February 2015 - BBClist - maillist.psb.ugent.be

Deadline registration: Life Science Courses at Avans University of Applied Sciences
by Sari van Heel - Vauhkala 27 Feb '15

27 Feb '15

Dear members of BBClist, Please note that the deadline for course registration for these three courses of the Research Group Analysis Techniques in Life Science (Avans University of Applied Sciences, Breda, the Netherlands) is Friday 6 March 2015: 1) Principles, parameters and applications of PCR; 7 April 2015 Registration fee: €400,- Website : http://www.alsavans.nl/avans-training-2545.htm 2) Real-time PCR in molecular diagnostics; 8-10 April 2015 Registration fee: €900,- Website: http://www.alsavans.nl/avans-training-2548.htm 3) Introduction to Next Generation Sequencing; technologies and data analysis; 14-17 April 2015 Registration fee: €1100,- Website: http://www.alsavans.nl/avans-training-2542.htm The digital registration form is available on the website. Should you have any questions, please do not hesitate to contact us by email at: si.vanheel-vauhkala(a)avans.nl<mailto:si.vanheel-vauhkala@avans.nl> Kind regards, Ms. Sari van Heel-Vauhkala Secretary Research Group Analysis Techniques in Life Science Disclaimer ( http://www.avans.nl/over-avans/e-mail-disclaimer )

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FW: Postdoctoral research fellow in biostatistics/bioinformatics
by Sander Canisius 26 Feb '15

26 Feb '15

Postdoctoral research fellow in biostatistics/bioinformatics Position as postdoctoral fellow available for three years at Department of Genetics, Institute for Cancer Research, Norwegian Radium Hospital, Oslo, Norway http://www.universitetstillinger.no/job/32r3o *Research environment* Institute for Cancer Research has since its foundation in 1954 played a central role within the field of cancer research both in Norway as well as internationally. The Institute has six research departments, a core facility and more than 320 employees, master students included. About 70% of the employees and projects are externally funded. Department of Genetics consists of four major research groups which include five project groups. The department is headed by Professor Anne-Lise Børresen-Dale, who is also leading a K.G. Jebsen-Center for Breast Cancer Research. The main research area of the department is on molecular biology and functional genomics of breast cancer to understand breast cancer progression and identify prognostic and predictive markers. In addition, one group is focusing on lung and pancreatic cancer. The department possesses large bio-banks of human tumor and blood samples and has long standing expertise in genome-wide technologies for the analysis of DNA, RNA and proteins. http://www.ous-research.no/genetics/ Oslo centre for biostatistics and epidemiology (OCBE) includes staff from University of Oslo and Oslo University Hospital and includes several professors, researchers, post-doctoral fellows and PhD students, making up a group of about 50. OCBE is internationally recognized, with interests spanning a broad range of areas of modern statistics and numerous collaborations with leading bio-medical research groups nationally and internationally. OCBE will have a major role in the recently funded prestigious centre for research-based innovation Big Insight, a consortium of academic, industrial and public partners. Big Insight will develop original statistical and machine learning methodologies and deep analytical tools to extract knowledge from complex and big data, with focus on two central themes: novel personalized solutions and sharper predictions of transient dynamics. *Project information* The post doctoral project is centered on development and progression of breast cancer using large scale genomic data from human tumor samples and mouse models. Such data include gene expression, copy number (SNP) and methylation data from microarray analysis of tumor samples ranging from benign lesions to invasive breast cancer, as well as targeted and exome sequencing data. The aim is to increase our understanding of how breast lesions develop and progress from the pre-invasive state and to the more aggressive invasive tumor stages and to identify markers of potentially clinical usefulness. The appointed candidate will be working in the group headed by Dr. Therese Sørlie, http://www.ous-research.no/sorlie/ . Co-supervisor will be Professor Arnoldo Frigessi, (OCBE) http://www.med.uio.no/imb/english/people/aca/frigessi/. In addition to own projects, the candidate is expected to supervise and contribute in the projects of other group members. Required professional and personal skills The candidate must have a PhD in statistics, mathematics, bioinformatics or other relevant science with a significant and documented competence in biostatistics. Experience with genomics data is necessary. The candidate must have full proficiency with some statistical software and language like R or plink. Knowledge of programming languages like C or Python is an advantage, but not necessary. Competence and/or experience with high dimensional data, multiple comparison, and dimension reduction is also an advantage. We are looking for a young researcher who has the interest in both developing new methods and analysis pipelines for high dimensional data and applying state of the art methods. The candidate is expected to work together with other scientists in a team. We will welcome a highly motivated and dedicated candidate, with the ability to work independently, but with good communication skills and who performs well in a team. Proficiency in the English language is a prerequisite. *We offer* * A challenging and friendly working environment * Favorable pension arrangement * Attractive welfare arrangements * Salary NOK 491 000 - 530 000 p. y. depending on qualifications *Application should include:* * Cover letter including motivation for the position * CV (summarizing education, positions and academic work) * Copies of educational certificates (PhD diploma) and letters of recommendation * List of publications and academic work that the applicant wishes to be considered * Contact information for two references * Foreign applicants should be prepared to provide an explanation of their diploma if needed. Please note that all documents should be in English or a Scandinavian language. * According to the Norwegian Freedom of Information Act (offentleglova) information about the applicant may be included in the public applicant list. Application deadline: 15.03.2015 Project start: July 2015 Contacts: Principal investigator: Therese Sørlie, tsorlie(a)rr-research.no, tel. +47 22781364, Co-supervisor Arnoldo Frigessi: arnoldo.frigessi(a)medisin.uio.no Administrative coordinator: Gry Geitvik, gryge(a)rr-research.no, TEL. +47 22781374

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[Gtpb] Bioinformatics Training Course IB15F Announcement / Reminder
by Pedro Fernandes 26 Feb '15

26 Feb '15

Dear all, The Applications for the Introductory Bioinformatics course, first instance in the 2015 Programme, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: March 20th 2015 Latest notification of acceptance: March 21st 2015 Course date: April 13th - April 17th 2015 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB15F/ This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Important NOTE: This is one of our most popular courses. It usually gets full very quickly. Applications are approved and accepted in order of arrival and we only have 20 seats. Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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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Three postdoc positions data analysis of clinical -omics data at GSK Vaccines (2.5 years)
by Robert Van den Berg 25 Feb '15

25 Feb '15

Dear all, I'm very excited to announce three postdoc positions at GSK Vaccines in collaboration with the Bill & Melinda Gates Foundation for the data analysis and interpretation of omics data collected in clinical research studies in the fields of malaria and TB vaccine development, and adjuvant mode of action. The positions are all for 2.5 years, based in Belgium, and will include a period (3 months up to 1 year) in the US visiting academic partners at the forefront of the field of systems vaccinology. The positions vary from a strong emphasis on data analysis, multivariate / longitudinal, integrating data from different sources, to a focus on bridging data analysis and biology with interpreting data to understand and improve the development of an adaptive immune response and learning / expanding novel immunological techniques. Please find below the links to the positions: https://careers.peopleclick.com/careerscp/client_gsk/external1931/jobDetail… https://careers.peopleclick.com/careerscp/client_gsk/external1931/jobDetail… https://careers.peopleclick.com/careerscp/client_gsk/external1931/jobDetail… Feel free to contact me if you have any questions. Please share it with people who might be interested. Kind regards, Robert Robert van den Berg Senior Manager Vaccines Research GSK Biologicals GSK Rue de l'institut 89 B1330, Rixensart Belgium Email robert.x.van-den-berg(a)gsk.com<mailto:robert.x.van-den-berg@gsk.com> Tel +32 2 656 8395 gsk.com<http://www.gsk.com/> | Twitter<http://twitter.com/GSK> | YouTube<http://www.youtube.com/user/gskvision> | Facebook<http://www.facebook.com/glaxosmithkline> | Flickr<http://www.flickr.com/photos/glaxosmithkline>

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Reminder: ICBO 2015, Call for Submissions, one week to go!
by Francisco Couto 25 Feb '15

