Comparative Genomics Co-op at Indigo

| Greater Boston Area
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Comparative Genomics Co-op

Please Submit applications by 6am on Tuesday, October 15th, 2019.

Indigo is a company dedicated to harnessing nature to help farmers sustainably feed the planet. With a vision of creating a world where farming is an economically desirable and accessible profession, Indigo works alongside its growers to apply natural approaches, conserve resources for future generations, and grow healthy food for all. Utilizing beneficial plant microbes to improve crop health and productivity, Indigo’s portfolio is focused on cotton, wheat, barley, corn, soybeans, and rice. The company, founded by Flagship Pioneering, is headquartered in Boston, MA, with additional offices in Memphis, TN, Research Triangle Park, NC, Sydney, Australia, Buenos Aires, Argentina, and São Paulo, Brazil.

This co-op will use computational methods to identify genes present in microbes that allow them to influence plant health. The co-op will compare the genomes of strains with different activities to find genes associated with those phenotypes. This role will require computational skills to combine and analyze data from multiple sources, run computational pipelines, and produce effective visualizations of data. This co-op should have strong knowledge and interest in microbial physiology and/or plant-microbe interactions to aid in interpretation of data and allow for participation in planning and/or execution of follow up experiments in the lab.


  • Use Python, SQL, and other computational languages to collect, analyze, and visualize data
  • Critically analyze experimental data to identify suitable datasets for comparative analyses
  • Meet with scientists conducting assays to learn about assay intricacies and relevant microbial features required for assay performance
  • Collect genomic data for microbes and run existing computational tools to compare their genomes
  • Analyze genomic differences between microbial strains with a biological mindset to identify differences that are relevant for microbial performance
  • Devise and implement novel computational analyses to identify and illustrate relevant genomic differences between microbes
  • Design follow up experiments to test hypotheses developed from comparative analyses
  • Accurately and concisely document work to communicate your results to others
  • Understand and embody our purpose & core values
    • Excited by Indigo’s mission; believes that Indigo can fundamentally change the agriculture industry; can clearly articulate passion for our mission and values
    • Optimistic and innovative; solution-oriented; shows no signs of cynicism
    • Will be widely viewed as someone who personifies our core values, is committed to them, and leans on them when making decisions. Specifically:
      • Demonstrates a track record of high integrity - doing the right thing, owning mistakes, conducting oneself honestly
      • Values, communicates and interacts with others with high levels of transparency and respect
    • Collaborates well across functions; creates an inspiring and collegial work environment


  • Proficiency in Python strongly preferred, with some experience in SQL desired
  • Experience writing clean, understandable code in environments like Jupyter Notebooks
  • Experience generating visualizations of complex data using packages like Matplotlib, Seaborn, ggplot, etc
  • Proven ability to look at complicated data and identify logical conclusions that can be acted upon
  • Strong background knowledge in genomic data and genomic assemblies, especially as it relates to microbes
  • Knowledge and fascination with how microbes work – how they generate energy, create interesting molecules, interact with their environment, etc
  • A strong desire to work at the interface of computational and biological sciences
  • Track record of effective professional communication of complex concepts through presentations/posters, etc
  • Experience working in a biological laboratory, especially with microbes and/or plants is a plus
  • Ability to communicate and collaborate with people from various scientific backgrounds

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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Technology we use

  • Engineering
    • JavascriptLanguages
    • PythonLanguages
    • RLanguages
    • TypescriptLanguages
    • GraphQLLanguages
    • ReactLibraries
    • ReduxLibraries
    • ExpressFrameworks
    • Node.jsFrameworks
    • MySQLDatabases
    • PostgreSQLDatabases


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!

An Insider's view of Indigo

What projects are you most excited about?

Our mission is to provide agronomists with unbiased real-time data we are collecting across thousands of acres at the ground level and from space. It's such a thrill to be working on the data and analysis perspective of this massively cross-disciplinary team that helps agronomists initiate data-powered conversations to provide substantial results.


Principal Data Scientist

What makes someone successful on your team?

A successful Indigo team member is someone willing to continuously learn and improve, regardless of experience or role. Whether you’re an Engineer, Account Manager, Business Analyst, or Scientist, successful team members keep the bigger picture in mind and bridge disciplines to solve problems facing the incredibly complex system that is agriculture


Software Product Manager

What are Indigo Perks + Benefits

Health Insurance & Wellness Benefits
Disability Insurance
Dental Benefits
Vision Benefits
Health Insurance Benefits
Life Insurance
Wellness Programs
Onsite Gym
Retirement & Stock Options Benefits
Company Equity
Performance Bonus
Child Care & Parental Leave Benefits
Generous Parental Leave
Flexible Work Schedule
Vacation & Time Off Benefits
Generous PTO
Paid Holidays
Paid Sick Days
Perks & Discounts
Commuter Benefits
Company Outings
Stocked Kitchen
Some Meals Provided
Recreational Clubs
Relocation Assistance
Fitness Subsidies
Professional Development Benefits
Job Training & Conferences
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