Computational Biologist I

  • Indigo
  • Boston, MA
  • Sep 17, 2020

Job Description


Computational Biologist I


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.      

The Computational Biologist will be use modern bioinformatics tools and method to screen Indigo’s microbial genomic library for functional traits beneficial to plant and will deliver hypothesis-driven microbial nominations to the screening pipeline. The Computational Biologist will contribute to enrich our internal microbial functional knowledgebase (MFKB) with current scientific knowledge on plant microbe interactions under biotic and abiotic stresses; generate hypotheses on microbial functions and their interactions with plant, and integrate multiple data streams to characterize strain performance and evaluate our strain nomination rationales.  The Computational Biologist will propose and conduct comparative genomic experiments to predict strain diversity, metabolic potential, and interaction with plant.




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

  • Apply comparative genomics to understand the modes of actions of our microbes and the plant responses to microbial treatments
  • Mine genomic data to find key environmental and phenotypic interactions between microbes and plants
  • Supplement publicly available data and knowledge into Indigo systems to improve nomination,
  • Contribute to the expansion and curation of the Indigo’s Microbial Functional Knowledgebase by conducting thorough reviews of current literature
  • Conduct integrative analyses on Indigo’s genomic and phenotypic data
  • Analyze the plant microbiome to understand influence of microbial communities on plant fitness and productivity
  • Leverage subject matter expertise and experience to contribute to the design of assays and data review


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

  • On a monthly basis, deliver a high-quality nomination set of 25-200 product candidates for biotic stresses to be tested in our pipeline, in line with the global product roadmap
  • Within 30 days, understand all aspects of product development process
  • Within 60 days, partner with team members to define a framework for measuring pipeline success of hypotheses
  • Within 60 days, take over leadership of Biotic Nomination Working Group and represent MXN on Biotic Indication Team
  • Within 60 days of taking over Biotic Nomination Working Group, run a process to collect feedback and define new/better ways of working with group
  • On an on-going basis, provide feedback to Bioinformatics team on tools, feature improvements, and prioritization of Software Engineering resourcing


Expand and upgrade criteria and rationales for microbial nominations into the pipeline to improve nomination success as measure by their performances in targeted screening assays


Collaborate with Bioinformatician and Software Engineer to refine tools and interfaces to genomic and phenotypic data such that scientists across the company can fully leverage the value of the Indigo data asset



  • A voracious learner who will always “ask the next question”
  • Outstanding communication skills – candidate will be working cross functionally across pipeline with
  • 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.

Organization Type



Food & Agriculture

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