Bioinformatics Engineer

Job Location
3595 John Hopkins Court
San Diego, CA 92121
Base, bonus and equity

We are proud to offer our employees a comprehensive and competitive benefits program. This is our way of enriching the lives of you and your loved ones, and rewarding you for your dedication to the company.

Job Description

The Bioinformatics Engineer is responsible for the design and implementation of a sequencing analysis pipeline at Sequenom. More specifically, the candidate will:•   Work in a clinical team that efficiently and accurately generates patient results•   Maintain and optimize bioinformatics pipelines within a CLIA environment•   Support laboratory and medical staff with results reporting and analytical review•   Use analytics to detect lab and computational issues, track metrics and monitor performance•   Perform appropriate documentation and testing•   Report lab status to team members and Lab directors•   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.
  • 3 years of experience in a high-throughput sequencing environment and experience with next-generation sequencing and data analysis
  • 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.

Sequenom is an EOE - Minority/Female/Disability/Vets

How to Apply

apply online at

or email resumes to

About Our Organization

Bringing the power of science to healthcare.


As a life sciences company, Sequenom (NASDAQ: SQNM) has a guiding vision:  enable healthier lives through the development of innovative products and services. We serve patients and physicians by providing early patient management information.

What makes this vision a reality? Our deep commitment to "Quality of Science." For us, only the highest quality is acceptable. We accept nothing less in the science that supports every product and service we offer. From design and development to manufacturing and marketing of innovative technology, instrumentation and tests, "Quality of Science" is the common element in everything we do.

Sequenom Center for Molecular Medicine (doing business as Sequenom Laboratories), a wholly-owned subsidiary of Sequenom, provides best-in-class laboratory testing services with a focus on prenatal and ophthalmological diseases and conditions. Our services include the market-leading MaterniT21® PLUS noninvasive prenatal laboratory-developed test intended for use in pregnant women at increased risk for fetal aneuploidies.

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