Pharmacometabonomics: data processing and statistical analysis

J Fu, Y Zhang, J Liu, X Lian, J Tang… - Briefings in …, 2021 - academic.oup.com
Individual variations in drug efficacy, side effects and adverse drug reactions are still
challenging that cannot be ignored in drug research and development. The aim of …

[HTML][HTML] Statistical and computational methods for integrating microbiome, host genomics, and metabolomics data

RA Deek, S Ma, J Lewis, H Li - eLife, 2024 - elifesciences.org
Large-scale microbiome studies are progressively utilizing multiomics designs, which
include the collection of microbiome samples together with host genomics and …

[HTML][HTML] Discrimination of missing data types in metabolomics data based on particle swarm optimization algorithm and XGBoost model

Y Yuan, J Du, J Luo, Y Zhu, Q Huang, M Zhang - Scientific Reports, 2024 - nature.com
In the field of data analysis, it is often faced with a large number of missing values, especially
in metabolomics data, this problem is more prominent. Data imputation is a common method …

Unconjugated bilirubin is associated with protection from early-life wheeze and childhood asthma

KN Turi, C McKennan, T Gebretsadik, B Snyder… - Journal of Allergy and …, 2021 - Elsevier
Background Wheeze and allergic sensitization are the strongest early-life predictors of
childhood asthma development; the molecular origins of these early-life phenotypes are …

Discovering metabolite quantitative trait loci in asthma using an isolated population

RK Johnson, T Brunetti, K Quinn, K Doenges… - Journal of Allergy and …, 2022 - Elsevier
Background Integration of metabolomics with genetics may advance understanding of
disease pathogenesis but has been underused in asthma genetic studies. Objective We …

[HTML][HTML] MIRTH: Metabolite imputation via rank-transformation and harmonization

BA Freeman, S Jaro, T Park, S Keene, W Tansey… - Genome Biology, 2022 - Springer
Out of the thousands of metabolites in a given specimen, most metabolomics experiments
measure only hundreds, with poor overlap across experimental platforms. Here, we describe …

High-dimensional logistic regression with missing data: Imputation, regularization, and universality

KA Verchand, A Montanari - arXiv preprint arXiv:2410.01093, 2024 - arxiv.org
We study high-dimensional, ridge-regularized logistic regression in a setting in which the
covariates may be missing or corrupted by additive noise. When both the covariates and the …

Estimation beyond Missing (Completely) at Random

T Ma, KA Verchand, TB Berrett, T Wang… - arXiv preprint arXiv …, 2024 - arxiv.org
We study the effects of missingness on the estimation of population parameters. Moving
beyond restrictive missing completely at random (MCAR) assumptions, we first formulate a …

[HTML][HTML] Plasma 25-hydroxyvitamin D concentrations are associated with polyunsaturated fatty acid metabolites in young children: Results from the vitamin d antenatal …

M Huang, RS Kelly, P Kachroo, SH Chu, K Lee-Sarwar… - Metabolites, 2020 - mdpi.com
Vitamin D deficiency contributes to a multitude of health conditions, but its biological
mechanisms are not adequately understood. Untargeted metabolomics offers the …

A statistical framework for GWAS of high dimensional phenotypes using summary statistics, with application to metabolite GWAS

W Huang, EC Hector, J Cape, C McKennan - arXiv preprint arXiv …, 2023 - arxiv.org
The recent explosion of genetic and high dimensional biobank and'omic'data has provided
researchers with the opportunity to investigate the shared genetic origin (pleiotropy) of …