Scientist I/ii, Bioinformatics

Title:                   Scientist I/II, Bioinformatics

Location:           Cambridge, MA, hybrid, or remote

Reports to:        Senior Director, Systems Biology

About Vedanta Biosciences:

Vedanta Biosciences is a late-stage biopharmaceutical company developing medicines for the treatment of gastrointestinal diseases. The company’s lead assets include potential first-in-class oral therapies, VE303, a Phase 3-ready candidate for recurrent C. difficile infection, and VE202, in a Phase 2 trial for ulcerative colitis. Vedanta’s pipeline has been built using the company’s industry-leading product engine for the development of therapies based on defined consortia of bacteria grown from pure clonal cell banks. The product engine, supported by foundational IP, includes one of the largest libraries of bacteria isolated from the human microbiome, vast clinical datasets, proprietary capabilities in consortium design, and end-to-end CGMP manufacturing capabilities at commercial launch scale.

The Role:

We are looking for a bioinformatician/computational biologist to join the Research and Development team to support of the development of Vedanta Biosciences’ portfolio of Live Biotherapeutic Products (LBPs). The candidate will lead the execution of existing microbiome analysis and bacterial genomics workflows, conduct benchmarking studies to evaluate these workflows and new approaches, and design, test, and implement bioinformatic process improvements. The candidate will lead the characterization of 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.

Here’s What You’ll Do:

• Lead the execution of bioinformatic workflows for processing and characterization of bacterial strain genomes and stool metagenomes.
• Conceptualize and establish novel bioinformatic microbiome analysis workflows in support of pre-clinical and clinical programs.
• Curate Vedanta’s collection of bacterial genomes and build reference genome databases.
• Develop bioinformatic methods for studying bacterial strain colonization. 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 communities.

Requirements:

• MS/PhD in bioinformatics, computational biology, or related quantitative field with 3+ years of working experience.
• 3+ years of experience in a scripting language, such as Rust, Perl, or Python are required.
• 1+ years of working experience in the development and operation of reproducible bioinformatic pipelines (i.e. Nextflow, Snakemake) is highly desirable.
• 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.
• Experience with cloud computing infrastructure (i.e. AWS, Google cloud) and version control (i.e. git) are highly desirable.
• Experience with software standardization (e.g. Docker, BioContainer) and relational database development (e.g. SQL, MySQL, RDS) are desirable.
• 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.