Computational Biologist at Indigo

| Greater Boston Area
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Computational Biologist 

at Indigo (View all jobs)

Boston, MA

Computational Biologist 

Indigo improves grower profitability, environmental sustainability, and consumer health through the use of natural microbiology and digital technologies. Utilizing beneficial plant microbes and agronomic insights, Indigo works with growers to sustainably produce high quality harvests. The company then connects growers and buyers directly to bring these harvests to market. Working across the supply chain, Indigo is forwarding its mission of harnessing nature to help farmers sustainably feed the planet. The company is headquartered in Boston, MA, with additional offices in Memphis, TN, Research Triangle Park, NC, Sydney, Australia, Buenos Aires, Argentina, and São Paulo, Brazil.      

As a member of the Microbial Informatics and Nominations Team, the Computational Biologist will employ computational methods that leverage Indigo’s microbial collection and sequence data assets to deliver hypothesis-driven microbial nominations to the product-development pipeline for novel microbial seed treatments. The position will primarily focus on the development of products targeting diverse biotic stresses across a range of host crops. The Computational Biologist will generate hypotheses around microbial functions and their interactions with plant hosts, integrate multiple data streams to characterize strain performance, and evaluate those hypotheses. This position will have the opportunity to directly impact the identification and development of novel microbial solutions to create a more sustainable agriculture.


Use bioinformatic methods and tools to identify microbial functional traits valuable for sustainable agriculture, synthesize hypotheses, and guide testing activities

  • Apply comparative genomics to propose and understand the potential modes of action of our microbial seed treatments across a range of crop hosts and stresses
  • Stay up-to-date and conduct thorough reviews of relevant literature in the areas of bioinformatics, plant-microbe interactions, and microbial physiology.
  • Contribute to the expansion and curation of the Indigo’s microbial data assets
  • Conduct integrative analyses on Indigo’s sequence-based and phenotypic data
  • Analyze datasets derived from microbial communities to understand the influence of these communities on host plant fitness and productivity
  • Leverage subject matter expertise and experience to contribute to the design of assays and data review
  • Collaborate with team members and software engineering to refine tools and interfaces for genomic and phenotypic data to enable scientists across the company to fully leverage the value of the Indigo data asset

Own microbial nominations into the pipeline for biotic stresses across all crops, globally.

  • Plan, generate, and deliver nomination sets of microbial product candidates targeting biotic plant stresses for pipeline testing
  • Become familiar with all aspects of the product development process and work collaboratively to contribute expertise and perform ad-hoc analyses in support of that process
  • Partner with team members to define a framework for measuring pipeline success of nomination hypotheses and integrate outcomes into future microbial nomination workflows
  • Represent the microbial informatics and nominations team in collaborative working groups and lead a group focused on the nomination strategy and execution of microbial treatments for biotic stresses
  • On an on-going basis, communicate feedback and ideas for new tools, improvement of existing tools, and general prioritization of computational needs.


  • A voracious learner who will always “ask the next question”
  • Outstanding communication skills – candidate will be working cross functionally across the microbial product-development pipeline
  • Team player – someone who thrives working in cross functional teams throughout the organization.
  • Easily adapts to new types of problems and questions. Flexible to different types of analysis and different stakeholders (e.g. lab science, field trials, commercial team).


  • PhD + 2 years industry and/or post-doc experience in a relevant field such as microbiology, computational biology, or plant biology
  • Required domain experience and publication history in comparative genomics, microbial ecology, microbial physiology
  • Experience in plant pathology assays, plant microbe interactions, and/or microbe-microbe interactions
  • Fluency with R and/or Python

Indigo is committed to living our values, specifically “creating a work environment where everyone feels respected, connected, and has opportunities to learn and grow.” As part of living our values, we strive to create a diverse and inclusive work environment where everyone feels they can be themselves and has an equal opportunity of succeeding.

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On the edge of Charlestown, we are within walking distance to restaurants and bars. The Sullivan Square T and bus stop is also right next door!
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