building B62J420 | Rue de l'Institut 89 | 1330 Rixensart | Belgium T: +3226568395 E: robert.x.van-den-berg(a)gsk.com<mailto:robert.x.van-den-berg@gsk.com> [Description: Description: cid:image001.jpg@01CD132C.27416BA0] Registered as GlaxoSmithKline Biologicals SA - Rue de l'Institut, 89 BE-1330 Rixensart - TVA BE 0440.872.918 RPM Nivelles. Deutsche Bank AG Bruxelles 826-0006444-59

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[Gtpb] GTPB Course Reminder - RNA-seq + Automatic Func. Annotation
by Pedro Fernandes 17 Apr '13

17 Apr '13

Course Reminder Applications are OPEN until May 7th 2013 Early decisions available. *TA-AFADM13* Transcriptome Assembly, Automatic Annotation and Data Mining with Ana Conesa and Fernando Garcia IMPORTANT DATES for TA-AFADM13 Deadline for applications: May 7th 2013 Notification of acceptance dates: EARLY: Apr 19th 2013 (on special request, see Application) NORMAL: May 8th 2013 Course date: May 20th - May 23rd 2013 http://gtpb.igc.gulbenkian.pt/bicourses/TA-AFADM13 This course is particularly suitable for those seeking training in using NGS data for tanscriptomics (RNA-seq), and in extensively annotating with Blast2GO, the most popular and powerful tool for this purpose. 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 first part of the course is a practical tutorial on Blast2GO, the most popular framework for functional annotation of sequences. Participants will also 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. visualization and enrichment analysis using the Gene Ontology. The second part of the course covers many relevant aspects of RNA-seq analysis, form quality control, to mapping, reconstruction of transcripts and differential expression. Participants will learn how to deal with RNAseq data both in the presence and absence of a reference genome. At the end of the course, participants can expect to have acquired skills to use multiple software tools to analise RNA-seq data and use Blast2GO. The course will be based on the use of 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. *Course Pre-requisites:* Basic knowledge in Molecular Biology and Statistics. Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS Tel +351 21 4407912 http://gtpb.igc.gulbenkian.pt _______________________________________________ Gtpb mailing list Gtpb(a)igc.gulbenkian.pt https://lists.igc.gulbenkian.pt/mailman/listinfo/gtpb

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FW: Vacancy Full professor of Bioinformatics at Wageningen University - new link
by Vleghels, Ingrid 17 Apr '13

17 Apr '13

Because of an update on the Wageningen-UR site a new link for this vacancy: http://www.wageningenur.nl/nl/Werken-bij/Vacatures/Show/Full-Professor-of-B… With kind regards, Ingrid Veghels ________________________________ From: Vleghels, Ingrid Sent: 16 April 2013 16:59 To: 'bbclist(a)psb.ugent.be' Subject: Vacancy Full professor of Bioinformatics at Wageningen University Dear sirs, Wageningen University seeks to appoint a full professor in Bioinformatics. Please use the link to find more information on this vacancy http://www.wageningenur.nl/en/Jobs/Vacancies/Show/Full-Professor-Bioinforma…. I hope you will be so kind to forward this link to the people on your e-mail list. With kind regards, Ingrid Vleghels Dr. Ingrid Vleghels Graduate School ‘Experimental Plant Sciences’ (EPS) Droevendaalsesteeg 1 Building RADIX-East (bldg. nr. 107) Bode 180 6708 PB Wageningen The Netherlands T: +31 317 484757 E: ingrid.vleghels(a)wur.nl<mailto:ingrid.vleghels@wur.nl> W: www.graduateschool-eps.info<http://www.graduateschool-eps.info>

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