Senior Bioinformatics Scientist (#10964)

Affymetrix (now part of Thermo Fisher Scientific)
Job Location
Santa Clara, CA
Job Description

Job ID: 10964  

Affymetrix, now part of Thermo Fisher Scientific

Position Summary:

The algorithms and data analysis department seeks a talented and motivated individual to join a small leadership group in the Axiom ® Genotyping custom program. The successful candidate will work closely with customers and consortia members to design Axiom ® genotype microarrays that meet the customer’s scientific and business objectives.   The array design process includes the usage and development of complex data models and imputation-aware algorithms to select optimal markers and probes.


Primary Duties and Responsibilities:

  1. Work closely with the customer to translate scientific requirements into a sequence of array design steps, and guide the customer through the design process.
  2. Provide detailed customer facing reports, that include careful verification of the customer submitted content.
  3. Mine the Affymetrix Genomic database for markers and probes that meet the customer design requirements. Content for arrays may be selected from several sources including, but not limited to, dbSNP, 1000 GP releases, Affymetrix’ Axiom® Genomic Database, or markers identified by sequencing
  4. Use, extend, and where applicable, develop new methods associated with array design, including probe scoring, selection of tagging markers, imputation-aware marker selection, evaluation of genetic coverage, and efficient database queries.
  5. Execute best practices genotyping to evaluate the performance of custom arrays after the design process is complete.





  1. PhD in Bioinformatics, Statistical Genetics, or Genome Science with experience in genotyping and/or genetics or equivalent experience
  2. 3 years working experience
  3. Excellent communication skills
  4. Strong initiative and demonstrated ability to take ownership of challenging problems.
  5. Knowledge of human genotyping imputation and Genome Wide Association Studies.
  6. Statistical computing language- R is preferred
  7. Scripting language such as Perl, or Python.
  8. Ability to query database with SQL
  9. Experience working with scientist customers or collaborators is a strong plus.
  10. Experience in analysis of microarray data considered a strong plus.


Level of Autonomy and Complexity:

  • Significant record of scientific achievement through multiple publications in peer-reviewed journals if applicable and full comprehension of established principles, theories, concepts to resolve an extensive range of issues
  • Displays success in scientific originality, independence, and technical skill
  • Employs judgment in choosing creative techniques to resolve complex issues requiring extensive analysis and evaluation of multiple factors
  • Contributes to establishment of organization's objectives, contributes to project/corporate strategy and recommends direction
  • Determines own methods for new projects; employs scope to determine goals for assignments
  • Thinks critically and creatively and demonstrates ability to work with complex projects to solve technical problems
  • Expanding use of statistical methods
  • Maintains knowledge of leading-edge principles and theories
  • Recognized as company leader in area of expertise
  • Provide significant intellectual contribution to programs on a cross-disciplinary level
How to Apply
About Our Organization

About Us

Affymetrix, now a part of Thermo Fisher Scientific, is a pioneer in creating breakthrough tools that are driving the genomic revolution. We provide leadership and support, partnering with customers in pharmaceutical, diagnostic, and biotechnology companies, as well as leading academic, government, and non-profit research institutes in their quest to use biology for a better world. More than 2,300 microarray systems have been shipped around the world, and more than 94,000 publications have referenced Affymetrix technologies (now a part of Thermo Fisher Scientific). 

We are an EEO/AA Employer of Minorities/Females/Veterans/Disability/Sexual Orientation and Gender 

About Thermo Fisher Scientific,

As the world leader in serving science, we empower our people to advance innovative technologies, develop meaningful solutions, and build rewarding careers. With revenues of $17 billion and the largest investment in R&D in the industry, we give our 50,000 extraordinary minds the resources and opportunities to make significant contributions to the world. Explore the professional possibilities at Thermo Fisher Scientific, and join us.

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