January 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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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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NBIC2013 – Call for abstracts
by Femke Francissen 21 Feb '13

21 Feb '13

Call for abstracts for the NBIC2013 NBIC2013 – the Netherlands Bioinformatics Conference 2013 Date: 16 & 17 April 2013 Venue: De Werelt, Lunteren, the Netherlands Website: http://www.aanmelder.nl/nbic2013 Call for abstracts You can submit an abstract for an oral presentation, a poster presentation and for a demo during the application showcase for the NBIC2013 programme. Note, there will be a specific session for Data & Technology. Abstracts can also be submitted for the two satellite meetings: the Metagenomics Satellite track and the NSBM Spring Meeting. Submit your abstract via the conference website: http://www.aanmelder.nl/nbic2013 Programme · 5 keynote speakers: Alexander van Oudenaarden, Janet Thornton, Uwe Sauer, Roeland van Ham and Jeroen Raes · Satellite meetings: Spring meeting of the Netherlands Society on Biomolecular Modelling (NSBM) & Metagenomics Satellite Track · Parallel sessions of contributed lectures · Parallel workshops · Poster presentations (NB: evening poster session!) · Industry meeting (BIUP) · RSG Retreat on April 15th Key dates · deadline for abstract submission: Monday March 4, 2013 · notification of selection for oral presentations: Friday March 22, 2013 · registration deadline: April 1, 2013 About The Netherlands Bioinformatics Conference 2013 (NBIC2013) is the 8th edition of the annual conference organized by the Netherlands Bioinformatics Centre (NBIC). NBIC2013 discusses the latest developments in bioinformatics and interrelated disciplines, and their wide-ranging applications in life sciences & health, agriculture, food & nutrition and industrial biotechnology. NBIC2013 offers a cross-disciplinary scientific program of (poster) presentations, application demonstrations and workshops, as well as other opportunities to exchange innovative ideas. More information Contact: Femke Francissen, e-mail: femke.francissen(a)nbic.nl<mailto:femke.francissen@nbic.nl>

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Metagenomics Satellite Track at the NBIC 2013 conference
by Sacha van Hijum 30 Jan '13

30 Jan '13

The Netherlands Metagenomics Platform cordially invites you to join the Metagenomics Satellite Track at the NBIC 2013 on April 17, 2013 in Lunteren, the Netherlands. Jeroen Raes of the Flemish Bioinformatics Institute and the Free University of Brussels will be present at this satellite meeting and will also give a keynote lecture during the NBIC2013 programme. Abstracts are solicited in any field related to metagenomics or computational analysis of microbial ecosystems. Topics include: - All areas of environmental sequencing (e.g. amplicon sequencing, shotgun metagenomics, metatranscriptomics, metaproteomics) - Prokaryotic, eukaryotic or viral systems - Sequencing strategies and technologies - Quality control, data pre-treatment - Read mapping, taxonomic and functional annotation - Comparative metagenomics - Metagenome assembly - Discovery of novel species, enzymes - Monitoring, public health surveillance - The tree of life, the rare biosphere - Microbial networks and ecosystem modeling - Host-microbe interactions (e.g. human, plants, corals) - Role of microbes in bioremediation, biogeochemical cycles - Visualisation To submit an abstract, please visit the abstract submission page: http://www.aanmelder.nl/nbic2013/wiki/Metagenomics%20satellite Please indicate that you are submitting your abstract for the Metagenomics Satellite track. -- Dr. Sacha van Hijum Group leader CMBI Bacterial Genomics Senior scientist bioinformatics NIZO food research B.V. Bioinformatics platform leader Top Institute Food and Nutrition T: +31(0)318 659 570 F: +31(0)318 650 400 M: +31(0)624782895 E: sacha.vanhijum(a)nizo.nl or svhijum(a)cmbi.ru.nl P.O. Box 20, 6710 BA EDE, The Netherlands Kernhemseweg 2, 6718 ZB EDE, The Netherlands

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NSBM Spring Meeting 2013
by Barbara van Kampen 28 Jan '13

28 Jan '13

Dear colleagues, It is our pleasure to invite you to the 2013 spring meeting of the (protein) structure bioinformatics society (NSBM). The meeting will take place in Lunteren on April 16 and run parallel with the first day of the annual two day NBIC meeting. We are proud to announce that two imminent scientists have accepted our invitation to participate in our club meeting.: Janet Thornton is the director of the EBI. She has been one of the worlds pioneers in protein structure bioinformatics. She recently was honoured by the British queen for her imminent role in science. Janet will present a key-note lecture and will present to 'us' a seminar on EBI specific bioinformatics topics. Daniel Hoffmann is a bioinformatics professor from the university of Duisburg-Essen. He has a background in mathematics/physics, but nevertheless is a wonderful teacher with great skills in making difficult concepts clear to the more bio-oriented scientists among us. Daniel has accepted our invitation to explain to us the concepts behind the recent developments in predicting structures from sequence alignments (see the articles by Nimwegen, Jones, and Marks and Sander). Additionally, we will have a poster session, and 6 poster presenters will be invited to present their poster in a seminar. Here all information can be found http://www.aanmelder.nl/nbic2013/: - The program of both the NBIC and NSBM meeting - How to register - How to submit the abstract. With kind regards, Gert Vriend NSBM

