Statistical challenges in longitudinal microbiome data analysis
The microbiome is a complex and dynamic community of microorganisms that co-exist
interdependently within an ecosystem, and interact with its host or environment. Longitudinal …
interdependently within an ecosystem, and interact with its host or environment. Longitudinal …
Dynamic interaction network inference from longitudinal microbiome data
Background Several studies have focused on the microbiota living in environmental niches
including human body sites. In many of these studies, researchers collect longitudinal data …
including human body sites. In many of these studies, researchers collect longitudinal data …
MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks
C Lo, R Marculescu - Proceedings of the 2018 ACM International …, 2018 - dl.acm.org
Recent studies have identified different microbiome profiles in healthy and sick individuals
for a variety of diseases; this suggests that the microbiome profile can be used as a …
for a variety of diseases; this suggests that the microbiome profile can be used as a …
Capturing the dynamics of microbial interactions through individual-specific networks
Longitudinal analysis of multivariate individual-specific microbiome profiles over time or
across conditions remains dauntin. Most statistical tools and methods that are available to …
across conditions remains dauntin. Most statistical tools and methods that are available to …
[HTML][HTML] Modeling microbial community networks: methods and tools
In the current research landscape, microbiota composition studies are of extreme interest,
since it has been widely shown that resident microorganisms affect and shape the …
since it has been widely shown that resident microorganisms affect and shape the …
Dynamic bayesian networks for integrating multi-omics time series microbiome data
ABSTRACT A key challenge in the analysis of longitudinal microbiome data is the inference
of temporal interactions between microbial taxa, their genes, the metabolites that they …
of temporal interactions between microbial taxa, their genes, the metabolites that they …
MPLasso: Inferring microbial association networks using prior microbial knowledge
C Lo, R Marculescu - PLoS computational biology, 2017 - journals.plos.org
Due to the recent advances in high-throughput sequencing technologies, it becomes
possible to directly analyze microbial communities in human body and environment. To …
possible to directly analyze microbial communities in human body and environment. To …
Capturing the dynamics of microbiomes using individual-specific networks
Background Longitudinal analysis of multivariate individual-specific microbiome profiles
over time or across conditions remains a daunting task. The vast majority of statistical tools …
over time or across conditions remains a daunting task. The vast majority of statistical tools …
Nested inference of pairwise interactions from strain frequency data across settings and context-dependent mutual invasibilities
How does coexistence of multiple species or pathogen strains arise in a system? What do
coexistence patterns in time and space reveal about the epidemiology, ecology and …
coexistence patterns in time and space reveal about the epidemiology, ecology and …
Multivariate statistical monitoring system for microbial population dynamics
K Ishiya, S Aburatani - Physical Biology, 2021 - iopscience.iop.org
Microbiomes in their natural environments vary dynamically with changing environmental
conditions. The detection of these dynamic changes in microbial populations is critical for …
conditions. The detection of these dynamic changes in microbial populations is critical for …