Best practices for analysing microbiomes

R Knight, A Vrbanac, BC Taylor, A Aksenov… - Nature Reviews …, 2018 - nature.com
Complex microbial communities shape the dynamics of various environments, ranging from
the mammalian gastrointestinal tract to the soil. Advances in DNA sequencing technologies …

Multi-omic integration of microbiome data for identifying disease-associated modules

E Muller, I Shiryan, E Borenstein - Nature Communications, 2024 - nature.com
Multi-omic studies of the human gut microbiome are crucial for understanding its role in
disease across multiple functional layers. Nevertheless, integrating and analyzing such …

[KNIHA][B] Multivariate data integration using R: methods and applications with the mixOmics package

KA Lê Cao, ZM Welham - 2021 - taylorfrancis.com
Large biological data, which are often noisy and high-dimensional, have become
increasingly prevalent in biology and medicine. There is a real need for good training in …

The changes of immunoglobulin G N-glycosylation in blood lipids and dyslipidaemia

D Liu, X Chu, H Wang, J Dong, SQ Ge, ZY Zhao… - Journal of translational …, 2018 - Springer
Background Alternative N-glycosylation has significant structural and functional
consequences on immunoglobulin G (IgG) and can affect immune responses, acting as a …

The statistical theory of linear selection indices from phenotypic to genomic selection

JJ Cerón‐Rojas, J Crossa - Crop Science, 2022 - Wiley Online Library
A linear selection index (LSI) can be a linear combination of phenotypic values, marker
scores, and genomic estimated breeding values (GEBVs); phenotypic values and marker …

sjive: Supervised joint and individual variation explained

EF Palzer, CH Wendt, RP Bowler, CP Hersh… - … statistics & data analysis, 2022 - Elsevier
Analyzing multi-source data, which are multiple views of data on the same subjects, has
become increasingly common in molecular biomedical research. Recent methods have …

Multi-region brain transcriptomes uncover two subtypes of aging individuals with differences in Alzheimer risk and the impact of APOEε4

AJ Lee, Y Ma, L Yu, RJ Dawe, C McCabe, K Arfanakis… - bioRxiv, 2023 - biorxiv.org
The heterogeneity of the older population suggests the existence of subsets of individuals
which share certain brain molecular features and respond differently to risk factors for …

Searching for a technology-driven acute rheumatic fever test: the START study protocol

AP Ralph, R Webb, NJ Moreland, R McGregor… - BMJ open, 2021 - bmjopen.bmj.com
Introduction The absence of a diagnostic test for acute rheumatic fever (ARF) is a major
impediment in managing this serious childhood condition. ARF is an autoimmune condition …

Longitudinal canonical correlation analysis

S Lee, J Choi, Z Fang… - Journal of the Royal …, 2023 - academic.oup.com
This paper considers canonical correlation analysis for two longitudinal variables that are
possibly sampled at different time resolutions with irregular grids. We modelled trajectories …

Model-based joint visualization of multiple compositional omics datasets

S Hawinkel, L Bijnens, KAL Cao… - NAR Genomics and …, 2020 - academic.oup.com
The integration of multiple omics datasets measured on the same samples is a challenging
task: data come from heterogeneous sources and vary in signal quality. In addition, some …