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Job Vacancy at the INCa-Synergie Bioinformatics Facility for Cancer Genomics, Lyon, France.
Experienced genomicist with statistical expertise
1-PROGRAMME
1.1- Background Recognizing the new opportunities offered by next generation sequencing technologies in the field of cancer genomics, the French National Cancer Institute (INCa) has pledged to provide a major contribution to the International Cancer Genome Consortium (ICGC- http://www.icgc.org/) through the study of two cancer types (hepatocellular carcinoma and HER2 amplified breast tumors). In the near future, INCa is considering contributing more tumor types. The entire sequencing of multiple pairs of tumor and matched germline DNAs has already been completed in France and other pairs are rapidly following. In order to overcome the challenges raised by the massive amount of sequence data that has been and will be generated by such programs, INCa and the Lyon community through the Synergie Lyon Cancer Foundation (http://www.synergielyoncancer.com/) are joining efforts to create a dedicated bioinformatics facility. The objective of the bioinformatics facility will be to empower the biomedical teams working in the field of cancer to best exploit the data generated through large scale genomic projects, notably those funded by INCa and in the first place those taking place within the ICGC.
1.2 Context The INCa-Synergie facility is located in a major French comprehensive cancer center (Centre Leon Berard) with a very active research department (http://oncora1.lyon.fnclcc.fr/englis...index_eng.html). It is in close proximity to the International Agency for Research on Cancer, IARC. The facility is integrated into the "Pole Rhone-Alpes de Bioinformatique, PRABI (http://www.prabi.fr/), which federates major bioinformatic teams. Thus the facility benefits both from strong biomedical and bioinformatics environments. It is acquiring a large HPC equipment. The facility will open over the coming months four positions for experienced bioinformaticians who will work under the supervision of the facility director, Pr. Gilles Thomas. This job description corresponds to one of these positions.
1.3 Description of duties Working in a team of experienced bioinformaticians and in close collaboration with French partner groups and international research centers, the candidate will be in charge of : initiating with investigators trained in mathematics, statistics, informatics and genomics and with the collaborating sequence production teams, methods for the efficient processing and analysis of nucleotide sequences, adapted to the huge volume of data produced by genomic technologies and notably by new high throughput DNA sequencing methods (quality control, identification and analysis of correlations, genome reconstruction and characterization algorithms). developing data mining tools to best characterize the reconstructed genomes and generate biological knowledge. testing and developing these methods and tools to a level that will allow their implementation in standard analytical packages that can be used by biomedical research teams. gaining expertise in developing and applying quality control procedures in accordance with the ISO 9001:2000 standard. continually evaluating new technology, algorithms and publications relevant to the scientific field. bringing his/her expertise in data mining to specific requests from the collaborating research teams.
2- REQUIRED QUALIFICATION
2.1 Education : Advanced university degree (Masters, PhD) in statistics and informatics.
2.2 Skills statistical modeling. descriptive and inferred statistics. simulation methods, model fitting, optimization. knowledge of the major genomic databases and their interfaces. thorough knowledge of the main computing and statistical packages (R, SAS, Stata, Matlab, Maple, Mathematica,). practical knowledge of scripting (Linux/UNIX) and programming languages (awk, perl/bioperl, python, C, C++, java), of database query (SQL) and markup (XML) languages. basic knowledge of web programming (php, html, ajax/javascript).
2.3 Professional experience At least two years of relevant professional experience at the international level in the field of statistical genomics.
2.4 Complementary information : Communication in French is not required but advanced English language, excellent communication and interpersonal skills are essential. The candidate should be self motivated, capable of working both independently and within a closely interacting team of scientists and be able to deliver a quality product with fixed deadlines.
3- CONTRACT AND SUBMISSION PROCEDURE
3.1 Contract : Fixed term appointment (two years, renewable once) will be offered to the successful candidate. At the end of a 4 year period and depending on circumstances, a long term position may be considered. Starting date will depend on availability of the successful candidate. It may be as early as October 2009.
3.2 Work location : Lyon, France
3.3 Submission procedure : Letter of motivation, curriculum vitae and addresses of three referees are to be provided in electronic form to the following e-mail address : [email protected], prior to September 15, 2009 . Acknowledgement of receipt will be forwarded to each candidate. Selected candidates will be invited to come to Lyon for an interview. Prior to the closing date, general enquiries about the opened position may be sent to the same e-mail address.
