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Bioinformatics Data Engineer III

Location: Somerville, Massachusetts, 02143, United States

About Finch

Finch Therapeutics is a clinical-stage microbiome therapeutics company leveraging its Human-First Discovery® platform to develop a novel class of orally administered biological drugs. With the capabilities to develop both complete and targeted microbiome therapeutics, Finch is advancing a rich pipeline of candidates designed to address a wide range of unmet medical needs. Finch’s lead candidate, CP101, is in late-stage clinical development for the prevention of recurrent C. difficile infection (CDI) and has received Breakthrough Therapy and Fast Track designations from the U.S. Food and Drug Administration. Finch is also developing FIN-211 for children with autism spectrum disorder and significant gastrointestinal symptoms. Finch has a partnership with Takeda focused on the development of targeted microbiome therapeutics for inflammatory bowel disease.


Position Summary

At Finch the Data Science team is an integral component of Research unit, and a core contributor to translational and development activities in the company. As a member of the Data Science team your mission is to work closely with scientists from multiple functions and lead the establishment, implementation, and refinement of our next-generation data ingestion, processing and analytical pipelines. You will develop the vision to continually advance our research data and analytics infrastructure, and empower scientists to generate and utilize novel types of biological data and implement advanced computational analysis techniques in research and clinical settings. You will architect the system to transition program-critical computational methods from development to stage-appropriate compliant environments. In doing all this you will ensure that Data Science team continues to serve the multifold needs of a rapidly growing, clinical-stage, company.  



  • Design, develop, and maintain applications to enable ingestion, rapid access, and analysis of data to accelerate discovery and enable decisions acrross research, development and translational groups 
  • Develop and maintain a software development lifecycle (SDLC) to support moving tools from research and development to validated and GXP environments  
  • Maintain infrastructure that allows scientists to process and analyze internally generated and/or externally acquired NGS data and results of bench assays
  • Orchestrate existing research tools and analytic assets developed by computational scientists via Docker, APIs, or CLIs
  • Work with a team of laboratory scientists and data scientists to rapidly specify, implement, and deploy fit-to-purpose software tools  
  • Evaluate commercial and open source tools to improve our bioinformatics research pipelines; implement pipelines into our research workflows  
  • Troubleshoot complex environment, software, and workflow problems related to deployment and operations
  • Support rollout, optimizationand improved scalability of Finch’s analysis pipelines 
  • Design easy to use, scalableand intuitive user interfaces for bench scientists  
  • Manage a small team of engineers



  • Bachelor’s or Master’sdegree in Bioinformatics, Computational Biology, Statistics, Engineering or Computer Science. Master’s degree and 2 years of scientific/clinical development experience or Bachelor’s degree and 5 years of similar experience.  
  • Proficiency in designing relational schemas to capture and represent multi-type data. Ability to design complex queries to generate clear representations of data from complex relational  schemas. 
  • Experience in orchestration tools such as Terraformand Cloudformation 
  • Experience with workflow management systems such as snakemake, airflowand nextflow  
  • Programming experience in scripting languages such as Python & R, using version control, Gitlab and continuous integration environments 
  • Basic understanding of pharmaceutical discovery process.
  • Experience indeveloping and supporting validated systems in translational/clinical settings. 
  • Familiarity with NGSanalysis methods and software 
  • Experience with bioinformatics pipeline developmentand software development cycle 
  • Familiarity with software release management and deployment (Git, CI/CD)
  • Familiarity withDevOps principles and best practices 
  • Knowledge of information security and compliance practices
  • Experience with BigQueryor Azure 
  • Experience with at least one modern front-end framework (React, Vue, Angular) 
  • Significant knowledge of REST APIs. This includes both REST development and integration with a variety of third party APIs 
  • Proficiency in needs gathering, follow-up communicationand project leadership 

 Ideal Candidate will also have

  • Understanding of basic concepts in microbiology, genomicsor transcriptomics 
  • Prior experience in managing scientists or engineers in pharmaceutical or biotechnology setting 
  • Experience in software engineering for clinical trials


More About Finch 

Here at Finch, we are determined to create the best work environment and experience for you through our formal benefits programs and fringe perks. Together, we hope that we’ll create a fun & supportive environment in and out of the workplace as we strive to create a new class of therapeutics together to help patients. 

  • Our formal benefits include medical, dental, and vision coverage through Harvard Pilgrim in addition to life insurance and long-term & short-term disability policies. We offer discretionary and flexible paid time off policies. Should you choose to start or grow your family while working at Finch, we aspire to lead our peers by offering several months of paid parental leave. We also offer a generous 401(k) contribution to help teammates save for life beyond Finch, as well as other savings and investment opportunities. 
  • We also try to keep the workplace an inspiring and motivating place to work with our fringe perks. Our facilities in Somerville, MA include an in-office gym with a shower and towel service (temporarily closed due to COVID), fully stocked kitchen with free snacks, iced coffee & flavored/sparkling waters on tap. We sponsor ride-sharing to and from the office from preset locations around Boston, Cambridge, and Somerville. We are always evaluating our fringe perks and hope to grow them alongside our team.  

*Only facility-dependent employees are working on-site in Somerville until further notice. 


Equal Opportunity Employer

We are committed to recruiting, developing, and retaining the most talented people from a diverse candidate pool.  All aspects of employment including the decision to hire or promote, will be based on aptitude, performance, and business need. We do not discriminate on the basis of race, color, religion, sex, national origin, age, physical or mental disability, marital status, sexual orientation, gender identity, gender expression, genetic information, military and veteran status, or any other legally protected status. Finch will make reasonable accommodations for qualified individuals with disabilities, in accordance with applicable law.