Software Engineer

Job Location
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

We currently have a great opportunity for a Software Engineer who will contribute to the development of series of web-based applications that are focused on the clinical interpretation of genetic findings from Next-Generation Sequencing as used in our clinical laboratories. The successful candidate will also assist in clinical data mining, testing and optimization of current pipelines, and support the effort of LIMS integration with the clinical pipelines. Responsibilities:

  • Lead design and development of applications for interrogating internal and external resources for clinical interpretation of genetic findings.
  • Lead design, and direct development of, a persistent data model to support existing and future applications.
  • Participate in large scale data mining of public and proprietary data repositories focused on extracting information related to clinical interpretation of the genetic findings.
  • Work closely with a multidisplinary team, including other software engineers, bioinformaticians, scientists and IT.
  • B.S., M.S., or Ph.D. in computer science or other applicable scientific or technical field (or equivalent experience) and a minimum of 3 years of related experience.
  • Experience in implementing bioinformatics, scientific algorithms, and data processing pipelines within the domain of Next-Generation Sequencing, and genetics or healtcare environment
  • Hands-on experience with programming in  Java , and familiarity with one or more of the following programming and scripting languages: Python, Perl, R.
  • Experienced with web application development tools and languages including PHP, HTML5, javascript, and/or JSP.
  • Experienced in Data Modeling and Database programming with one or more of the relational databases such as PostgreSQL, Oracle, Sand/or MySQL, and related interfaces.
  • Demonstrated experience and familiarity with working/interacting with  public genetics and oncology related  databases including NCBI, GenBank,TCGA, Clinvar, OMIM, COSMIC, dbSNP,HapMap, etc.
  • Demonstrated experience with processing popular genetic information related files and data formats such as .vcf, .bed, .wig, .bigwig, .sam, .bam, …
  • Experience working in a Linux/Unix operating environment.
  • Familiarity with common software development tools, application frameworks and practices (Version control, build automation, design patterns, algorithm development).
  • Strong interpersonal and communication skills with the ability to talk to computational and bench scientists.
  • Have experience in working in a multidisciplinary work environment of scientists, engineers, mathematician,  and statisticians.

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

How to Apply

Email resumes directly to

About Our Organization

Sequenom Laboratories, a wholly owned subsidiary of Sequenom, Inc., is a CAP-accredited and CLIA-certified molecular diagnostics laboratory, dedicated to the development and commercialization of laboratory-developed tests (LDTs) for prenatal diseases and conditions. Sequenom Laboratories holds or has access to intellectual property for noninvasive prenatal testing using circulating cell-free fetal nucleic acids.

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