- BBClist - maillist.psb.ugent.be

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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Vacancy for a PhD student at the Department of Bioinformatics - BiGCaT in Maastricht
by Chris Evelo 17 Jan '13

17 Jan '13

The department of Bioinformatics - BiGCaT at Maastricht University has a vacancy for a PhD student whose research topic will concentrate on the integration of genetic data in biological pathway approaches. A description of the vacancy and the procedures involved is available online at: www.academictransfer.com/16883 Dr. Chris Evelo, Maastricht University

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Doctoral Fellowship "Computational Biodiversity"
by bvkampen＠cmbi.ru.nl 16 Jan '13

16 Jan '13

Dear Colleague, Please forward the attached advertisement for a doctoral fellowship on "Computational Biodiversity" to interested parties. Thanks, Daniel

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Development of R software for data analysis-workshop in Hasselt University in 13/03/2013
by Martin OTAVA 16 Jan '13

16 Jan '13

Dear All, We would like to invite you for the workshop “Development of R software for data analysis”. The workshop is co organized by OpenAnalytics and CenStat and will take place in Hasselt University on 13/03/2013 from 09:00 to 17:30. The workshop will be focused on the use of R software and R Applications in a dynamic and changing working environment (see the program below). The workshop is free of charge but registration is mandatory and can be done online using the following link: http://www.uhasselt.be/Workshop-R We are looking forward to see you in the workshop, Martin Otava, Pushpike Thilakarathne and Tobias Verbeke. Program of the workshop 08:30-09:00: Coffee + Welcome 09:00-10:30: Tobias Verbeke (Open Analytics): Proper working environment and best practices when developing R code + R packaging 10:30-11:00: Coffee break. 11:00-12:30: Tobias Verbeke: Proper working environment and best practices when developing R code + R packaging 12:30-13:30: Lunch 13:30-14:00: Ziv Shkedy (Hasselt University): Lost in translation or maybe not ? translation of data analysis framework into a set of a R packages 14:00-15:00: Setia Pramana(Karolinska Institutet): Development of GUIs and packaging. 15:00-15:30: Pushpike Thilakarathne (Hasselt University): Development of an R package for Biomarkers validation with survival outcome 15:30-16:00: Coffee break. 16:00-16:45: Tobias Verbeke: The R Service Bus (RSB): Integrating R in Work flows and Processes 16:45-17:30: Tobias Verbeke: The R Service Bus (RSB) + summary of the workshop. 17:30: Reception. Martin Otava PhD student Interuniversity Institute for Biostatistics and statistical Bioinformatics (I-Biostat) Center for Statistics, Universiteit Hasselt Agoralaan 1 - 3590 Diepenbeek, Belgium Tel.: 32 - 11 - 268201 E-mail: otava.martin(a)uhasselt.be

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Job Opening: Bioinformatician at OpenAnalytics (Belgium)
by Tobias Verbeke 15 Jan '13

15 Jan '13

L.S. OpenAnalytics is an international company providing data analysis services and products across geographies and industrial sectors. We are currently looking to expand our bioinformatics team with a candidate who fits the following profile: Bioinformatician: MSc / PhD in Computational Biology, Computer Science or Bioinformatics A detailed description can be found at http://www.openanalytics.eu/jobs Strong R and BioConductor skills are an important asset for the position. Kind regards, Tobias Verbeke -- Tobias Verbeke Manager OpenAnalytics BVBA Jupiterstraat 20 2600 Antwerp Belgium E tobias.verbeke(a)openanalytics.eu M +32 499 36 33 15 http://www.openanalytics.eu

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Course Introduction to Next Generation Sequencing
by Jeanie van Driel - Blom 15 Jan '13

15 Jan '13

Dear reader, We, Avans University of Applied Sciences, Research Group Analysis Techniques in Life Science, organize an international shortcourse on next generation sequencing in Breda at April 2013. Aim of the course: DNA sequencing technologies are currently developing at an incredible speed and new applications are presented monthly, incl. DNA/RNA profiling, ChIP-seq, re-sequencing, de novo genome sequencing and metagenomics. The aim of this course is to introduce next generation sequencing technologies, highlight different applications of these new technologies, and show ways to analyse data. Please visit the course website for detailed information: http://www.alsavans.nl/avans-training-2542.htm Looking forward to meeting you in Breda Best regards Jeanie van Driel-Blom Avans university of applied science p.o. box 90116 4800 RA Breda The Netherlands --------------------------------------------------------------------------- Op deze e-mail zijn de volgende voorwaarden van toepassing: The following conditions apply to this e-mail: http://emaildisclaimer.avans.nl ---------------------------------------------------------------------------

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CAPRI2013 meeting
by Barbara van Kampen 15 Jan '13

15 Jan '13

Dear all, The 5th international CAPRI meeting (Critical Assessment of Predicted Interactions) will take place in Utrecht on April 17-19. This meeting brings together leading experts in the field of modelling biomolecular interactions and functions as an important catalyst for innovation. The meeting is open to all interested groups, even if not participating to CAPRI. The three day program is divided into a number of thematic sessions and short presentations. It will host 20 regular lectures and 10 short talks where we will grant the stage to young researchers, mainly post-docs and PhD students. Following the tradition of the meeting, the selection of speakers wil be made based on the submitted abstracts. Selected speakers are also invited to contribute to the special issue of Proteins dedicated to CAPRI that will be published late 2013. In addition, poster sessions will take place during lunches and in the first evening with welcome drinks. Posters will be on display for the entire duration of the meeting. Registration is going well and we have already received quite some abstracts for contributions. We have extended the deadline for submitting abstracts for talks to January 20th. Selected contributors will be notified by February 8th. So if you have not yet submitted an abstract for a talk at CAPRI2103, please visit: www.capri2013.nl <http://www.capri2013.nl/> To ensure smooth planning of the evaluation meeting and the publication of the CAPRI Special Issue in Proteins there are a number of key dates you should be aware of. January 20: Deadline for abstract submission February 8: Oral presentations and short talks are selected April 17-19: Utrecht meeting June 1: Submission deadline for papers of the Special Issue of Proteins The preliminary programme and registration information are available from the CAPRI2013 web site. Looking forward to see you in Utrecht. Best regards Alexandre Bonvin & CAPRI committee

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