[HTML][HTML] Statistical analysis of metagenomics data

ML Calle - Genomics & informatics, 2019 - ncbi.nlm.nih.gov
Understanding the role of the microbiome in human health and how it can be modulated is
becoming increasingly relevant for preventive medicine and for the medical management of …

Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities

D Jiang, CR Armour, C Hu, M Mei, C Tian… - Frontiers in …, 2019 - frontiersin.org
The advent of large-scale microbiome studies affords newfound analytical opportunities to
understand how these communities of microbes operate and relate to their environment …

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies

D Reichart, EL Lindberg, H Maatz, AMA Miranda… - Science, 2022 - science.org
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic
cardiomyopathy (ACM) convey high risks for the development of heart failure through …

Modeling idiopathic autism in forebrain organoids reveals an imbalance of excitatory cortical neuron subtypes during early neurogenesis

A Jourdon, F Wu, J Mariani, D Capauto, S Norton… - Nature …, 2023 - nature.com
Idiopathic autism spectrum disorder (ASD) is highly heterogeneous, and it remains unclear
how convergent biological processes in affected individuals may give rise to symptoms …

NetCoMi: network construction and comparison for microbiome data in R

S Peschel, CL Müller, E Von Mutius… - Briefings in …, 2021 - academic.oup.com
Motivation Estimating microbial association networks from high-throughput sequencing data
is a common exploratory data analysis approach aiming at understanding the complex …

Normalization and microbial differential abundance strategies depend upon data characteristics

S Weiss, ZZ Xu, S Peddada, A Amir, K Bittinger… - Microbiome, 2017 - Springer
Background Data from 16S ribosomal RNA (rRNA) amplicon sequencing present
challenges to ecological and statistical interpretation. In particular, library sizes often vary …

zCompositions—R package for multivariate imputation of left-censored data under a compositional approach

J Palarea-Albaladejo, JA Martín-Fernández - Chemometrics and Intelligent …, 2015 - Elsevier
Abstract zCompositions is an R package for the imputation of left-censored data under a
compositional approach. It is pertinent when the analyst assumes that the relevant …

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping

BS Beresford-Jones, SC Forster, MD Stares, G Notley… - Cell host & …, 2022 - cell.com
Human health and disease have increasingly been shown to be impacted by the gut
microbiota, and mouse models are essential for investigating these effects. However, the …

Meta-analysis reveals reproducible gut microbiome alterations in response to a high-fat diet

JE Bisanz, V Upadhyay, JA Turnbaugh, K Ly… - Cell host & …, 2019 - cell.com
Multiple research groups have shown that diet impacts the gut microbiome; however,
variability in experimental design and quantitative assessment have made it challenging to …

Compositional data analysis in time-use epidemiology: what, why, how

D Dumuid, Ž Pedišić, J Palarea-Albaladejo… - International journal of …, 2020 - mdpi.com
In recent years, the focus of activity behavior research has shifted away from univariate
paradigms (eg, physical activity, sedentary behavior and sleep) to a 24-h time-use paradigm …