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CAMDA'12 Announcement
by Yves Moreau 21 Jan '13

21 Jan '13

On behalf of the organizers of CAMDA'12. Best regards, Yves Moreau ============== Dear Colleagues, With great pleasure we announce the 12th International Conference on the Critical Assessment of Massive Data Analysis (CAMDA) in Berlin, Germany, July 19-20, 2013, held as official Satellite Meeting to ISMB/ECCB. CAMDA focuses on innovative methods to analyze massive data sets from life sciences. Over two days, researchers from bioinformatics, computer sciences, statistics, genetics, molecular biology, and other fields present novel approaches to analyze Big Data. An essential part of CAMDA is its competitive challenge where big heterogeneous data sets are analyzed and outcomes and methods compared. Academic and industrial researchers worldwide are invited to take the CAMDA challenge, to show their expertise in handling Big Data, and to present their results. Submitted abstracts are selected for oral and poster presentations. As in last years, the prestigious CAMDA prize will be awarded for the best presentation. Selected submissions are published in the CAMDA Proceedings as an open access PubMed indexed special issue of Systems Biomedicine. You can find additional information about the challenge data sets, submissions, etc. at www.camda.info. Some key dates are: - Abstract submission deadline for oral presentation / 20 May 2013 - Abstract submission deadline for poster presentation / 25 May 2013 - Notification of accepted contributions / 30 May 2013 - Early registration closes / 1 June 2013 As in past years, contest presentations are complemented by high profile keynotes (with recent speakers including Sandrine Dudoit, Mark Gerstein, John Quackenbush, Terry Speed, John Storey, Eran Segal, and others). This year, we are delighted to welcome Atul Butte of the Stanford University School of Medicine, CA, USA! We look forward to seeing you in Berlin! The organizers and chairs of CAMDA 2013 Chairs: Joaquin Dopazo, CIPF, Spain Sepp Hochreiter, Johannes Kepler University, Austria David Kreil, Boku University, Austria Simon Lin, Marshfield Clinic, U.S.A. Local organizer: Djork-Arné Clevert, Johannes Kepler University, Austria Contact: camda(a)bioinf.jku.at Conference website: http://www.camda.info

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PhD position @ Ghent University - Bioinformatics/Ribosome Profiling
by Gerben Menschaert 18 Jan '13

18 Jan '13

Research context This job opening has been created in the context of an FWO research grant entitled: “Complementary use of ribosome profiling and positional proteomics for mapping the translation initiation and nascent protein modification landscape in human cell lines”. The PhD student will be working in a multi-disciplinary environment within a collaboration of three different research groups: the Proteomics and CompOmics groups of the VIB Department of Medical Protein Research, and the BioBix-Lab of Bioinformatics and Computational Genomics. Job description High-throughput applications such as next-generation sequencing are frequently applied in modern biological and medical research. Recent technology advancements enable protein translation measurement on the RNA level by massive sequencing of ribosome-captured messenger RNA footprints. This work will focus on the intersection between the state-of-the-art fields of high-throughput RNA sequencing and high-throughput positional proteomics analysis. Specific tasks include preprocessing, statistical validation and genome-wide visualization of sequencing and proteomics data, and development of a toolbox integrating experimental sequencing data and search space optimization for mass spectrometry based proteomics research. A start date of 1 March 2013 is proposed but this is flexible depending on the availability of the successful candidate. Profile The successful candidate will have obtained or will obtain a Master’s degree in a relevant field (life sciences, informatics, statistics, biology, (bio-) engineering) and will have a keen interest/knowledge in bioinformatics and data processing. Experience in computational genomics or proteomics is considered an advantage. Experience with programming languages (notably Perl, Java, C++) and/or relational database systems (e.g., MySQL, SQLite) is also considered an advantage. Contact Please submit a cover letter, a full c.v., and a list of at least two contact persons (with name, email, address, phone number) for letters of reference to petra.vandamme(a)vib-ugent.be, or: Prof. Dr. Petra Van Damme, VIB Department of Medical Protein Research , A. Baertsoenkaai 3, B-9000 Gent, BELGIUM. Links http://www.vib.be/en/research/scientists/Pages/kris-gevaert-Lab.aspx http://www.biobix.be http://www.compomics.com

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PhD position in KU Leuven / Université du Québec à Chicoutimi
by Francisco Bonachela Capdevila 18 Jan '13

