Senior Researcher Position

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Amar Annamalai
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Senior Researcher Position

Senior Researcher Position in Bioinformatics and Systems Biology based at CNRS-EISBM in Lyon in relation with the IMI eTRIKS Consortium on Information and Knowledge Management Services

We are seeking an experienced individual to lead the Biomedical Personal Data Protection & Ethics activities of the newly formed eTRIKS Consortium, funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations.
Scientific Project: The eTRIKS Consortium is dedicated to delivering European Translational Information and Knowledge Management Services initially for all IMI projects, then for other European translational research projects. These projects encompass translational bioinformatics, clinical research informatics, health/clinical informatics and the development of new analytical tools. They use tranSMART as part of the software knowledge management platform:;
Job context: She/he will be working closely with academic partners at Imperial College in London and the Luxembourg Center for Systems Biomedicine, and the academic and pharmaceutical partners of eTRIKS. The selected candidate will be based in Lyon-Gerland within the CNRS-EISBM team led by Charles Auffray, hosted by Claude Bernard University and the Lyonbiopole competitive cluster on the Charles Mérieux campus:;
Job description: The ideal candidate should be able to proactively lead the development and implementation of complex workstreams based on data analysis and modeling methods, and engage multiple academic and industrial partners in a pre-competitive collaborative innovation effort, based on the specific needs of eTRIKS project partners. The objective is to reach international harmonization of the use of analytical and modeling methods in the context of the fast evolving area of translational research and systems medicine.
In particular the candidate is expected :
- to contribute to enhancement of the underlying tranSMART system with required analytical functions for analysis and integration of clinical and omics data;
- to develop advanced analytical methods and workflows (e.g. power calculation in clinical study design), and novel approaches for disease and target specific knowledge enrichment (e.g. pathways/disease network models);
- to outreach to network disease modelling communities (e.g. Sage Bionetworks, openBEL, Garuda);
- to provide scientific support for eTRIKS users on the use of analytics features of the system through training materials and reusable workflows.
Required Experience/Skills: Candidates should have a proven track record of research, management and implementation of the ethical and legal (i.e. personal data protection) frameworks of biomedical research and their interaction with information and communication technology. The required proven skills and experience include:
- PhD or MS/Engineering degree in biomedical and/or computational research
- Significant experience in academic or industrial biomedical research
- Statistical programming languages such as R, Matlab, Perl, Python, C
- Working in a UNIX/Linux HPC environment with relational databases
- Omics data analysis using ontologies and controlled vocabularies
- Experience in integration of heterogeneous high-dimensional data types
- Knowledge in network inference, analysis and modeling
- Development of data analysis workflows and supporting software
- Rigour, autonomy and excellent relational and teamwork skills
- Proven distributed project management and communication skills in English
Contract Duration: Available immediately for two years with possible one-year extension.
Salary: Depending on qualifications and experience, based on CNRS salary grid.
Application: Send CV, cover letter and names of two references to Charles Auffray
Email: eval(unescape('%64%6f%63%75%6d%65%6e%74%2e%77%72%69%74%65%28%27%3c%61%20%68%72%65%66%3d%22%6d%61%69%6c%74%6f%3a%6a%6f%62%73%40%65%69%73%62%6d%2e%6f%72%67%22%3e%6a%6f%62%73%40%65%69%73%62%6d%2e%6f%72%67%3c%2f%61%3e%27%29%3b'))
- Auffray C, Chen Z, Hood L. (2009) Systems medicine: the future of medical genomics and heathcare. Genome Med. 1:29.
- Szalma S, Koka V, Khasanova T, Perakslis, ED. (2010) Effective knowledge management in translational medicine. Translational Med 8:68.
- Szalma S, Koka V, Khasanova T, Perakslis ED. (2010) How informatics can potentiate precompetitive open-source collaboration to jump-start drug discovery and development. Clin Pharmacol Therapeutics 87:614-616.
- Hood L, Balling R, Auffray C. (2012) Revolutionizing medicine in the 21st century through systems approaches. Biotechnol. J. 7:992-1001.

Deadline:April 19, 2013

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