Encoded Therapeutics

Bioinformatics Scientist

Encoded Therapeutics Inc. is a biotechnology company advancing precision medicines for a broad range of genetic disorders. Our mission is to unlock new opportunities for viral gene therapy through genomics-driven discovery. We focus on delivering life-changing advances for individuals with genetic disorders not addressable with current approaches. For more information, please visit www.Encoded.com.

Position details

We are looking for a talented and experienced Bioinformatics Scientist having a strong computational and software development background to join our R&D team. This is a unique opportunity to work at the intersection of genomics and computing and participate in the development of a diverse therapeutic pipeline driven by a transformative core technology. This position offers the opportunity to work with large genomics datasets and deeply influence technology development.

The successful candidate will be excited and motivated to have a big impact as we are building out the computational team at Encoded. They would have demonstrated a solid understanding of genomics, programming languages, next-generation sequencing (NGS) technologies, SQL databases, and Laboratory Information Management Systems (LIMS). They should be a team player, with a desire to partner with other genomics scientists in assay development and troubleshooting.

Workplace Model: Hybrid/SSF


  • Process and analyze next-generation sequencing (NGS) data generated on Illumina and 10x platforms
  • Develop database schemas and manage our SQL database that stores our sequencing data and results
  • Partner with scientists across departments to design, troubleshoot experiments and help in interpretation
  • Perform custom sequence alignment, processing, QC and visualization of our novel RNA/DNA-sequencing assays
  • Assist in managing our cloud-computing environment that runs NGS processing jobs at scale using AWS Batch
  • Partner with other members of the computational group to explore and prototype computational approaches


  • PhD in Bioinformatics or related field with 0-2+ years industry experience
  • Demonstrated desire and skills to work in a collaborative setting is critical
  • Strong biological background and computational expertise
  • Independent and creative thinking
  • Experience working with transcriptomics data is a must. Knowledge of sequencing technologies such as RNA-Seq, ChIP-Seq, ATAC-Seq, Single Cell Seq
  • Grasp of basic molecular biology and genomics – laboratory experience is a plus
  • Understanding of and experience with whole genome transcriptome alignment and quantification tools
  • Experience programming in a high-level language such as Python, Ruby or R; Python is preferred
  • Familiarity with building bioinformatics pipelines using a workflow management system such as Snakemake
  • Experience developing databases to store scientific data. Knowledge of SQL and some experience with LIMS
  • Familiarity with cloud computing infrastructures on AWS and working with cloud-based tools such as AWS Batch, Data Pipeline, RDS/Redshift is a plus

Preferred Qualifications

  • Drug development experience is a plus


  • Comprehensive benefits package, including competitive employer premium contributions
  • Meaningful stock option grants
  • PTO, sick time, and holiday pay
  • Generous Parental Leave program
  • Pre-tax medical and dependent care programs
  • STD, LTD, Life and AD&D
  • Professional development opportunities
  • Team-building events
  • Fully stocked kitchen
  • Purple Tie dry cleaning service
  • Fitness center

Encoded is an Equal Opportunity Employer and prohibits discrimination and harassment of any kind. Encoded is committed to the principle of equal employment opportunity for all employees and to providing employees with a work environment free of discrimination and harassment. All employment decisions at Encoded are based on business needs, job requirements and individual qualifications, without regard to race, religion or belief, color, national origin, gender, status as a protected veteran, status as an individual with a disability, or any other status protected by the laws or regulations in the location in which we operate. Encoded will not tolerate discrimination or harassment based on any of these characteristics. Encoded encourages applicants of all ages.

If you need assistance or an accommodation due to a disability, you may call us at +1 650-491-0272.

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