18 Jan '13

PROJECT OUTLINE INTEGRATIVE ANALYSIS OF GENOMICS, EPIGENOMICS AND TRANSCRIPTOMICS The rapid evolution of analytical strategies in the last years has permitted an exhaustive analysis of biological processes providing us with different views of the origin of genetic diseases. Enormous datasets including genomics, transcriptomics and epigenomics have been regularly generated by Systems Biology approaches and new bioinformatics strategies must be developed to find relevant patterns and retrieve useful information from them. The individual approach to analyze those databases does not seem to be sufficient while integrative strategies start to be used, which provide us with a multi-perspective vision of the biological processes and diseases. At the Laprise lab in the context of the Canada Research Chair in asthma at UQAC, Chicoutimi, Québec both genomic, transcriptomics and epigenomics analysis have been run since 2000. The expertise of CODeS group, KULAK, Belgium includes integrative and combinatorial optimization approaches in, among others, bioinformatics. The doctoral project will be developed under both GEPROMIC and CODeS groups and new bioinformatics methodologies will have to be designed and developed with aim to integrate data from the previously mentioned heterogeneous biological databases in an efficient and relevant manner. TIME FRAME From beginning 2013 to end of the 2016, the project on integrative genomics in asthma will be performed. CANDIDATE REQUIREMENTS The candidate should have a master degree in Bioinformatics, Bio-engineering, Biomedical Sciences, Engineering or Computer Sciences and demonstrate deep knowledge in programming (e.g. perl, Java), computational statistics (e.g. R) and/or machine learning. Experience with sequence data or genome-wide data sets will be assets. The candidate should have good organizational skills, interest for interdisciplinary research, good presenting skills and be able to work independently. LOCATION The Ph.D. research will be conducted partially in the Katholieke University of Leuven campus Kortrijk and in the Université du Québec à Chicoutimi. CONTACT DETAILS Please contact Dr. Catherine Laprise (catherine_laprise(a)uqac.ca) and Dr. Francisco Bonachela-Capdevila (Francisco.BonachelaCapdevila(a)kuleuven-kortrijk.be <mailto:Francisco.BonachelaCapdevila@kuleuven-kortrijk.be>). When applying please ensure you include a CV, a covering letter and your student record. CLOSING DATE Closing date: 3 February 2013

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Vacancy NGS data manager
by Tim De Meyer 17 Jan '13

17 Jan '13

Dear sir/madam, please forward to the bbclist. Thank you, Tim De Meyer *Vacancy: Data manager next-generation sequencing data* ** *When to start?* As soon as possible, August 2013 the latest. ** *Job description* High-throughput applications, such as next-generation sequencing, are becoming increasingly important in contemporary biological and medical scientific research. The lab for Bioinformatics and Computational Genomics "BIOBIX" (Dept. of Mathematical Modelling, Statistics and Bioinformatics at the Faculty of Bioscience Engineering, Ghent University), performs research in close collaboration with the sequencing team of NXTGNT, with typical applications in cancer and cardiovascular diseases. BIOBIX particularly focuses on the (pre-)processing, bioinformatics and statistical data-analysis of the obtained data. BIOBIX is recruiting a new, enthusiastic co-worker to join our team of "genome hackers", initially for a period of 4 years. Your most important task is the daily management of huge quantities of next-generation sequencing data, being data transfer, safe storage and back-up, and automated data-preprocessing. In addition you'll also be involved in our research, particularly in the "PLASTOSCINE" basic research project attempting to elucidate learning processes in the brain on a molecular level. *Your profile* You have a professional bachelor's degree or master degree in industrial sciences in the field of bioinformatics (broad sense), or equivalent by experience. Final year students are welcome to apply as well. Solid knowledge of molecular biology, PERL and SQL are absolutely required, as well as profound experience of working in a LINUX (command line) environment. Experience with website-development, server maintenance (hard- and software) and statistical data-analysis (preferably in R) are appreciated. You like to work in a team, but you're also flexible and accountable to solve problems independently. You have strong operational troubleshooting and diagnostic skills. Proficiency in English is a requirement. *Contact* Send your CV, motivation letter and 2 reference letters (optional) to Tim.DeMeyer(a)UGent.be <mailto:Tim.DeMeyer@UGent.be>by the 1st of March, 2013. ** ** ** -- ___________________________ Prof. Tim De Meyer, PhD MRP Nucleotides 2 Networks BIOBIX Lab. for Bioinformatics and Computational Genomics BW10 - Dept. of Mathematical Modelling, Statistics and Bioinformatics Faculty of Bioscience Engineering Coupure Links 653, 9000 Ghent Ghent University - Belgium www.biobix.be / www.nucleotides2networks.be / www.researcherid.com/rid/D-3892-2011 Tel.: +3292649922 (office)

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Bioinformatics jobs in Denmark
by Olivier Sand 17 Jan '13

17 Jan '13

Dear all, Please find in attachment two job ads. Best regards, -- Olivier Sand, PhD Responsable Bioinformatique EGID FR3508 European Genomics Institute for Diabetes CNRS UMR8199 Genomique et Maladies Metaboliques Institut de Biologie de Lille 1, Rue du Professeur Calmette B.P. 245 CS 50447 59021 Lille Cedex France Tel: 33 (0)3 20 87 10 71 Fax: 33 (0)3 20 87 10 31 olivier.sand(a)good.ibl.fr http://www-good.ibl.fr/

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