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Research Associate – Computational Expert in Structural Biology or Deep Sequencing – Influenza Research
by Judy Fonville 01 Mar '13

01 Mar '13

Dear BBC list, Our group is currently advertising a position for a Computational Expert in Structural Biology or Deep Sequencing (Centre for Pathogen Evolution, Department of Zoology, University of Cambridge). Information on the post is attached to this email. If you know anybody who might be interested, please feel free to forward this information to them. http://www.zoo.cam.ac.uk/zooone/administration/vacancy.html http://www.zoo.cam.ac.uk/zooone/administration/FI_PF00982.pdf Best wishes, Judy Fonville

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Senior Project Manager
by Johann Pellet 28 Feb '13

28 Feb '13

Senior Project Manager 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 contribute to the management of community engagement and outreach activities in 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: http://www.etriks.org; http://www.transmartproject.org Job context: She/he will be working closely with the academic and pharmaceutical partners of eTRIKS, interfacing with the community of users in IMI, FP7 and Horizon 2020. 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:http://www.eisbm.org; http://workshop.eisbm.org Job description: The ideal candidate should be able to proactively lead the development of the community of users of the eTRIKS platform, engaging multiple academic and industrial partners in a pre-competitive collaborative innovation effort. 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 establish and maintain interactions with IMI & non-IMI translational projects regarding their knowledge management and informatics needs; • to coordinate the activities of eTRIKS with the open source development community around the eTRIKS platform; • to coordinate the provision of education to IMI and non-IMI translational scientists, patient advocacy groups, commercial service providers regarding the mission and services of the eTRIKS consortium. Required Experience/Skills: • PhD or MBA/Engineering degree in biomedical/computational research • Significant experience in academic or industrial project management • Experience in Open Innovation and Agile project management • Familiarity with a UNIX/Linux HPC environment with relational databases • Knowledge 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: jobs(a)eisbm.org More information at: http://job.eisbm.org/senior-project-manager-etriks/ References: - 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.

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Senior Researcher Position
by Johann Pellet 28 Feb '13

28 Feb '13

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: http://www.etriks.org; http://www.transmartproject.org 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: http://www.eisbm.org; http://workshop.eisbm.org 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: jobs(a)eisbm.org More information at: http://job.eisbm.org/senior-research-position-etriks/ References: - 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.

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Personal Data Protection Manager in Lyon
by Johann Pellet 27 Feb '13

27 Feb '13

Personal Data Protection Manager 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: http://www.imi.europa.eu/. 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: http://www.etriks.org; http://www.transmartproject.org Job context: She/he will be working closely with academic partners at Imperial College in London and the Luxembourg Center for Systems Biomedicine, with Sanofi and the 9 other 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: http://www.eisbm.org; http://workshop.eisbm.org Job description: The ideal candidate should be able to proactively lead complex workstreams on data security and privacy monitoring and compliance, and engage multiple academic and industrial partners in a pre-competitive collaborative innovation effort. The objective is to reach international harmonization of personal data protection rules in the context of the fast evolving area of translational research and systems medicine. 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: • Previous significant experience in data protection and/or ethics in Europe • Experience in biomedical and clinical research in academy and/or industry • Proven distributed project management and communication skills in English • Experience in information security (technical knowledge would be a plus) 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: jobs(a)eisbm.org References: - 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. More information at: http://job.eisbm.org/personal-data-protection-manager-etriks/

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Two Junior Post-doctoral Positions in Bioinformatics and Systems Biology in Lyon
by Johann Pellet 27 Feb '13

