Bioinformatics Scientist

Hybrid or Remote, MA

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.

Mission of the Position

We are seeking a highly motivated and experienced Bioinformatics Scientist to join our team at Allonnia. As a Bioinformatics Scientist, you will play a crucial role in advancing our cutting-edge research in genomics and bioinformatics. Your responsibilities will encompass data analysis and interpretation, algorithm/pipeline development, experimental design support, resource management, continuous learning, and problem-solving.

Key Criteria/Requirements

  • PhD degree in bioinformatics, computational biology, or related field
  • Minimum 3 years’ experience in bioinformatics, interpretation, and visualization
  • Minimum 2 years’ experience in environmental microbiology
  • Experience analyzing genomics and metagenomic data sets.
  • Familiarity with database management and data security.
  • 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

Algorithm/Pipeline Development and Customization:

  • Develop and maintain bioinformatics algorithms and pipelines to address Allonnia’s research needs.
  • Optimize and validate pipelines and methods to improve accuracy, efficiency.
  • Enhance and add new features to existing pipelines to make them more robust and efficient.
  • Develop and document protocols, pipelines, algorithms that are built in relation to bioinformatics.
  • Ensure utilization of bioinformatics best practices (e.g., version control, unit testing, code documentation/validation)

Architect, Build and Maintain Environmental & Genomic Database

  • Collaborate with Allonnia’s database engineer to maintain and develop the genomic portion of the database.
  • Ensure data quality, security, management, and efficient data retrieval of all bioinformatics data.
  • Manage computational resources, including hardware and software licenses to support bioinformatics analysis efficiently.

Conduct Data Analysis, Develop Insights & Implications 

  • Analyze a variety of biological and genomic data including but not limited to amplicon sequencing, whole genome sequencing, metagenomics, gene expression and other microbial ‘omics based datasets.
  • Collaborate with the wet-lab team to 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
  • Tackle complex biological and data-related challenges that may arise during research of product development.

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
  • Resourcefulness/Initiative
  • Organization/Planning
  • Team Player
  • Communications – Oral & Written
  • Energy/Drive


JOB CODE: 1000055