25 Feb '15

ICBO2015 Call for submissions *** Relevant dates *** Conference paper submission: Mar 2, 2015 Conference paper notification: Apr 6, 2015 Camera-ready conference papers: Apr 20, 2015 Workshop paper, software demonstration and early career submission: Apr 13, 2015 Workshop paper, software demonstration and early career notification: May 11, 2015 Camera-ready workshop papers, software demonstration papers/abstracts and early career abstracts: May 25, 2015 Demos and Poster abstract submissions: May 18, 2015 Demos and Poster abstract notifications: June 8th, 2015 Camera-ready poster abstracts: June 15th, 2015 *** Topics *** Ontologies are knowledge representation tools widely used in the semantic description of biological and medical data from creation to publication and consumption for research and software applications including expert systems. To be maximally effective for a wide range of diverse purposes, such ontologies must be of good quality and work well together. Therefore, issues like good ontology design, ontology coordination, methods for harnessing ontologies for research and applications, and ontology maintenance need to be addressed. The International Conference on Biomedical Ontology (ICBO) series is designed to meet this need. ICBO 2015, the sixth event in the highly successful series, will bring together representatives of all major communities involved in ontology use and development in biomedical research, health care, and related areas. *** Call for Papers *** ICBO 2015 is soliciting submissions of novel (not previously published nor concurrently submitted) research papers in the areas of the application of ontologies to biomedical problems, ontology design and ontology interoperability, at any stage in the process from data creation to use in applications or scientific analyses. Submissions will be welcome from a broad range of approaches to ontology building and use. In addition, we would like to invite contributions showcasing methods for ontology-based research, including statistical methods, and contributions addressing the challenges associated with working with multiple ontologies at the same time, including ontology development, visualization, annotation of data, analysis, and applications. We will accept full-length research and application papers (5 pages), poster submissions (2 page abstracts), software demonstrations (2 page abstracts), and early career researcher symposium submissions (2 page abstracts). A selection of successful poster abstracts will be invited to give flash presentations during the conference. We are also looking for submissions of half-day or full-day workshops and tutorials. Workshops should be working sessions with a specific outcome that can be subsequently presented at the main conference. Tutorials are educational events and may involve hands-on practicals. Submission of papers is via EasyChair ( https://www.easychair.org/conferences/?conf=icbo2015) according to the templates provided on the conference web site. A Best Paper Award, Best Poster Award, Best Demonstration Award, and a Best Early Career Paper Award will be conferred to the author(s) at the conference, selected by the Organizing Committee. All accepted papers and abstracts will be published in an issue of CEUR-WS ( http://ceur-ws.org/) In addition, authors of selected papers will be invited to submit an extended version for publication in a special issue of the Journal of Biomedical Semantics (JBMS), an open-access journal published by BioMed Central (BMC). Note that publication in the JBMS special issue will incur article processing charges. *** Contact *** For more information please email icbo2015(a)googlegroups.com *** Organizing Committee *** Scientific Chairs: Francisco Couto (Lisboa, Portugal) and Janna Hastings (Cambridge, UK) Local Chair: Catia Pesquita (Lisboa, Portugal) Program Chair: Stefan Schulz (Graz, Austria) Workshop and Tutorial Chairs: Melanie Courtot (Vancouver, Canada) and João Ferreira (Lisboa, Portugal) Proceedings and Special Issue Chair: Dietrich Rebholz-Schuhmann (Zurich, Switzerland) Early Career Chair: Pierre Grenon (London, UK) Poster and Demonstrations Chair: Matthew Horridge (Stanford, USA) Sponsorship and Publicity: Emanuel Santos (Lisboa, Portugal) and Pedro Fernandes (Oeiras, Portugal)

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Postdoc and PhD position in evolutionary systems biology
by Katrijn Vannerum 24 Feb '15

