[BioC] job advertisement

[Zhenyu Xu]

Dear All,

 Sorry to bother those who are not interested.

We have 2 open positions at Sophia Genetics (http://www.sophiagenetics.com) 
If you are interested, please contact Dr Zhenyu Xu (zxu at sophiagenetics.com). The deadline for the application is 31st Aug 2013.

best,
zhenyu


About the company: 
 	Sophia Genetics SA helps clinical laboratories that perform routine clinical genetic analysis for personalized healthcare to overcome the cost and complexity related to the bioinformatics analysis, highly secured banking and reliable interpretation of the massive quantity of patient data generated by Next Generation Sequencing. We are situated on the PSE, on the EPFL campus near Lausanne; 10 minutes walk from Lake Geneva.Our goal is to simplify and enhance genetic testing providing the most efficient bioinformatics solution for clinical genetic data analysis.Our solution combines a client - server data management and visualization tool with a high performance bioinformatics pipeline to analyze genetic sequence data. We use a wide range of technology, including JAVA, JavaScript, Hadoop HDFS and many open source R, C, C++, Python and Perl tools, in a predominantly Linux environment.The challenge is to provide a scalable, parallel analysis solution, together with a simple to use graphical user interface to give geneticists a manageable way to handle the large amounts of data, and help them interpret the increasingly complicated results in a compact, graphical way.Today Sophia Genetics is active in Switzerland and is preparing to enter the rest of Europe. 

Job description 1 (Bioinformatician):  

The successful candidates will be involved in clinical next generation sequence (NGS) data analysis methods development. You will be responsible for NGS data alignment and variant calling algorithm development. You will be expected to explore and identify statistical properties of different NGS experiment design. The successful candidates should be able to read research publications and catch the front-end of the algorithm development in clinical NGS application.

As an established startup we want people that are motivated, enthusiastic and flexible – you must be willing to get involved with all aspects of the system. You must be goal driven and able to work independently on a project to completion as well as being comfortable in a team.

The successful applicant should have expertise in statistical modeling ideally with a theoretical / statistical physics background. The applicant must be able to demonstrate excellence in the following areas:
	• Experience in high-throughput data analysis
	• Experience in statistical modelling of large volume data
	• Familiarity with common machine learning techniques
	• Strong C/C++ skills
	• Strong data analysis experience using R/Matlab

Job description 2 (Software Engineer / Developer):  

The successful candidate will take the main development role of re-engineering and optimizing the pipeline for genome sequence alignment and variant detection. This will involve choosing appropriate parallelization techniques for currently sequential operations, as well as the implementation and parallelization of bioinformatics algorithms. As an established startup we want people that are motivated, enthusiastic and flexible – you must be willing to get involved with all aspects of the system. You must be goal driven and able to work independently on a project to completion as well as being comfortable in a team.

You will have an MSc or PhD in Computer Science, Bioinformatics or equivalent and several years of experience developing applied numerical solutions.

You will be expected to show the following abilities:

	• Good analytical and creative problem solving skills
	• C/C++ proficiency including multithreading
	• Solid background in algorithmic complexity and string, tree, indexing etc. algorithms
	• Good knowledge of parallelization techniques - MPI, Hadoop MapReduce, GPU solutions
	• Comfortable with script languages such as Python, Perl
	• Knowledge of R / Bioconductor would be an advantage
	• Previous experience with Exome/WGS data analysis would be an advantage
	• Some experience with JAVA / MySQL would be an advantage