Sr Bioinformatics Scientist & Environmental Microbiologist

Remote - Boston, MA

Mission of the Position

Your role will be to 1) develop and execute Allonnia’s environmental bioinformatics strategy and 2) build the capability (people, process, tools, insight) to enable discovery of microorganisms that uniquely sets Allonnia apart to deliver commercial remediation, upcycling, and sensing solutions.  

Company Description & Purpose

Allonnia’s purpose is to create transformative solutions for a waste-free, pollution-free world through leveraging the power of biotechnology and engineered systems that degrade or sequester pollutants and upcycle waste. Our ethos at Allonnia is to work in harmony with nature, combining biology and technology to fast forward time and bring Nature’s future solutions to the present day. Through this collaboration we will unlock the potential in waste and enable a world where nothing is wasted. Allonnia is backed by Battelle, Ginkgo Bioworks, Viking Global, General Atlantic, EVOK and Cascade Investments.

Key Criteria/Requirements

  • PhD degree in bioinformatics, biology or science
  • Minimum 3 years’ experience in bioinformatics
  • Minimum 2 years’ experience in environmental microbiology
  • Experience analyzing genomics and/or metagenomic data sets
  • Experience developing code for complex problems requiring integration of multiple data sources
  • Demonstrated experience with high level scripting language (Python and R)
  • Experience with bioinformatics best practices
  • Demonstrated ability to understand and develop machine learning algorithms in the bioinformatics field
  • Excellent communication and organization skills
  • Ability to simplify the complex; ability to translate technical concepts into simple terms
  • Ability to distill insights from data and visualize findings
  • Willingness to challenge others/critical thinking
  • Ability to collaborate to achieve common goals
  • Boston-based preferred

Responsibilities & Measurable Accountabilities

Develop Environmental Bioinformatics Strategy  

  • Collaborate with Allonnia’s executive leadership team to develop the environmental bioinformatics strategy
  • Develop an aspirational vision with hypotheses and plan how to prove or disprove.
  • Clearly document the path to value creation from bioinformatics
  • Clearly document risks with mitigation plans
  • Clearly document phased approach to building the bioinformatics capability (people, process, tools, insights), including costs and funding opportunities
  • Develop prioritized list of markets of interest, data sets required and translation of value to Allonnia and customers Identify 
  • IP ownership and security features relevant for Allonnia and stakeholders

Architect, Build and Maintain Environmental & Genomic Database

  • Complete the master database design that is flexible and integrates multiple data sources (including metagenomics, environmental data, treatment plant data)
  • Build the platform with necessary security, tools, and infrastructure to support the strategy
  • Build the database and begin to populate with available data
  • Develop protocols and the process to clean and maintain the database 
  • Complete documentation of the database architecture and maintenance plan

Conduct Data Analysis, Develop Insights & Implications 

  • Develop and document protocols to prepare data for analysis
  • Develop and document algorithms to process the data
  • Develop analytic practices using data mining techniques and software
  • Build analytical models and conduct analysis to enable discovery of microorganisms that have unique capabilities to remediate and upcycle waste
  • Extract insights from the analysis that are directly applicable to active projects to commercialize products
  • Synthesize, interpret, and communicate results that derive value 
  • Debrief and document project learnings; apply and leverage learnings from one project to the next

Drive for excellence; be the subject matter expert on emerging bioinformatics trends and best practices

  • Keep abreast of emerging methods through literature and conference participation
  • Ensure utilization of bioinformatics best practices (e.g., version control, unit testing, code documentation/validation)
  • Build relationships with thought leaders 
  • Regularly assess process and tools to ensure cutting edge methods and tools are in place

Thought Leadership & Brand Advancement

  • 2 case studies to share at conferences/associations per year

Allonnia Core Values


Committing to work on the right things as individuals and as a company, making a difference every day


Working with passion and curiosity to learn every day, creatively delivering results to the world


Fostering a high trust environment that embraces constructive debate, achieving success together

  Key Competencies

  • Intelligence
  • Strategic Skills
  • Analysis Skills
  • Leading Edge
  • Integrity
  • Resourcefulness/Initiative
  • Organization/Planning
  • Excellence
  • Team Player
  • Communications – Oral & Written
  • Energy/Drive
  • Tenacity

JOB CODE: 1000006