24 Feb '15

From: Steven Maere <steven.maere(a)psb.vib-ugent.be<mailto:steven.maere@psb.vib-ugent.be>> Date: 23 Feb 2015 15:19:38 CET Subject: Postdoc and PhD position in evolutionary systems biology To: Steven Maere <stmae(a)psb.vib-ugent.be<mailto:stmae@psb.vib-ugent.be>> Dear colleagues, I'm currently looking for a postdoc to study the evolution of transcriptional systems after gene duplication using mechanistic genotype-phenotype mapping models. Because of budget restrictions, this person should not have obtained his/her PhD in Belgium (giving him/her a different status under Belgian tax law). I would be grateful if you could forward the following information to potential candidates. Many thanks, Steven

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Job opportunity : Structural bioinformatician - Product developer
by Marianne Rooman 23 Feb '15

23 Feb '15

Job opportunity : Structural bioinformatician - Product developer Context: The possibility of introducing targeted mutations in proteins to rationally modify their stability, thermal resistance, solubility or affinity for other partners is an important goal in protein science, which has applications in a wide series of biotechnological and biopharmaceutical processes. We developed a suite of software tools that predict the effect of point mutations on the thermodynamic and thermal stabilities on the basis of the experimental or modeled tertiary structure of the wild type protein. These tools are extremely helpful in limiting the number of mutations to be tested experimentally, as shown in a number of test cases. In order to provide access to this suite of software, we have set up a SaaS platform called dezyme and plan to create a company to provide services. In this framework, we are looking for a Bioinformatician. Job description: The main task will be the development of software (in C) and application to protein optimization, and involve teamwork with a business developer. More specifically this job will include: - Extension and optimization of existing software for the design of more stable proteins ; - Evaluation of the advantages compared to existing in silico methods ; - Application of software tools to optimize systems of interest for customers ; - Positioning of the software offering in industrial processes and in complement to experimental methods like directed mutagenesis. Profile: - Master in Bioinformatics, Informatics or Bioengineer - Autonomous and voluntary personality - Professional experience preferred but not required - Good knowledge of English Employment status: Freelance, Full time; 6 months at the University Libre de Bruxelles and afterwards in a startup Contact: Send your application with CV and motivation letter to Marianne Rooman (mrooman(a)ulb.ac.be) --------------------------------------------------------------- Marianne Rooman 3BIO-BioInfo - BioModeling, BioInformatics & BioProcesses Université Libre de Bruxelles 50 Roosevelt Ave, CP 165/61, 1050 Brussels, Belgium Phone: +32 2 650 2067 Email: mrooman(a)ulb.ac.be ----------------------------------------------------------------

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FW: APC Post-Doc (Bioinformatician) position in Southern Irelnd
by Claesson, Marcus 20 Feb '15

20 Feb '15

See http://www.teagasc.ie/opportunities/postdoctoral/ or, more specifically 1) Experienced Post-Doctoral Researcher - Bioinformatician (Ref: EPD/APCB1/0215)<http://www.teagasc.ie/opportunities/postdoctoral/Information_for_Candidates…> or 2) Teagasc Post-Doctoral Research Fellow in Bioinformatics Level 1 (PD1)/Level 2 (PD2)<http://www.teagasc.ie/opportunities/postdoctoral/Information_for_Candidates…> Teagasc, Food Research Centre, Moorepark, Fermoy, Co Cork Closing Date: no later than 12 midnight on Thursday 5 March 2015 Dr Paul Cotter Principal Research Officer, Teagasc Food Research Centre Moorepark, Cork Ireland Principal Investigator, Alimentary Pharmabiotic Centre Adjunct Lecturer, Cork Institute of Technology Tel. +353 (0)25 42694 http://orcid.org/0000-0002-5465-9068 Attention: This e-mail is privileged and confidential. If you are not the intended recipient please delete the message and notify the sender. Any views or opinions presented are solely those of the author. This email was scanned by Teagasc and has been certified virus free with the pattern file currently in use. This however cannot guarantee that it does not contain malicious content. Tabhair aire: Tá an r-phost seo faoi phribhléid agus faoi rún. Mura tusa an duine a bhí beartaithe leis an teachtaireacht seo a fháil, scrios é le do thoil agus cuir an seoltóir ar an eolas. Is leis an údar amháin aon dearcaí nó tuairimí a léirítear. Scanadh an r-phost seo le Teagasc agus deimhníodh go raibh sé saor ó víoras leis an bpatrúnchomhad atá in úsáid faoi láthair. Ní féidir a ráthú leis seo áfach nach bhfuil ábhar mailíseach ann.

