Staff Scientist Bioinformatics

Thermo Fisher Scientific
Job Location
Santa Clara, CA
Job Description

The successful candidate will be involved in creating designs for commercial and custom probe arrays as well as genotyping panels by next-generation sequencing. The candidate will interact with many different scientists from different companies and assist them to define the best design strategy for their research needs. The candidate will also be responsible for project management, data analysis, documentation, and deliverable preparation for the various scientific services projects for different applications, such as whole genome and/or targeting genotyping, copy number variation assays, and gene expression.



  • Interface with several cross-functional groups within the company and with our scientific customers
  • Work closely with the customer to translate scientific requirements into a sequence of array design steps, and guide the customer through the design process.
  • Provide detailed customer facing reports that include careful verification of the customer submitted content.
  • 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
  • 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.
  • Execute best practices genotyping to evaluate the performance of custom arrays after the design process is complete.
  • Use, extend, and where applicable, develop new pipelines for expression and genotyping data analysis
  • Work on applications of microarray and next generation sequencing platforms, including some or all of the following: detection of rare variants, detection of gene fusions, detection of deletions and other structural variants, quantitation of differential gene expression.



  • PhD in computational biology, biostatistics, bioinformatics, Statistical Genetics, or Genome Science or similar or MS in related disciplines plus 3+ yrs experience
  • Excellent communication skills along with the ability to work as part of a team
  • Strong initiative and demonstrated ability to take ownership of assign tasks
  • Ability to work in a fast paced, collaborative environment and meet deadlines
  • Must possess strong organizational skills
  • Proficiency in Linux/Unix including shell scripting
  • Statistical computing language - R is preferred
  • Solid experience with Python and/or Perl, in a Unix environment
  • Solid experience with relational databases, and proficiency with SQL and/or Oracle
  • Experience in analysis of microarray data considered a strong plus.
  • Knowledge of bioinformatics and specific knowledge of next generation sequencing
  • Experience in human genotyping imputation, Genome Wide Association Studies, annotation databases, as well as the ability to handle very large bioinformatics datasets and develop automated workflows, is a strong plus

Thermo Fisher Scientific is an EEO/Affirmative Action Employer and does not discriminate on the basis of race, color, religion, sex, sexual orientation, gender identity, national origin, protected veteran status, disability or any other legally protected status.

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