About the Talk
Presenter
Assoc. Prof. Dr. Niranjan Nagarajan
Dr. Nagarajan is Associate Director and Senior Group Leader at the Genome Institute of Singapore, and Associate Professor in the Department of Medicine and the Department of Computer Science at the National University of Singapore. His research focuses on developing state-of-the-art genome analytics tools and using them to study the role of microbial communities in human health. His team works at the interface of genetics, computer science and microbiology, using a systems biology approach to understand host–microbiome–pathogen interactions in a range of disease conditions.
Abstract
The structure and function of diverse microbial communities is underpinned by undefined ecological interactions. With the rapid adoption of next-generation sequencing to study microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but has the disadvantage that ecological interpretation is not possible. We present an expectation maximisation algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalised Lotka–Volterra). Benchmarking against ten state-of-the-art correlation-based methods showed that BEEM-Static can infer the presence and direction of ecological interactions even with relative abundance data (AUC-ROC > 0.85). Applying BEEM-Static to a large public dataset of human gut microbiomes (n = 4,617) identified multiple stable equilibria that better reflect ecological enterotypes.
Date: April 13th, 2021 – 10:00 AM (GMT+3)
Language: English