Bioinformatics Engineer II


Emeryville, CA, US
  • Job Type: Full-Time
  • Function: Research Sci/Assoc/Mgr
  • Post Date: 02/21/2021
  • Website:
  • Company Address: 5980 Horton Street Suite 105, Emeryville, CA, 94608

About Zymergen

We are a science and material innovation company rethinking biology and reimagining the world. A World Economic Forum Tech Pioneer, we partner with nature to create never-before imagined materials and products across industries – from agriculture to electronics, consumer care to pharmaceuticals, and more.

Job Description

Zymergen is developing its cloud-based data analysis infrastructure to support automated strain design and the discovery of natural products with commercial applications. Our Metagenomics Software team uses advanced machine learning techniques to search our massive, proprietary DNA sequence database to discover gene clusters encoding pathways that produce these natural products. This team is in need of an experienced bioinformatics engineer to:

  • Enhance the efficiency of our natural product discovery pipeline
  • Automate metagenomic bioinformatics tools for use in a high throughput environment
  • Work with laboratory scientists to design effective storage, search and display technologies to facilitate their work with the outputs of these tools 

Job Description and Specific Responsibilities

You will help us build workflows to extract actionable insights from our proprietary collection of metagenomics data, which we leverage to produce valuable   molecules, improve microbial performance and identify novel traits of benefit to commercial applications.  You will work as a member of a bioinformatics engineering team that collaborates closely with laboratory scientists and data analysts. Finally, you will have a chance to develop novel tools and systems to support development of disruptive capabilities for our new product development efforts.

Immediate responsibilities include:

  • Technical scoping of solutions to requirements, which require technical expertise and understanding of timelines and effort.
  • Porting prototype/exploratory workflows into more robust and reusable components.
  • Promoting software best practices by reviewing pull requests from other engineers and upholding agreed-upon code quality standards.
  • Improving scalability of computationally intensive workflows.
  • Ingestion and output of diverse data formats.
  • Collaborating across multiple functional teams.




  • BS, MS or Ph.D. in Bioinformatics, Computational Biology, Computer Science or a related field
  • 2+ years professional experience

Required Skills:

  • Mastery of bioinformatics tools, data, and concepts. Familiarity with current trends in the metagenomics and natural product discovery literature
  • Demonstrated experience with software engineering best practices and developing well-documented, production code
  • Excellent written and oral communications skills
  • Strong skills in bioinformatics pipeline development
  • Comfort with software deployment and coding in a Linux environment, version control (git), unit testing

Nice to have:

  • Experience structuring large, multi-dimensional biological datasets, using DB and data warehousing technologies as appropriate
  • Experience with statistics and/or machine learning
  • AWS / Docker expertise
  • Python is a key tool for the group and company. A successful candidate will be able to thrive in a python-forward environment

Personality traits:

  • Ability to communicate with stakeholders from different teams across Zymergen and collaborate while maintaining positive relationships 
  • Creativity, independent thinking, and self-motivation 
  • A passion for challenging new problems outside of one’s comfort zone, and the drive to deliver impac


Additional Details
Zymergen’s approach embodies a “data-driven research” mindset.  You will gain access to big data generated by our high-throughput robotics capability, allowing you to analyze and learn from real experimental data acquired at industry-leading precision and scale.  We store all data, both positive and negative, to enable continuous learning and analyses that inform subsequent experimentation.  This ever-growing body of knowledge guides the evolution of our approaches and the design of our platform.

We take our software engineering mindset into the biological domain.  We seek to continually optimize the performance of our microbes through a “design, build, test, analyze, learn” (DBTAL) loop.  Our lab automation, data warehouses, bioinformatics tools, data science and ML modeling serve to efficiently iterate through the DBTAL loop.  We are even able to transfer our learned biological optimizations across programs.  The problems of metabolic engineering are challenging and unique.  You will have many opportunities to pioneer novel strategies to attack these problems with us. 

Legal authorization to work in the U.S. is required. Zymergen may agree to sponsor an individual for an employment visa now or in the future if there is a shortage of individuals with particular skills for this job.

In compliance with federal law, all persons hired will be required to verify identity and eligibility to work in the United States and to complete the required employment eligibility verification form upon hire.

Founded in 2013 and headquartered in the SF Bay Area, Zymergen is a science and material innovation company rethinking biology and reimagining the world. A World Economic Forum Tech Pioneer, Zymergen partners with nature to create never-before imagined materials and products across industries – from agriculture to consumer electronics, personal care to pharmaceuticals, and more. The company’s materials are in use today, creating value for Fortune 1000 companies and major corporations across the globe. Our clients have sold over $1 billion worth of products using Zymergen microbial strains. For more information visit:

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Disclaimer: Local Candidates Only
This company does NOT accept candidates from outside recruiting firms. Agency contacts are not welcome.