Experienced genomicist with statistical expertise
1-PROGRAMME
1.1- Background Recognizing the new opportunities offered by next generation sequencing technologies in the field of cancer genomics, the French National Cancer Institute (INCa) has pledged to provide a major contribution to the International Cancer Genome Consortium (ICGC- http://www.icgc.org/) through the study of two cancer types (hepatocellular carcinoma and HER2 amplified breast tumors). In the near future, INCa is considering contributing more tumor types. The entire sequencing of multiple pairs of tumor and matched germline DNAs has already been completed in France and other pairs are rapidly following. In order to overcome the challenges raised by the massive amount of sequence data that has been and will be generated by such programs, INCa and the Lyon community through the Synergie Lyon Cancer Foundation (http://www.synergielyoncancer.com/) are joining efforts to create a dedicated bioinformatics facility. The objective of the bioinformatics facility will be to empower the biomedical teams working in the field of cancer to best exploit the data generated through large scale genomic projects, notably those funded by INCa and in the first place those taking place within the ICGC.
1.2 Context The INCa-Synergie facility is located in a major French comprehensive cancer center (Centre Leon Berard) with a very active research department (http://oncora1.lyon.fnclcc.fr/englis...index_eng.html). It is in close proximity to the International Agency for Research on Cancer, IARC. The facility is integrated into the "Pole Rhone-Alpes de Bioinformatique, PRABI (http://www.prabi.fr/), which federates major bioinformatic teams. Thus the facility benefits both from strong biomedical and bioinformatics environments. It is acquiring a large HPC equipment. The facility will open over the coming months four positions for experienced bioinformaticians who will work under the supervision of the facility director, Pr. Gilles Thomas. This job description corresponds to one of these positions.
1.3 Description of duties Working in a team of experienced bioinformaticians and in close collaboration with French partner groups and international research centers, the candidate will be in charge of : initiating with investigators trained in mathematics, statistics, informatics and genomics and with the collaborating sequence production teams, methods for the efficient processing and analysis of nucleotide sequences, adapted to the huge volume of data produced by genomic technologies and notably by new high throughput DNA sequencing methods (quality control, identification and analysis of correlations, genome reconstruction and characterization algorithms). developing data mining tools to best characterize the reconstructed genomes and generate biological knowledge. testing and developing these methods and tools to a level that will allow their implementation in standard analytical packages that can be used by biomedical research teams. gaining expertise in developing and applying quality control procedures in accordance with the ISO 9001:2000 standard. continually evaluating new technology, algorithms and publications relevant to the scientific field. bringing his/her expertise in data mining to specific requests from the collaborating research teams.
2- REQUIRED QUALIFICATION
2.1 Education : Advanced university degree (Masters, PhD) in statistics and informatics.
2.2 Skills statistical modeling. descriptive and inferred statistics. simulation methods, model fitting, optimization. knowledge of the major genomic databases and their interfaces. thorough knowledge of the main computing and statistical packages (R, SAS, Stata, Matlab, Maple, Mathematica,). practical knowledge of scripting (Linux/UNIX) and programming languages (awk, perl/bioperl, python, C, C++, java), of database query (SQL) and markup (XML) languages. basic knowledge of web programming (php, html, ajax/javascript).
2.3 Professional experience At least two years of relevant professional experience at the international level in the field of statistical genomics.
2.4 Complementary information : Communication in French is not required but advanced English language, excellent communication and interpersonal skills are essential. The candidate should be self motivated, capable of working both independently and within a closely interacting team of scientists and be able to deliver a quality product with fixed deadlines.
3- CONTRACT AND SUBMISSION PROCEDURE
3.1 Contract : Fixed term appointment (two years, renewable once) will be offered to the successful candidate. At the end of a 4 year period and depending on circumstances, a long term position may be considered. Starting date will depend on availability of the successful candidate. It may be as early as October 2009.
3.2 Work location : Lyon, France
3.3 Submission procedure : Letter of motivation, curriculum vitae and addresses of three referees are to be provided in electronic form to the following e-mail address : [email protected], prior to September 15, 2009 . Acknowledgement of receipt will be forwarded to each candidate. Selected candidates will be invited to come to Lyon for an interview. Prior to the closing date, general enquiries about the opened position may be sent to the same e-mail address.