Watchmaker Genomics is an early-stage life science company based in Boulder, Colorado. Our team is passionate about innovation and values collaboration, creativity and scientific rigor. We believe the intersection of biology, engineering and computer science presents exciting opportunities for developing novel technologies that promote research and improve human health. Watchmaker Genomics specializes in the design, development and production of DNA- and RNA-modifying enzymes that enable high-growth applications in genomics, molecular diagnostics and personalized medicine.

Position Summary

Watchmaker Genomics is inviting applications for the full-time position of Director of Computational Biology and Software. This position reports to the Chief Scientific Officer and will be responsible for building a foundational R&D computational biology program. This includes building and overseeing both robust internal analytical pipeline development and on-going ad hoc R&D data analysis and mathematical model development. This individual will lead the design, development, and implementation of novel algorithms and software packages for analyzing large sequencing data sets. These efforts will play a central role in the analysis of novel enzymes for RNA/DNA manipulation (derived from internal rational design and directed evolution efforts), and modules or kits for analysis of nucleic acids in a variety of experimental contexts. Additionally, this individual will ultimately lead the development of software products for the analysis of complex data sets. The development of automated analytical pipelines requires rigorous, scalable software development and testing, as well as a deep understanding of existing tools for sequence data analysis. Additionally, the R&D data analysis will require both strong sequence analysis and quantitative/statistical analysis. The ideal candidate will also have a firm understanding of the basic molecular biology of sequencing library preparation. 

The successful candidate will thrive in a dynamic, fast-paced working environment and contribute directly to our company culture and success. The ideal candidate has a proven track record of managing effective teams, and is driven by scientific curiosity, quality engineering, and mathematical rigor.

  • Establish a highly innovative and efficient R&D computational biology program
  • Develop novel algorithms for the analysis of a wide variety of sequencing data sets
  • Build upon a culture of collaboration R&D in which bench scientists and computational scientists operate in concert to drive rigorous, efficient, and innovative product development
  • Build and manage a well-engineered and documented code base
  • Contribute to strategies for efficient data management for the purpose of maximizing learning from new and historical datasets
  • Train and manage a team of bioinformatics scientists and software engineers
  • Contribute strategic vision on role of data analytics in Watchmaker’s product offerings
  • Participate in customer collaborations and product support
  • Identify opportunities for internal process improvement
Required Qualifications and Experience

The candidate should have a Ph.D. with 5+ years of industry experience (or an M.Sc with 8+ years industry) in bioinformatics, computational biology, mathematics/statistics, or physics. The candidate must have a proven track record of high-throughput sequencing data analysis in addition to a strong foundation in quantitative data analysis. Strong software engineering skills and a basic understanding of methods of sequencing library preparation are required. Experience in or excitement to learn other areas including computational structural biology, in silico bioprospecting, data extraction from large biological databases (e.g. GEO, TCGA, JGI genome database, etc), and analysis of enzyme evolution data are expected.

The following skills and experience are requirements for the position:

  • Rigorous data analysis skills, including solid statistics and advanced bioinformatics
  • Proven background in managing effective software engineering and data analysis teams
  • An understanding of existing tools for sequencing data analysis, including GATK, bwa, MACS, STAR, kallisto, DESeq2, and others
  • Proficiency in Python and familiarity with R as well as statically typed languages such as C++, Java or Rust is required
  • A basic understanding of molecular biology techniques such as PCR and sequencing library preparation
  • Adherence to best practices in software engineering, including fluency with version control (particularly git), CI/CD, linting, testing, when to use OOP  over procedural paradigms
  • Basic understanding of principles of database design and management
  • Ability to manage and coordinate bioinformatics scientists and software engineers in a dynamic, fast-paced development environment
  • A firm understanding of scalable software engineering practices and of modern frameworks for software scalability such as AWS, Kubernetes, and Docker
  • Strong interpersonal skills and an ability to work as an effective leader of a goal-oriented team
  • Adept and creative problem-solving skills
  • Demonstrated ability to plan, build, troubleshoot, complete and scalable software solutions to advanced data analysis problems
  • Excellent organizational skills and outstanding attention to detail
  • Excellent written and verbal communication skills
Education Requirements
  • Ph.D. (plus a minimum of 5 years of relevant industry experience) or an M.Sc (plus a minimum of 8 years of relevant industry experience) in bioinformatics, computational biology, mathematics/statistics, or physics.

The budgeted range for this position starts at $140,000 – $190,000 + bonus + equity; actual pay will be adjusted based on skills and experience. Employees are eligible for Flexible Time Off, Holidays, Medical, Dental, Vision, Life/AD&D, and a 401(k) retirement plan.

Application Requirements

Applications without a Letter of Motivation will not be considered. Local candidates preferred.

  • Letter of motivation
  • Curriculum vitae, highlighting relevant qualifications and experience

If selected to participate in the interview process, the names and contact information of two references who are able to assess your suitability for the position in terms of the specified requirements will be requested.

Watchmaker Genomics is committed to being an equal opportunity employer and creating a culturally diverse environment. All qualified applicants will receive consideration for employment without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, disability status, age, or veteran status or any other characteristics as protected by applicable law.