27 Feb '13

Two Junior Post-doctoral Positions in Bioinformatics and Systems Biology at CNRS-EISBM in Lyon in relation with the IMI U-BIOPRED Consortium on Severe Asthma We are looking for several dynamic and self-driven candidates thrilled to join an international cross-disciplinary team of biologists, clinicians and computer scientists from academy and industry in their efforts to overcome the hurdles in understanding and treating severe asthma. Scientific Project: The U-BIOPRED Consortium (Unbiased BIOmarkers for PREDiction of respiratory disease outcomes) aims at understanding severe asthma phenotypes through an integrative systems biology approach. It involves scientists from universities, research institutes, hospitals, the pharmaceutical industry and small companies across Europe. It is funded by the Innovative Medicines Initiative (IMI) of the European Commission 7th Framework Programme and the European Federation of Pharmaceutical Industries and Associations: http://www.imi.europa.eu/; http://www.ubiopred.european-lung-foundation.org Job context: She/he 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: http://www.eisbm.org; http://workshop.eisbm.eu The successful candidates will participate in the computational analysis of clinical and high-diemensional data (genetic, transcriptomic, proteomic, lipidomic, breathomic) produced by all U-BIOPRED academic and industrial partners and companion projects to identify biomarker fingerprints, and integrate them into severe asthma phenotype handprints of clinical utility. Job description: The ideal candidates hold a PhD degree specializing in analysis, integration, clustering and modelling of complex, heterogeneous biological datasets. He/she will collaborate closely with a multi-disciplinary team of computer scientists, bioinformaticians, biologists and medical doctors. Excellent communication, management and reporting skills in English are essential for this role, which entails travelling across Europe for joint working sessions at partners sites. Required Experience/Skills: - PhD degree in biomedical and/or computational research - Knowledge in statistical analyses and clustering of omics data - Experience in integration of heterogeneous high-dimensional data types - Knowledge in network inference, analysis and modelling - Experience with graphical models such as Bayesian networks - Rigour, autonomy and excellent relational and teamwork skills Contract Duration: Available immediately for one year with a possible extension. Salary: Depending on qualifications and experience, based on CNRS salary grid. Application: Send CV, cover letter and two references to Charles Auffray Email: jobs(a)eisbm.org References: - Auffray C, Adcock IM, Chung KF, Djukanovic R, Pison C, Sterk P. (2010) An integrative systems biology approach to understanding pulmonary diseases. - Wheelock CE, Goss VM, Balgoma D, Nicholas B, Brandsma J, Skipp PJ, Snowden S, D’Amico A, Horvath I, Chaiboonchoe A, Ahmed H, Ballereau S, Rossios C, Chung KF, Montuschi P, Fowler SJ, Adcock IM, Postle AD, Dahlen SE, Rowe A, Sterk PJ, Auffray C, Djukanovic R, the U-BIOPRED Study Group. (2013) Application of ‘omics technologies to biomarker discovery in inflammatory lung diseases. Eur Respir J. Feb 8.

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Position for a bioinformatician (post-doc) in Guadeloupe, France
by fred opperdoes 27 Feb '13

27 Feb '13

Research Project: Complete Genome Analysis of Naegleria fowleri and Naegleria lovaniensis Background Naegleria is a free-living amoeboflagellate found in freshwater feeding on bacteria. One species, N. fowleri, causes primary amoebic meningoencephalitis (PAM) in man, a rare but rapidly fatal central nervous system disease occurring after exposure to contaminated water. The pathogenic N. fowleri is frequently encountered in thermal waters together with its closest relative, the nonpathogenic N. lovaniensis. Sequences of the internal transcribed spacers (ITS) and the 5.8S ribosomal gene allows to distinguish eight types of N. fowleri, which have an uneven distribution in the world. Objectives : By comparing the genome of N. lovaniensis and that of N. fowleri, identify the genes responsible for the pathogenicity and confirm its probable descent from N. lovaniensis. By comparing the genome of the three most common N. fowleri types (2, 3 and 5) found in PAM cases, confirm the pathogenicity genes and identify suitable markers for phylogenetic analyses of N. fowleri strains. Methods : The complete genome sequence of three strains of N. fowleri belonging to 3 different types and one strain of N. lovaniensis will be determined using an illumina technology, before the arrival of the bioinformatician. The bioinformatician will reconstitute the complete genome of the 4 strains. To assemble the sequences he/she will be able to rely on the complete genome sequence of Naegleria gruberi (41 Mb) available at GenBank. He/she will work at the Pasteur Institute of Guadeloupe in a scientific environment of young scientists investigating the molecular epidemiology of Mycobacterium tuberculosis. He/she will have access to the computers of the Pasteur Institute in Paris through internet. Terms: The project will last for two years. The salary will depend on the finances from a grant for a post doctoral fellowship from the Guadeloupe region. This outcome of the grant will be known around September 2013. If the grant is accepted, the postdoctoral fellowship could begin at the end of 2013. The gross salary will be around 32,000 euros. For further information and for applications contact: Dr. Antoine Talarmin Directeur Institut Pasteur de Guadeloupe Morne Jolivière BP484 97183 Abymes Cedex Guadeloupe France ATALARMIN(a)pasteur-guadeloupe.fr tel : 05 90 89 69 40

