Host-Microbiome (Gut-Brain Axis) 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 and we are obsessed with uncertainty quantification. The gut microbiome and host-microbiome interactions are our primary areas of focus at this time. One area of particular interest to us is the gut-brain axis.
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For this project there will be a special emphasis on integrating new data modalities into our models for probing host-microbe interactions. A few examples include: the use of digital ELISA to measure low abundance host inflammatory markers in feces (in collaboration with the Walt Lab) as well as the use of spatial transcriptomics (e.g. Multiplexed Error-Robust FISH (MERFISH)) to obtain measurements of the spatial organization of bacteria and their local transcriptional environment.
Other projects in the lab include the design of bacteriotherapies (bugs-as-drugs), developing methods to learn microbial dynamics at ecosystem-scale, studying the impact of phages on microbial communities, methods for tracking low abundance pathogens, and methods for integrating multiple data modalities and prior knowledge (from other studies, databases, or foundation models (e.g. Alphafold)) in time-series models. We focus on Bayesian methods that can propagate measurement uncertainty so that we can assess confidence in model parameters and to help prioritize follow-up experiments. ML techniques applied include: variational inference, Bayesian non-parametric models, discrete relaxation techniques (for making discrete models differentiable), and deep learning.
Qualifications
- PhD from a quantitative discipline (those with a pure bio background will be co-advised)
- Solid programming skills in Python; this isn’t a software engineering job, but 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) brief research statement (not to exceed 2 pages); (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.