DisBalance: a platform to automatically build balance-based disease prediction models and discover microbial biomarkers from microbiome data

The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants

(2021) Anders B. Dohlman et al.   Cell Host & Microbe

MicroPhenoDB Associates Metagenomic Data with Pathogenic Microbes, Microbial Core Genes, and Human Disease Phenotypes

(2021) Guocai Yao et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

A pilot integrative analysis of colonic gene expression, gut microbiota and immune infiltration in primary sclerosing cholangitis-inflammatory bowel disease: association of disease with bile acid pathways

(2020) Mohammed Nabil Quraishi et al.   Journal of Crohns & Colitis

Effects of Primary Sclerosing Cholangitis on Risks of Cancer and Death in People With Inflammatory Bowel Diseases, Based on Sex, Race, and Age

(2020) Palak J. Trivedi et al.   GASTROENTEROLOGY

Updated review of research on the gut microbiota and their relation to depression in animals and human beings

(2020) Zhongli Yang et al.   MOLECULAR PSYCHIATRY

AI finds microbial signatures in tumours and blood across cancer types

(2020) Nadim J. Ajami et al.   NATURE

Colonic microbiota is associated with inflammation and host epigenomic alterations in inflammatory bowel disease

(2020) F. J. Ryan et al.   Nature Communications

Interpretable Log Contrasts for the Classification of Health Biomarkers: a New Approach to Balance Selection

(2020) Thomas P. Quinn et al.   mSystems

Review article: bugs, inflammation and mood-a microbiota-based approach to psychiatric symptoms in inflammatory bowel diseases

(2020) Anne K. Thomann et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Major Trends in Gastroenterology and Hepatology Between 2010 and 2019

(2020) J.S. Bajaj et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

An ecological framework to understand the efficacy of fecal microbiota transplantation

(2020) Yandong Xiao et al.   Nature Communications

A comparison of isometric and amalgamation logratio balances in compositional data analysis

(2020) Michael Greenacre et al.   COMPUTERS & GEOSCIENCES

Pathophysiology of Inflammatory Bowel Diseases

(2020) John T. Chang   NEW ENGLAND JOURNAL OF MEDICINE

Heat Shock Factor 1-dependent extracellular matrix remodeling mediates the transition from chronic intestinal inflammation to colon cancer

(2020) Oshrat Levi-Galibov et al.   Nature Communications

The role of the gut microbiome and its metabolites in metabolic diseases

(2020) Jiayu Wu et al.   Protein & Cell

GutBalance: a server for the human gut microbiome-based disease prediction and biomarker discovery with compositionality addressed

(2020) Fenglong Yang et al.   BRIEFINGS IN BIOINFORMATICS

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Risk of colorectal cancer in inflammatory bowel diseases

(2019) Muhammad Shahid Nadeem et al.   SEMINARS IN CANCER BIOLOGY

GMrepo: a database of curated and consistently annotated human gut metagenomes

(2019) Sicheng Wu et al.   NUCLEIC ACIDS RESEARCH

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

Microbiome Multi-Omics Network Analysis: Statistical Considerations, Limitations, and Opportunities

(2019) Duo Jiang et al.   Frontiers in Genetics

Understanding sequencing data as compositions: an outlook and review

(2018) Thomas P Quinn et al.   BIOINFORMATICS

Variable Selection in Compositional Data Analysis Using Pairwise Logratios

(2018) Michael Greenacre   Mathematical Geosciences

Urbanization and the gut microbiota in health and inflammatory bowel disease

(2018) Tao Zuo et al.   Nature Reviews Gastroenterology & Hepatology

Balances: a New Perspective for Microbiome Analysis

(2018) J. Rivera-Pinto et al.   mSystems

The Gut Microbiota and Autism Spectrum Disorders

(2017) Qinrui Li et al.   Frontiers in Cellular Neuroscience

A phylogenetic transform enhances analysis of compositional microbiota data

(2017) Justin D Silverman et al.   eLife

Microbiome Datasets Are Compositional: And This Is Not Optional

(2017) Gregory B. Gloor et al.   Frontiers in Microbiology

Balance Trees Reveal Microbial Niche Differentiation

(2017) James T. Morton et al.   mSystems

propr: An R-package for Identifying Proportionally Abundant Features Using Compositional Data Analysis

(2017) Thomas P. Quinn et al.   Scientific Reports

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

It's all relative: analyzing microbiome data as compositions

(2016) Gregory B. Gloor et al.   ANNALS OF EPIDEMIOLOGY

Compositional analysis: a valid approach to analyze microbiome high-throughput sequencing data

(2016) Gregory B. Gloor et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Impact of the gut microbiota on inflammation, obesity, and metabolic disease

(2016) Claire L. Boulangé et al.   Genome Medicine

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

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

(2015) Hongzhe Li   Annual Review of Statistics and Its Application

The Microbiome in Inflammatory Bowel Disease: Current Status and the Future Ahead

(2014) Aleksandar D. Kostic et al.   GASTROENTEROLOGY

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Ulcerative Colitis Complicated with Primary Biliary Cirrhosis

(2011) Fujimasa Tada et al.   INTERNAL MEDICINE

Normal gut microbiota modulates brain development and behavior

(2011) R. D. Heijtz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Balance-dendrogram. A new routine of CoDaPack

(2008) S. Thió-Henestrosa et al.   COMPUTERS & GEOSCIENCES