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[Gtpb] Bioinformatics Training Course IB15F Announcement/Reminder
by Pedro Fernandes 20 Feb '15

20 Feb '15

Dear all, The Applications for the Introductory Bioinformatics course, first instance in the 2015 Programme, are now OPEN. IMPORTANT DATES for this Course Deadline for applications: March 20th 2015 Latest notification of acceptance: March 21st 2015 Course date: April 13th - April 17th 2015 Details are available here: http://gtpb.igc.gulbenkian.pt/bicourses/IB15F/ This is an entry level course aimed that those with a reasonable biological background but no significant experience with bioinformatics. The course is broadly based around a series of exercises in which a combination of simple analytical tools and reference to publicly available databases is applied to the investigation of a single human gene. The training manual for the course is comprised of detailed instructions for the tasks undertaken. Included are, questions (with answers) and discussion of and the interpretation of the results achieved. Participants are asked to imagine an interest in the disease aniridia. Course exercises then provide extremely detailed instruction leading participants to discover the gene primarily associated with this disease and all that is interesting about that gene and its protein products. This course will also provide a soft introduction to Next Generation Sequencing (NGS) data analysis. This part of the course aims at providing basic skills that are needed when one needs to process NGS data, such as evaluating data quality, trimming sequences, changing data formats, visualising data, etc. Then, participants will learn how to address a simple transcriptomics problem, stepwise, using open source bioinformatics tools. Important NOTE: This is one of our most popular courses. It usually gets full very quickly. Applications are approved and accepted in order of arrival and we only have 20 seats. Best wishes Pedro Fernandes GTPB Coordinator -- Pedro Fernandes Instituto Gulbenkian de Ciência Apartado 14 2781-901 OEIRAS PORTUGAL 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: PhD or Postdoc in Bioinformatics
by a.schlicker＠nki.nl 13 Feb '15

13 Feb '15

-------- Original Message -------- Subject: PhD or Postdoc in Bioinformatics Date: Wed, 11 Feb 2015 19:46:34 +0100 From: Mario Albrecht <info(a)mario-albrecht.de> Open PhD and Postdoc positions in Bioinformatics Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria Deadline: 28 February 2015 Contact: Prof. Dr. Mario Albrecht, Institute for Knowledge Discovery, Graz University of Technology, Graz, Austria, info(a)mario-albrecht.at Find further information on the open PhD and Postdoc bioinformatics positions at http://www.medbioinf.at and below! Note: Please send your application to info(a)mario-albrecht.at as well! Please forward this mail to your colleagues, thank you! Open full-time bioinformatics PhD student position for molecular network research until 28 February 2015, for details see http://mibla.tugraz.at/14_15/Stk_8/8.html#112 and as follows: Molecular networks and proteins are involved in many biological processes. Therefore, we aim at the development and application of computational network methods for the analysis and prediction of molecular interactions and their structural and functional changes due to sequence mutations. The mutations might occur in disease genes or bacterial and viral genomes. Based on the analysis results, we also want to develop innovative bioinformatics approaches for modeling pathways and their changes as well as for the design and prioritization of follow-up experiments. Open full-time bioinformatics postdoc position for integrative omics research until 28 February 2015, for details see http://bioinf.tugraz.at/images/Postdoc.pdf and as follows: Cancer is the leading cause of death and involves altered lipid metabolism. The rate-limiting enzyme in triacylglyceride degradation, the adipose triglyceride lipase (ATGL), might not participate only in lipid mobilization and degradation, but also in signaling pathways by generating lipid signaling molecules. Therefore, we aim at the large-scale elucidation of the functional role of ATGL in cancer progression using different omics strategies combined with computational approaches. Novel bioinformatics methods are developed for analyzing the data of molecular proteomics and metabolomics networks related to lipolysis in cancer.

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