Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis

J **a, DS Wishart - Current protocols in bioinformatics, 2016‏ - Wiley Online Library
Abstract MetaboAnalyst (http://www. metaboanalyst. ca) is a comprehensive Web application
for metabolomic data analysis and interpretation. MetaboAnalyst handles most of the …

Guiding the choice of informatics software and tools for lipidomics research applications

Z Ni, M Wölk, G Jukes, K Mendivelso Espinosa… - Nature …, 2023‏ - nature.com
Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across
biology and biomedicine. These generate extremely large raw datasets requiring …

[HTML][HTML] Tau PTM profiles identify patient heterogeneity and stages of Alzheimer's disease

H Wesseling, W Mair, M Kumar, CN Schlaffner, S Tang… - Cell, 2020‏ - cell.com
To elucidate the role of Tau isoforms and post-translational modification (PTM) stoichiometry
in Alzheimer's disease (AD), we generated a high-resolution quantitative proteomics map of …

Using MetaboAnalyst 4.0 for comprehensive and integrative metabolomics data analysis

J Chong, DS Wishart, J **a - Current protocols in bioinformatics, 2019‏ - Wiley Online Library
Abstract MetaboAnalyst (https://www. metaboanalyst. ca) is an easy‐to‐use web‐based tool
suite for comprehensive metabolomic data analysis, interpretation, and integration with other …

[HTML][HTML] Enterosignatures define common bacterial guilds in the human gut microbiome

C Frioux, R Ansorge, E Özkurt, CG Nedjad, J Fritscher… - Cell Host & Microbe, 2023‏ - cell.com
The human gut microbiome composition is generally in a stable dynamic equilibrium, but it
can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent …

Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation

H **, C Zhang, M Zwahlen, K Von Feilitzen… - Nature …, 2023‏ - nature.com
Cell lines are valuable resources as model for human biology and translational medicine. It
is thus important to explore the concordance between the expression in various cell lines vis …

An atlas of genetic scores to predict multi-omic traits

Y Xu, SC Ritchie, Y Liang, PRHJ Timmers, M Pietzner… - Nature, 2023‏ - nature.com
The use of omic modalities to dissect the molecular underpinnings of common diseases and
traits is becoming increasingly common. But multi-omic traits can be genetically predicted …

Clinical, radiological, and laboratory characteristics and risk factors for severity and mortality of 289 hospitalized COVID‐19 patients

J Zhang, Y Cao, G Tan, X Dong, B Wang, J Lin, Y Yan… - Allergy, 2021‏ - Wiley Online Library
Background The coronavirus disease 2019 (COVID‐19) has become a global pandemic,
with 10%‐20% of severe cases and over 508 000 deaths worldwide. Objective This study …

Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor

SMA Islam, M Díaz-Gay, Y Wu, M Barnes, R Vangara… - Cell genomics, 2022‏ - cell.com
Mutational signature analysis is commonly performed in cancer genomic studies. Here, we
present SigProfilerExtractor, an automated tool for de novo extraction of mutational …

Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair

FC Simões, TJ Cahill, A Kenyon… - Nature …, 2020‏ - nature.com
Canonical roles for macrophages in mediating the fibrotic response after a heart attack
include extracellular matrix turnover and activation of cardiac fibroblasts to initiate collagen …