Using MetaboAnalyst 3.0 for comprehensive metabolomics data analysis

J Xia, 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 …

Gene set analysis: challenges, opportunities, and future research

F Maleki, K Ovens, DJ Hogan, AJ Kusalik - Frontiers in genetics, 2020 - frontiersin.org
Gene set analysis methods are widely used to provide insight into high-throughput gene
expression data. There are many gene set analysis methods available. These methods rely …

MicrobiomeAnalyst 2.0: comprehensive statistical, functional and integrative analysis of microbiome data

Y Lu, G Zhou, J Ewald, Z Pang, T Shiri… - Nucleic Acids …, 2023 - academic.oup.com
Microbiome studies have become routine in biomedical, agricultural and environmental
sciences with diverse aims, including diversity profiling, functional characterization, and …

KOBAS-i: intelligent prioritization and exploratory visualization of biological functions for gene enrichment analysis

D Bu, H Luo, P Huo, Z Wang, S Zhang, Z He… - Nucleic acids …, 2021 - academic.oup.com
Gene set enrichment (GSE) analysis plays an essential role in extracting biological insight
from genome-scale experiments. ORA (overrepresentation analysis), FCS (functional class …

An inflammatory state remodels the immune microenvironment and improves risk stratification in acute myeloid leukemia

A Lasry, B Nadorp, M Fornerod, D Nicolet, H Wu… - Nature cancer, 2023 - nature.com
Acute myeloid leukemia (AML) is a hematopoietic malignancy with poor prognosis and
limited treatment options. Here we provide a comprehensive census of the bone marrow …

Using MicrobiomeAnalyst for comprehensive statistical, functional, and meta-analysis of microbiome data

J Chong, P Liu, G Zhou, J Xia - Nature protocols, 2020 - nature.com
MicrobiomeAnalyst is an easy-to-use, web-based platform for comprehensive analysis of
common data outputs generated from current microbiome studies. It enables researchers …

Using MetaboAnalyst 4.0 for comprehensive and integrative metabolomics data analysis

J Chong, DS Wishart, J Xia - 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] IL4I1 is a metabolic immune checkpoint that activates the AHR and promotes tumor progression

A Sadik, LFS Patterson, S Öztürk, SR Mohapatra… - Cell, 2020 - cell.com
Aryl hydrocarbon receptor (AHR) activation by tryptophan (Trp) catabolites enhances tumor
malignancy and suppresses anti-tumor immunity. The context specificity of AHR target …

Metabolic dynamics and prediction of gestational age and time to delivery in pregnant women

L Liang, MLH Rasmussen, B Piening, X Shen, S Chen… - Cell, 2020 - cell.com
Metabolism during pregnancy is a dynamic and precisely programmed process, the failure
of which can bring devastating consequences to the mother and fetus. To define a high …

Comprehensive genomic analysis identifies novel subtypes and targets of triple-negative breast cancer

MD Burstein, A Tsimelzon, GM Poage… - Clinical Cancer …, 2015 - AACR
Purpose: Genomic profiling studies suggest that triple-negative breast cancer (TNBC) is a
heterogeneous disease. In this study, we sought to define TNBC subtypes and identify …