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.
Vedanta is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person’s race, color, gender, age, religion, national origin, ancestry, disability, veteran status, genetic information, sexual orientation or any characteristic protected under applicable law. Vedanta will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law.
Vedanta Biosciences requires all employees to be fully vaccinated against COVID-19 and newly hired employees must be fully vaccinated prior to their employment start date. Vedanta Biosciences will consider accommodations for individuals who are unable to be vaccinated against COVID-19 due to a qualifying medical condition or disability or a sincerely held religious objection.
Top Skills
What We Do
The trillions of microbes that call us home –the human microbiome – perform critical functions that preserve our health including helping develop our immune system, manufacturing nutrients such as vitamins, and harvesting energy from the diet. Alterations of the human microbiome are increasingly recognized as a key factor in autoimmune, metabolic, infectious and many other diseases.
For millions of years, humans have co-evolved with this community of microbes, communicating in an ancient language that holds critical clues about how autoimmune and infectious diseases develop. This language is based on a system of signals that our resident microbes use to successfully colonize us, such as byproducts of bacterial metabolism and factors that bacteria use to adapt to human niches. Recent discoveries have shown that most of these signals do not lead to disease, rather, they promote our long-term survival.
Vedanta is developing a novel class of therapies that modulate pathways of interaction between the human microbiome and the host immune system. Vedanta was co-founded by PureTech Health and a group of world renowned experts in immunology and microbiology
