Bioinformatics Scientist 1 - Medical Genomics at Illumina, Inc.

Posted in General Business 7 days ago.

Type: Part-Time
Location: San Diego, California

Job Description:

Position Summary:

Medical genomics research at Illumina is seeking an individual who wants to make a direct impact on the diagnosis of human disease. The group applies a wide array of sequencing based assays such as WGS, RNA-seq, methylation in order to push the boundaries of sequencing based diagnostics in rare disease, oncology, autoimmune disease, neonatal and other domains.

As a bioinformatics scientist, you will be applying your biological, computational, informatic and data driven insights to enable the diagnosis of disease, pilot new methods, build pipelines, aggregate data across multiple sources and showcase the future of medicine. You will also have the opportunity to work on large scale data and engage with other talented scientists at Illumina.


  • Analyze NGS datasets using commonly used methods and tools. Summarize the results of analyses and provide visualizations for discussion with other researchers.

  • Contribute to the development of software for the tracking of patient samples.

  • Contribute to the assessment, benchmarking and development of existing or novel bioinformatics tools.

  • Maintain and support existing workflows and computational pipelines

  • Provide clear documentation of tools, workflows and analyses.

  • Maintain code repositories.

  • Communicate analytic findings in informal and formal settings.

  • Stay informed about the current state of the field

  • Engage in collaborative research with internal and external teams.


  • Masters or PhD degree in computational biology, oncology, bioinformatics, computer science or or similar technical field

  • Experience with bioinformatics analysis of NGS data including the file formats and commonly applied tools and methods (WGS, RNA-seq, variant calling, structural variation).

  • Proficiency in python, R, java, and/or c++ with the ability to analyze data sets or develop functional implementations of analytic, algorithmic or data processing pipelines.

  • Familiarity with public databases such as gnomAD, refseq/ensembl transcripts, COSMIC, clinvar

  • Experience with linux environments, high performance computing, or cloud environments

  • Ability to extract and manipulate data from databases such as MySQL/postgres or MongoDB

  • Understanding of scientific literature

  • Ability to clearly communicate ideas, summarize scientific literature

  • Team oriented, comfortable with fast paced environment

  • Demonstrated ability to perform essential tasks with moderate oversight

Preferred Experience

  • Prior experience analyzing oncology data (somatic analysis, copy number/structural variation, ctDNA) data. Knowledge on the current state of tools, methods and relevant public databases.

  • Knowledge of different -omics technologies (WGS, RNA-seq, etc)

  • Familiarity with building pipelines, workflow tools and Docker/Singularity

  • Experience with version control systems

At Illumina, we strive to foster a diverse and inclusive workplace by cultivating an environment in which everyone contributes to our mission. Built on a strong foundation, Illumina has always been rooted in openness, collaboration, and seeking alternative views and perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and demonstrate our collective commitment to diversity and inclusion in the communities we live and work. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. If you require accommodation to complete the application or interview process, please contact To learn more, visit: