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Principal Research Associate/Scientist, Bioinformatics

Cambridge, MA
About Vedanta Biosciences, Inc.
Vedanta is pioneering the development of a new class of therapies based on defined bacterial consortia that act by modulating the human microbiome. Modulation of the human microbiota holds enormous promise to treat a broad range of immune and infectious diseases in ways that are completely different to existing drug classes. Breakthrough discoveries of our scientific team in the field of mucosal immunology have led to the first rationally designed drug candidates in the microbiome field.

We believe that in the near future, doctors will have an entirely new option to treat patients: bacterial consortia therapeutics. We are enabling this new drug class with groundbreaking and industry-leading scientific work powered by large-scale capabilities to identify, screen, and manufacture bacteria with drug-like properties. Our team is at the core of all we do - and we're excited to meet new team members!  
About Us, About You

At Vedanta, we value diversity in all its forms and are looking for candidates with a wide variety of perspectives, backgrounds, education, and experiences. We believe that a diverse and inclusive workforce builds the strongest team possible.

We're proud of our workplace culture. Our Vedanta Values inspire us to be the best professionals and colleagues possible. Our values are:
Respect - Collaboration - Execution - Effective Communication - Problem Solving - Scientific Thoroughness

About the role

We are looking for a bioinformatician/computational biologist to support the Research and Development team in the operation of existing microbiome analysis and bacterial genomics workflows, conduct benchmarking studies to evaluate these workflows, and design, test, and implement process improvements. In support of the development of Vedanta Biosciences’ portfolio of Live Biotherapeutic Products (LBPs), the candidate will characterize bacterial isolate genomes, develop tools for predicting strain function or growth potential from genomic content, curate Vedanta’s growing database of cultured isolates, and support pre-clinical and clinical microbiome analyses. We are looking for an individual who is independent, curious, self-motivated, scientifically rigorous, and excited to collaborate with Vedanta’s diverse team of researchers. The job title and level will correspond to the experience and skills of the selected candidate. Candidates interested in fully remote work are encouraged to apply.
Here's what you'll do:
  • Lead the bioinformatic processing and characterization of bacterial strain genomes.
  • Curate Vedanta’s collection of bacterial genomes and build reference genome databases.
  • Conceptualize and benchmark bioinformatic microbiome analysis workflows.
  • Develop bioinformatic methods for predicting bacterial strain function or growth potential from genomic content.
  • Work with long- and short-read sequencing technologies to assemble and annotate bacterial isolate genomes.
  • Develop and apply algorithms for taxonomic clustering and classification in complex microbial community.
  • MS/PhD in bioinformatics, computational biology, or related quantitative field with 3+ years of working experience.
  • 3+ years of experience in a programming language, such as Rust, Perl, or Python, are required.
  • Analytical experience with metagenomic and hybrid bacterial genome assembly, binning, annotation, and taxonomic identification (e.g. MEGAHIT, metaSPAdes, UniCycler) is required.
  • Analytical experience with microbiome and microbial community ecology datasets is required.
  • Experience with assembly-independent strain characterization tools (e.g. StrainPhlAn, PanPhlAn etc.) is highly desirable.
  • Working experience in the development and operation of reproducible bioinformatic pipelines (e.g. Snakemake or Nextflow, versioning with Git) is highly desirable.
  • Experience with cloud computing infrastructure, shell scripting and data analyses is desirable. Experience with SQL programming and relational database management is preferred.
  • Highly organized and motivated individual. Detail oriented. Must be a team player, able to work well in a group setting as well as independently in a fast-paced environment.
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