Bacteriotherapy design, “bugs-as-drugs” (using control theory principles) Postdoctoral Fellow
Opening for a Postdoctoral Research Fellow to join the Gibson Lab at Harvard Medical School (HMS), Brigham and Women’s Hospital (BWH), and the Broad Institute of MIT and Harvard. We leverage tools from machine learning (ML) and control theory to better understand biological systems. While specific research questions may evolve over time, a key hallmark of our work is the careful co-design of computational and experimental models. Biological systems are simply too complex to be probed through either paradigm alone.
This specific project is focused on designing bacteriotherapies using control theory principles. Bacteriotherapies are defined communities of bacteria for use as a therapeutic (“bugs-as-drugs”). We have already completed dense time series gnotobiotic studies with humanized (pre-print) and conventional mice (unpublished - ongoing NSF project), and using models trained on that data you will design cocktails of bacteria that will then be tested in mouse experiments that will be carried out by our friends in the Massachusetts Host Microbiome Center. You will also have the opportunity to develop your own models for learning dynamics from longitudinal data. These new models may include using neural ODEs, integrating multiple data modalities (including spatial), or even using embeddings from large DNA sequence models as priors in the model.
Qualifications
- PhD from a quantitative discipline or direct experience with the research topic in the posting
- Solid programming skills in Python; you will need to be able to develop efficient implementations and apply your work to real data
- Strong publication track record
- Ability to reside in the U.S. and legally work in the country.
About the lab and fellow appointment
The Gibson Lab is physically located in the Division of Computational Pathology at BWH. All fellows have a triple appointment at BWH, HMS and the Broad. If necessary to conduct you work an official appointment at MIT can also be secured. For more information please go to the lab website: https://gibsonlab.io
Applications Process
Submit: (1) cover letter or research statement; (2) curriculum vitae; (3) two most relevant publications; (4) names and contact information of three individuals who can serve as references to: Travis Gibson, tegibson@bwh.harvard.edu. If you wish to chat briefly over Zoom before submitting materials to learn more details about our ongoing work, please inquire about this possibility