Genotype to Phenotype: Design of an Extensible Experimental Platform for Characterizing Microbes
Creators
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Jensen, Paul Anthony
(Researcher)1
-
Al Habib, Shantal
(Researcher)2
-
Baker, Scott
(Researcher)3
- Bernstein, David (Researcher)4
- David, Benjamin (Researcher)1
-
DeBenedictis, Erika
(Researcher)2
-
Eisen, Jonathan A.
(Researcher)5
-
Fitch, Lauren
(Researcher)6
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Hoarfrost, Adrienne
(Researcher)7
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Knight-Connoni, Victoria
(Researcher)8
-
Koblitz, Julia
(Researcher)9
-
Mahadevan, Radhakrishnan
(Researcher)10
- Milshteyn, Sasha (Researcher)11
-
Nattermann, Una
(Researcher)12
-
Reimer, Lorenz Christian
(Researcher)9
-
Stork, Devon
(Researcher)12
-
Surae, Satnam
(Researcher)13
- Winnifrith, Adam (Researcher)14
-
Wood-Charlson, Elisha M.
(Researcher)15
- Kelly, Peter (Researcher)2
-
1.
University of Michigan
-
2.
Align to Innovate
-
3.
Pacific Northwest National Laboratory
-
4.
University of Vermont
-
5.
University of California, Davis
- 6. ArkeaBio
-
7.
University of Georgia
- 8. ATCC
-
9.
Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures
-
10.
University of Toronto
- 11. Transition Biomining Inc.
- 12. Pioneer Labs
- 13. Twig Bio
-
14.
University of Oxford
-
15.
Lawrence Berkeley National Laboratory
Contributors
-
1.
University of Toronto
- 2. Tatta Bio
- 3. University of Wisconsin
Description
Currently, there are no predictive models of microbial growth under various conditions that utilize data generated specifically for machine learning applications, and that are collected under consistent experimental conditions. This project aims to develop an extensible experimental platform and standardized data ontology for collecting phenotypic measurements of microbes grown in various cultivation conditions. Our goal is to understand and predict how environmental conditions interact with microbial genotypes to affect phenotypes such as growth and function. To do this, we will generate a comprehensive, machine learning-ready dataset comprising growth data for 1,000 culturable microbial strains across 1,000 cultivation conditions, resulting in one million unique experiments. Each strain will be cultured under controlled conditions, and growth measurements will be systematically collected along with a suite of additional phenotypic assays. This dataset will provide a deeper understanding of microbial growth dynamics and phenotypes across diverse environmental conditions, ultimately enabling the development of robust predictive models
Files
10.5281_zenodo.14990500_GenotypeToPhenotype.pdf
Files
(4.2 MB)
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Additional details
Related works
- Cites
- Publication: 10.1038/s41564-023-01376-0 (DOI)
Dates
- Created
-
2025-03-13