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NBIC2013 - reminder abstract submission - deadline March 4
by Femke Francissen 27 Feb '13

27 Feb '13

** NBIC2013 - reminder abstract submission ** NBIC2013 Date: 16 & 17 April 2013 Venue: De Werelt Conference Centre, Lunteren, the Netherlands Website: http://www.aanmelder.nl/nbic2013/ Abstract submission - deadline March 4 Only 5 days left to submit your abstract for an oral presentation at the NBIC2013 or one of her satellite meetings: * NBIC2013 programme: any bioinformatics related subject * Data & Technology session: data management, -stewardship and -interoperability * NSBM Spring Meeting 2013: protein structure and structural bioinformatics (April 16) * Metagenomics Satellite Track: metagenomics and computational analysis of microbial ecosystems (April 17) You can also submit an abstract for a poster presentation or demo! Submit your abstract now: http://www.aanmelder.nl/nbic2013/wiki/Abstract%20submission About NBIC 2013 is the 8th edition of the annual conference organized by the Netherlands Bioinformatics Centre (NBIC)<http://www.nbic.nl/>. 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 about the conference programme: http://www.aanmelder.nl/nbic2013/ Register here: http://www.aanmelder.nl/nbic2013/subscribe?survey_id=53415 Use #NBIC2013 to Tweet about the conference!

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Junior PI meeting: a satellite of ISMB-ECCB 2013
by Magali Michaut 26 Feb '13

26 Feb '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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Reminder: Metagenomics Satellite Track at the NBIC 2013 conference
by Sacha van Hijum 26 Feb '13

26 Feb '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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Position for a Bioinformatician/Computational biologist in France
by Irene YUJNOVSKY 21 Feb '13

21 Feb '13

Position for a Bioinformatician/Computational biologist A position is open in the Gronemeyer laboratory at IGBMC for a bioinformatician to work in the analysis and integration of genome-wide biological data, develop bioinformatics tools and establish data analysis pipelines for High-Throughput Sequencing data (ChIP Seq, RNA Seq, ChIA-PET, etc). Candidates must be highly motivated to work on biological questions and flexible to interact with the various members of the laboratory. They should have a degree in computational biology, bioinformatics, statistics or equivalent level of knowledge. Candidates must be comfortable working in UNIX/Linux environments and possess excellent programming skills (R, perl, python, etc). Experience in web developing would be considered an advantage. Operating language in the laboratory is English. Applications including a cover letter, curriculum vitae and the names of two referees should be sent by March 15th to: Dr. Irene Yujnovsky at ireneyuj(a)igbmc.fr Information about the institute and the laboratory can be found at: http://www.igbmc.fr/research/department/2/team/21/ Information about the laboratory's bioinformatics expertise: http://archive.igbmc.fr/recherche/Prog_FGC/Eq_HGron/bioinfotools.html

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