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ARS Home » Pacific West Area » Davis, California » Western Human Nutrition Research Center » Immunity and Disease Prevention Research » Research » Research Project #444878

Research Project: Advancing Methods and Applications in Metagenomics Sequence Analysis

Location: Immunity and Disease Prevention Research

Project Number: 2032-51530-026-040-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Sep 11, 2023
End Date: Oct 31, 2025

This collaborative project with UC Davis is extending a longstanding research collaboration between the Western Human Nutrition Research Center (WHNRC) and the University of California, Davis (UCD) that currently includes a postdoctoral researcher funded by the Agricultural Research Service (ARS) via the Oak Ridge Institute for Science and Education (ORISE) program. This postdoctoral fellow is jointly supervised by the WHNRC research scientist and the UCD collaborator and is working in the collaborator’s laboratory for the purpose of analyzing DNA sequence data from WHNRC study samples to develop new methods to characterize the functional capacity of the intestinal microbome by developing and applying new Artificial Intelligence (AI) methods. The objective of the current project is to adapt AI predictions of protein structure to better annotation of microbial sequences via structural homology and to apply new methods to metagenome and metatranscriptome sequencing projects.

Aim 1) Using AI methods, predict protein structures of microbial genes. Conduct alignment of candidate sequences using structural homology and evaluate against existing methods using sequence homology using microbial genes that have been experimentally validated. Aim 2) Sequence samples from the Mouse Fiber Diversity Study and the WHNRC Fiber Intervention Study and apply techniques developed in Aim 1.