Title:                  Scientist, Computational Biology 

Location:          Cambridge, MA  

Reports to:       Associate Director, Research  

The Role:

We are hiring a computational biologist to contribute to our microbial community design and in vitro microbial community modeling functions. The Computational Biologist will join a team of microbiologists and systems biologists focused on designing and controlling gut microbial communities in vitro and in vivo. They will develop new algorithms for designing microbial communities to meet specific objectives and evaluate these design principles with experimental data. 

Here’s What You’ll Do:

• Identify metabolite-microbe associations from longitudinal datasets.
• Develop intervention strategies for controlling microbial community behavior. 
• Develop new analytical workflows for paired analysis of metabolomics and DNA sequencing data
• Analyze, interpret, and manage bacterial growth data from hundreds of experiments.
• Collaborate with our Bioinformatics team to automate and scale analytics methods to optimize reproducibility and turnaround time.
• Integrate metabolomics data from in vitro experiments with Vedanta’s bacterial strain library to better characterize metabolic behavior across the library.
• Support Process Development efforts to improve and understand bacterial fermentation processes.
• Support Analytical Development in efforts to characterize Live Biotherapeutic Products using novel sequencing methods.

Requirements:

• PhD in the life sciences or engineering, or MS/BS with at least 5 years of post-degree experience. 
• Significant experience with time-series modeling (mechanistic or data-driven) OR genome-scale metabolic network modeling. Experience applying these approaches to study bacteria preferred.
• Demonstrated experience programming with Python (please share links to public code contributions or projects, e.g., a github/gitlab profile, in your resume or cover letter if available).
• Command line experience in Unix-like systems (e.g., Linux, macOS, Windows Subsystem for Linux). 

Preferred Qualifications

• Experience analyzing metabolomics and/or sequencing data in microbial ecology studies. Previous work with gut microbes is a plus.
• Knowledge of compositional data analysis methods for studying microbial communities.
• Experience analyzing processed metabolomics data (e.g., relative intensities or absolute concentrations). Familiarity with processing raw spectra from any equipment (NMR/MS) is a plus.
• Experience combining supervised machine learning with mechanistic/hypothesis-based models.
• Experience formulating and solving optimization problems is a plus (linear programming, integer programming).
• Previous wet lab experience, especially with automation, is a plus (but this role does not involve performing wet lab experiments).
• 3+ years writing Python code.
• Experience with git, Amazon Web Services, and Jupyter. Experience with Nextflow is a plus.