Lyon -Experienced genomicist with statistical expertise]

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 andthe 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/english_version/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 :
synergie_vacancies@prabi.fr, 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.



  _________________

--
Aurélie Laugraud
PRABI
Bât.Mendel 2è étage
16 rue Raphael Dubois
69622 Villeurbanne Cedex
tel: 0472432826




--
Magali Michaut, PhD
http://baderlab.org/MagaliMichaut