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 …

Functional effects of the microbiota in chronic respiratory disease

KF Budden, SD Shukla, SF Rehman… - The lancet Respiratory …, 2019 - thelancet.com
The composition of the lung microbiome is increasingly well characterised, with changes in
microbial diversity or abundance observed in association with several chronic respiratory …

Microbiome-wide association studies link dynamic microbial consortia to disease

JA Gilbert, RA Quinn, J Debelius, ZZ Xu, J Morton… - Nature, 2016 - nature.com
Rapid advances in DNA sequencing, metabolomics, proteomics and computational tools are
dramatically increasing access to the microbiome and identification of its links with disease …

Molecular networking as a drug discovery, drug metabolism, and precision medicine strategy

RA Quinn, LF Nothias, O Vining, M Meehan… - Trends in …, 2017 - cell.com
Molecular networking is a tandem mass spectrometry (MS/MS) data organizational
approach that has been recently introduced in the drug discovery, metabolomics, and …

The gut–liver axis in sepsis: interaction mechanisms and therapeutic potential

X Zhang, H Liu, K Hashimoto, S Yuan, J Zhang - Critical care, 2022 - Springer
Sepsis is a potentially fatal condition caused by dysregulation of the body's immune
response to an infection. Sepsis-induced liver injury is considered a strong independent …

Computational metabolomics: a framework for the million metabolome

K Uppal, DI Walker, K Liu, S Li, YM Go… - Chemical research in …, 2016 - ACS Publications
“Sola dosis facit venenum.” These words of Paracelsus,“the dose makes the poison”, can
lead to a cavalier attitude concerning potential toxicities of the vast array of low abundance …

Recent advances in metabolism and toxicity of tyrosine kinase inhibitors

Q Zhao, ZE Wu, B Li, F Li - Pharmacology & Therapeutics, 2022 - Elsevier
Small molecule tyrosine kinase inhibitors (TKIs) are widely used as anticancer drugs
approved by US FDA. However, the toxicities of TKIs to multiple organs have greatly limited …

[HTML][HTML] A restructuring of microbiome niche space is associated with Elexacaftor-Tezacaftor-Ivacaftor therapy in the cystic fibrosis lung

LM Sosinski, KA Neugebauer, LAJ Ghuneim… - Journal of Cystic …, 2022 - Elsevier
Abstract Background Elexacaftor-Tezacaftor-Ivacaftor (ETI) therapy is showing promising
efficacy for treatment of cystic fibrosis (CF) and is becoming more widely available since …

Longitudinal microbial and molecular dynamics in the cystic fibrosis lung after Elexacaftor–Tezacaftor–Ivacaftor therapy

C Martin, DV Guzior, CT Gonzalez, M Okros… - Respiratory …, 2023 - Springer
Background Cystic fibrosis (CF) is a genetic disorder causing poor mucociliary clearance in
the airways and subsequent respiratory infection. The recently approved triple therapy …

Uncovering the Carboxylated Metabolome in Gut Microbiota–Host Co-metabolism: A Chemical Derivatization-Molecular Networking Approach

YZ Wang, YY Chen, XZ Wu, PR Bai, N An… - Analytical …, 2023 - ACS Publications
Gut microbiota–host co-metabolites serve as essential mediators of communication between
the host and gut microbiota. They provide nutrient sources for host cells and regulate gut …