Statistical normalization methods in microbiome data with application to microbiome cancer research

Y **a - Gut microbes, 2023 - Taylor & Francis
Mounting evidence has shown that gut microbiome is associated with various cancers,
including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have …

[HTML][HTML] Review and revamp of compositional data transformation: A new framework combining proportion conversion and contrast transformation

Y Zhang, J Schluter, L Zhang, X Cao, RR Jenq… - Computational and …, 2024 - Elsevier
Due to the development of next-generation sequencing technology and an increased
appreciation of their role in modulating host immunity and their potential as therapeutic …

Beyond normalization: incorporating scale uncertainty in microbiome and gene expression analysis

MP Nixon, GB Gloor, JD Silverman - Biorxiv, 2024 - pmc.ncbi.nlm.nih.gov
Though statistical normalizations are often used in differential abundance or differential
expression analysis to address sample-to-sample variation in sequencing depth, we offer a …

Assessment of Distinct Gut Microbiome Signatures in a Diverse Cohort of Patients Undergoing Definitive Treatment for Rectal Cancer

DM Hein, LA Coughlin, N Poulides… - Journal of …, 2024 - meridian.allenpress.com
Introduction Disparities in incidence and outcome of rectal cancer are multifactorial in
etiology but may be due, in part, to differences in gut microbiome composition. We used …

Explicit Scale Simulation for analysis of RNA-sequencing with ALDEx2

GB Gloor, MP Nixon, JD Silverman - bioRxiv, 2023 - biorxiv.org
In high-throughput sequencing (HTS) studies, sample-to-sample variation in sequencing
depth is driven by technical factors, and not by variation in the scale (eg, total size, microbial …