Scientist, Bioinformatics

Scientist, Bioinformatics 150 150 checkerspot

Title: Scientist, Bioinformatics

Type: Full-Time

Location: Berkeley, CA

Supervisor: Senior Director, Molecular Biology


Checkerspot designs performance materials at a molecular level.  It does this by optimizing microbes to biomanufacture unique structural oils produced in nature, but not previously accessible at commercial scale.  A certified B-Corporation, Checkerspot’s first materials are next generation polyurethanes and textile finishes designed to improve the performance of consumer products.  The company is currently commercializing a performance composite engineered into skis and sold through its WNDR® Alpine brand, as well as algal oil formulated into miDori® BioWick and sold in partnership with Beyond Surface Technologies.  Checkerspot’s mission is to expand the palette of molecular building blocks for high performance and sustainable materials. 


Our company culture can best be understood through experience.  Come get to know us!  We’d like to be known more by what we do than what we say.


We seek an enthusiastic, team-oriented, problem solver to join our Molecular Biology & Strain Development group as a Bioinformatics Scientist.  Key responsibilities will include:  

  • Coordinating with the Molecular Biology team and NextGen Sequencing CROs to execute both genomic and transcriptomic sequencing programs in both novel microbial systems and in higher plants and performing subsequent analyses including haplotyping, gene annotation, and variant analyses
  • Aggregation, Q/C, and warehousing of raw NGS data for subsequent analyses; developing, organizing and maintaining databases for a variety of research and manufacturing data
  • Developing pipelines for long- and short-read genomic assembly, error correction, haplotype phasing, and gene annotation in order to generate reference genomes for a number of novel microbes
  • Developing de novo transcriptome assembly and annotation pipelines for RNAseq data derived from the analyses of higher plant tissues and from a number of novel microbes
  • Using comparative phylogenomics to assist the Molecular Biology scientists in gene discovery efforts in non-model higher plants 
  • Performing differential gene expression analyses using RNAseq data derived from platform organisms grown under different experimental conditions
  • Assisting in structure-function analyses of newly identified enzymes
  • Advising on the development and maintenance of local and cloud-based IT infrastructure to support current and future bioinformatics needs 
  • Producing high-quality documentation for newly developed approaches
  • Assisting in the preparation of written examples for IP and regulatory filings


  • M.S. (or higher degree) in bioinformatics, computational biology, systems biology, genetics, or related field, and a sound understanding of both biology and data science; or B.S. in physics, statistics, computer science and at least 4 years of industry experience in bioinformatics; or an equivalent combination of education and experience
  • A deep appreciation that bioinformatics must generate actionable data and insights that support efforts at the bench
  • Proficiency in Python or other relevant programming languages in a Unix environment
  • Experience with cloud computing and data storage and some familiarity with server storage architecture and optimization
  • Demonstrated expertise in creating pipelines for genome and transcriptome assembly and annotation, as well as haplotype phasing and contaminating sequence removal
  • Experience in novel gene discovery and/or comparative phylogenomics, metabolomics, and/or gene expression analysis
  • Excellent written and oral communication skills with scientific peers AND executive partners
  • Experience with the Geneious Prime suite of molecular biology and sequence analysis tools is a plus but not required
  • Ability to manage large datasets and draw conclusions from them
  • Comfortable working in a fast-paced, dynamic environment
  • Committed to the highest standards for protecting data integrity and security
  • Must be legally authorized to work in the United States on a full-time basis


Checkerspot offers its employees a competitive benefits and compensation package. 

Checkerspot is an Affirmative Action and Equal Opportunity Employer and all qualified applicants will receive consideration for employment without regard to race, color, religion, gender, sexual orientation, national origin, genetic information, age, disability, veteran status, or any other legally protected basis.

For consideration, please submit your résumé and brief cover letter: