Machine learning methods for microbiome studies

Autism Spectrum Disorder and the Gut Microbiota in Children: A Systematic Review

(2020) Navya Bezawada et al.   ANNALS OF NUTRITION AND METABOLISM

The neuroactive potential of the human gut microbiota in quality of life and depression

(2019) Mireia Valles-Colomer et al.   Nature Microbiology

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

(2019) Michael Zimmermann et al.   SCIENCE

The role of inflammation and the gut microbiome in depression and anxiety

(2019) Jason M. Peirce et al.   JOURNAL OF NEUROSCIENCE RESEARCH

MetaNN: accurate classification of host phenotypes from metagenomic data using neural networks

(2019) Chieh Lo et al.   BMC BIOINFORMATICS

Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

(2019) Gil Sharon et al.   CELL

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Machine learning to predict microbial community functions: An analysis of dissolved organic carbon from litter decomposition

(2019) Jaron Thompson et al.   PLoS One

Long-term benefit of Microbiota Transfer Therapy on autism symptoms and gut microbiota

(2019) Dae-Wook Kang et al.   Scientific Reports

Association Between Gut Microbiota and Autism Spectrum Disorder: A Systematic Review and Meta-Analysis

(2019) Mingyu Xu et al.   Frontiers in Psychiatry

Application of machine learning techniques for creating urban microbial fingerprints

(2019) Feargal Joseph Ryan   Biology Direct

Interplay between the human gut microbiome and host metabolism

(2019) Alessia Visconti et al.   Nature Communications

MicroPheno: predicting environments and host phenotypes from 16S rRNA gene sequencing using a k-mer based representation of shallow sub-samples

(2018) Ehsaneddin Asgari et al.   BIOINFORMATICS

Progress of analytical tools and techniques for human gut microbiome research

(2018) Eun-Ji Song et al.   JOURNAL OF MICROBIOLOGY

Taxonomic classification for microbiome analysis, which correlates well with the metabolite milieu of the gut

(2018) Yoshihisa Wakita et al.   BMC MICROBIOLOGY

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) Claire Duvallet et al.   Nature Communications

Gene expression-based biomarkers for discriminating early and late stage of clear cell renal cancer

(2017) Sherry Bhalla et al.   Scientific Reports

Clustering of Subgingival Microbiota Reveals Microbial Disease Ecotypes Associated with Clinical Stages of Periodontitis in a Cross-Sectional Study

(2017) Sébastien Boutin et al.   Frontiers in Microbiology

Normalization and microbial differential abundance strategies depend upon data characteristics

(2017) Sophie Weiss et al.   Microbiome

A Machine Learning Approach for Using the Postmortem Skin Microbiome to Estimate the Postmortem Interval

(2017) Hunter R. Johnson et al.   PLoS One

Molecular subtypes of pancreatic cancer based on miRNA expression profiles have independent prognostic value

(2016) Junghyun Namkung et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Glycosyltransferase Gene Expression Profiles Classify Cancer Types and Propose Prognostic Subtypes

(2016) Jahanshah Ashkani et al.   Scientific Reports

Gut microbiota and obesity

(2015) Philippe Gérard   CELLULAR AND MOLECULAR LIFE SCIENCES

Potential of fecal microbiota for early-stage detection of colorectal cancer

(2014) G. Zeller et al.   Molecular Systems Biology

Ensemble Positive Unlabeled Learning for Disease Gene Identification

(2014) Peng Yang et al.   PLoS One

Diabetes, obesity and gut microbiota

(2013) Amandine Everard et al.   BEST PRACTICE & RESEARCH IN CLINICAL GASTROENTEROLOGY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Human Gut Microbiota Changes Reveal the Progression of Glucose Intolerance

(2013) Xiuying Zhang et al.   PLoS One

The Human Microbiome: Our Second Genome

(2012) Elizabeth A. Grice et al.   Annual Review of Genomics and Human Genetics

Positive-unlabeled learning for disease gene identification

(2012) Peng Yang et al.   BIOINFORMATICS

Tumor Classification of Six Common Cancer Types Based on Proteomic Profiling by MALDI Imaging

(2012) Stephan Meding et al.   JOURNAL OF PROTEOME RESEARCH

The gut microbiota, obesity and insulin resistance

(2012) Jian Shen et al.   MOLECULAR ASPECTS OF MEDICINE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization

(2012) Xingpeng Jiang et al.   PLoS One

AUC-RF: A New Strategy for Genomic Profiling with Random Forest

(2011) M. Luz Calle et al.   HUMAN HEREDITY

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges

(2011) Susanne Schmitt et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Study Design, Precision, and Validity in Observational Studies

(2009) Melissa D.A. Carlson et al.   JOURNAL OF PALLIATIVE MEDICINE