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Evolutionary-scale interpretation of protein functions in the human gut microbiome

Research Project
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01.10.2023
 - 30.09.2027

Thanks to over a decade of metagenomics efforts, we have a catalogue of over 170 million unique putative proteins from the human gut microbiome. About 40% of these do not have function assigned (dark proteins), hence limiting our understanding of the well-established relationship between the gut microbiome and human health. Current homology-based methods used for functional assignment have reached their limits because of the availability of reference data. But we are now in a new Era of computational biology, where deep-learning-based approaches allow us to predict protein structures (e.g. AlphaFold2), functions (e.g. deepFRI), and molecular mechanisms at extremely high levels of detail. This opens the door to further model protein interactions and remote evolutionary relationships (e.g. the Protein Universe Atlas) at unprecedented scales. Following up on these developments, our aim is to construct an integrative view of putative molecular functions and biological roles of proteins from the human gut microbiome by combining deep learning-driven, structure-based function prediction with a large-scale view of the protein universe.

Funding

Evolutionary-scale interpretation of protein functions in the human gut microbiome

SNF Projekt (GrantsTool), 10.2023-09.2027 (48)
PI : Schwede, Torsten.
CI : Soares Pereira, Joana Maria.

Members (3)

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Torsten Schwede

Principal Investigator
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Joana Maria Soares Pereira

Co-Investigator
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Tomasz Kosciolek

Co-Investigator