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Next Generation Sequencing Bioinformatician
1-PROGRAMME
1.1 Context
INCa-Synergie Lyon Cancer is bioinformatics facility platform dedicated to the next generation sequencing technologies in the field of cancer genomics. Recognizing the new opportunities offered by next generation sequencing technologies for 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 several cancer types.
In order to overcome the challenges raised by the massive amount of sequence data that has been and will be generated, INCa and the Lyon community through the Synergie Lyon Cancer Foundation (http://www.synergielyoncancer.fr/) 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. Pr. Gilles Thomas is the director of the facility.
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 regional bioinformatics teams. Thus the facility benefits both from strong biomedical and bioinformatics environments. It has acquired and is extending a large HPC equipment. The present staff includes two bioinformaticians, two biostatisticians and one database manager.
1.2 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 :
• contribute to the challenges of processing, analyzing, visualizing and annotating the huge volume of data generated by NGS technologies
• help identify germline and somatic variants in tumor samples (point mutations, indels, structural variants...)
• be responsible for the annotation and interpretation of the called variants
• do a technology watch of existing and emerging methods for NGS data
• benchmark (some of) the existing software (performance of algorithms, specificity, sensitivity)
• carry out a wide range of computational genomics duties
• collaborate with investigators trained in mathematics, statistics, computer sciences and genomics
2- REQUIRED QUALIFICATION
2.1 Education:
Advanced university degree (Masters, PhD) in bioinformatics.
2.2 Skills
• Working in a GNU/Linux environment
• Major scripting languages : Perl (BioPerl), Python (BioPython), shell/awk
• Understanding relational database schemes, writing efficient SQL queries
• Knowing biological data formats
• Good knowledge of annotation databases, interfaces & web services (Ensembl,UCSC, NCBI ...)
• Ability to carry out integration of data across dipartite data resources.
• Good background in biology and genetics (gene, protein, transcript, pathway, snp, allele...)
Previous experience in cancer genomics field would be highly valued.
Additional skills that would be appreciated
• Previous experience in handling & managing NGS data and softwares
• Other programming skills (C, C++, Java)
• Previous experience in a cluster computing environment
• Knowledge of R
2.3 Professional experience
At least two years of relevant professional experience at the international level in the field of bioinformatics is required. Prior experience in quality assurance procedures will be highly appreciated.
2.4 Complementary information:
Excellent 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. Oral and written communication in the group is in English.
3- CONTRACT AND SUBMISSION PROCEDURE
3.1 Contract :
Fixed term appointment (3 years) will be offered to the successful candidate. Starting date is as soon as possible from September. The salary will be based on the french public research institution
wages and slightly adjusted according to the successful candidate experience.
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] before July 31st 2011 . Acknowledgement of receipt will be forwarded to each candidate. Selected candidates will be invited to come to Lyon, France for an interview. General enquiries about the open position may be sent to the same e-mail address.
1-PROGRAMME
1.1 Context
INCa-Synergie Lyon Cancer is bioinformatics facility platform dedicated to the next generation sequencing technologies in the field of cancer genomics. Recognizing the new opportunities offered by next generation sequencing technologies for 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 several cancer types.
In order to overcome the challenges raised by the massive amount of sequence data that has been and will be generated, INCa and the Lyon community through the Synergie Lyon Cancer Foundation (http://www.synergielyoncancer.fr/) 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. Pr. Gilles Thomas is the director of the facility.
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 regional bioinformatics teams. Thus the facility benefits both from strong biomedical and bioinformatics environments. It has acquired and is extending a large HPC equipment. The present staff includes two bioinformaticians, two biostatisticians and one database manager.
1.2 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 :
• contribute to the challenges of processing, analyzing, visualizing and annotating the huge volume of data generated by NGS technologies
• help identify germline and somatic variants in tumor samples (point mutations, indels, structural variants...)
• be responsible for the annotation and interpretation of the called variants
• do a technology watch of existing and emerging methods for NGS data
• benchmark (some of) the existing software (performance of algorithms, specificity, sensitivity)
• carry out a wide range of computational genomics duties
• collaborate with investigators trained in mathematics, statistics, computer sciences and genomics
2- REQUIRED QUALIFICATION
2.1 Education:
Advanced university degree (Masters, PhD) in bioinformatics.
2.2 Skills
• Working in a GNU/Linux environment
• Major scripting languages : Perl (BioPerl), Python (BioPython), shell/awk
• Understanding relational database schemes, writing efficient SQL queries
• Knowing biological data formats
• Good knowledge of annotation databases, interfaces & web services (Ensembl,UCSC, NCBI ...)
• Ability to carry out integration of data across dipartite data resources.
• Good background in biology and genetics (gene, protein, transcript, pathway, snp, allele...)
Previous experience in cancer genomics field would be highly valued.
Additional skills that would be appreciated
• Previous experience in handling & managing NGS data and softwares
• Other programming skills (C, C++, Java)
• Previous experience in a cluster computing environment
• Knowledge of R
2.3 Professional experience
At least two years of relevant professional experience at the international level in the field of bioinformatics is required. Prior experience in quality assurance procedures will be highly appreciated.
2.4 Complementary information:
Excellent 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. Oral and written communication in the group is in English.
3- CONTRACT AND SUBMISSION PROCEDURE
3.1 Contract :
Fixed term appointment (3 years) will be offered to the successful candidate. Starting date is as soon as possible from September. The salary will be based on the french public research institution
wages and slightly adjusted according to the successful candidate experience.
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] before July 31st 2011 . Acknowledgement of receipt will be forwarded to each candidate. Selected candidates will be invited to come to Lyon, France for an interview. General enquiries about the open position may be sent to the same e-mail address.