Bioinformatics Engineer

Sequenom, Inc.
Job Location: 
San Diego, CA
Competitive salary, bonus, stock options
Job Description: 

Come join SEQUENOM, the company that is committed to providing the best genetic analysis for research, agricultural applications, molecular medicine and non-invasive prenatal diagnostics research. We are growing and our success depends on the talents, efforts and achievements of our exceptional employees. We offer compensation and employee benefit packages that are top in the industry. So come join the team at SEQUENOM and feel the same passion we do for how we are changing medical technology.

The Bioinformatics Engineer is responsible for the design and implementation of a sequencing analysis pipeline at Sequenom. More specifically, the candidate will:

• Develop tools for automating DNA sequence assemblies and sequence data quality reporting
• Develop and maintain high performance computational platform for sequence data analysis pipeline
• Develop and maintain database infrastructure and LIMS for the sequencing data
• Perform appropriate documentation and testing
• Support multiple-site operation


The position requires excellent communication skills and the ability to coordinate with projects from within multiple departments and multiple sites. Project management skills are required as well as the ability to lead the implementation process.

The Qualified Candidate will have:
• Master’s degree in molecular biology, bioinformatics, or related field; Ph.D. preferred
• 3 years of experience in a high-throughput sequencing environment and experience with next-generation sequencing and data analysis
• knowledge of nucleic acid hybridization kinetics and properties, PCR kinetics and properties
• Familiarity with genomic browser(s) content and functionality
• Demonstrated expertise with PERL and shell scripting, and experience with Java
• Experience with unit testing
• Demonstrated expertise with relational database systems - SQL server, Oracle, MySQL, PostgreSQL
• Experience with statistical software, such as R
• Experience developing software for research purposes
• Broad knowledge of UNIX/Linux
• Ability to troubleshoot research-grade software, both internally developed as well as third-party provided.
• Ability to present information in a clear and concise manner to a multidisciplinary team of scientists, engineers and programmers
• Experience with high-performance computing environments. Proven experience with a mainstream cluster job manager – SGE, LSF/OpenLava, PBS/Torque.
• Proven experience with deployment of a data analysis pipeline in a distributed computing environment.

Contact Information: 

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