4.7 Article

Guild-based analysis for understanding gut microbiome in human health and diseases

Related references

Note: Only part of the references are listed.
Article Biotechnology & Applied Microbiology

Malassezia and Staphylococcus dominate scalp microbiome for seborrheic dermatitis

Qingbin Lin et al.

Summary: Seborrheic dermatitis (SD) is a common disease of the human scalp, with dysbiosis of the scalp microbiome being associated with SD. Specific fungi and bacteria have been identified as potential biomarkers for SD. The etiology of SD is multi-pathogenetic-dependent on the linkage of several microbes with host.

BIOPROCESS AND BIOSYSTEMS ENGINEERING (2021)

Article Gastroenterology & Hepatology

Microbial imbalance in inflammatory bowel disease patients at different taxonomic levels

Mohammad Tauqeer Alam et al.

GUT PATHOGENS (2020)

Article Microbiology

Core Gut Bacteria Analysis of Healthy Mice

Jingjing Wang et al.

FRONTIERS IN MICROBIOLOGY (2019)

Review Oncology

Role of the intestinal microbiome in colorectal cancer surgery outcomes

Lelde Lauka et al.

WORLD JOURNAL OF SURGICAL ONCOLOGY (2019)

Article Biochemistry & Molecular Biology

Functional sequencing read annotation for high precision microbiome analysis

Chengsheng Zhu et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Microbiology

Deciphering the trophic interaction between Akkermansia muciniphila and the butyrogenic gut commensal Anaerostipes caccae using a metatranscriptomic approach

Loo Wee Chia et al.

ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY (2018)

Article Multidisciplinary Sciences

Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes

Liping Zhao et al.

SCIENCE (2018)

Editorial Material Genetics & Heredity

Causality in dietary interventions-building a case for gut microbiota

Yan Y. Lam et al.

GENOME MEDICINE (2018)

Article Microbiology

Evaluating the profound effect of gut microbiome on host appetite in pigs

Hui Yang et al.

BMC MICROBIOLOGY (2018)

Article Gastroenterology & Hepatology

Tumour-associated and non-tumour-associated microbiota in colorectal cancer

Burkhardt Flemer et al.

Article Biochemistry & Molecular Biology

Microbial strain-level population structure and genetic diversity from metagenomes

Duy Tin Truong et al.

GENOME RESEARCH (2017)

Article Multidisciplinary Sciences

Strains, functions and dynamics in the expanded Human Microbiome Project

Jason Lloyd-Price et al.

NATURE (2017)

Article Multidisciplinary Sciences

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

Michiru Nishita et al.

SCIENTIFIC REPORTS (2017)

Article Biochemistry & Molecular Biology

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Ron Caspi et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Biochemical Research Methods

MOCAT2: a metagenomic assembly, annotation and profiling framework

Jens Roat Kultima et al.

BIOINFORMATICS (2016)

Article Biochemical Research Methods

Weakly supervised learning of biomedical information extraction from curated data

Suvir Jain et al.

BMC BIOINFORMATICS (2016)

Review Biochemistry & Molecular Biology

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

Minoru Kanehisa et al.

JOURNAL OF MOLECULAR BIOLOGY (2016)

Review Multidisciplinary Sciences

Microbiome-wide association studies link dynamic microbial consortia to disease

Jack A. Gilbert et al.

NATURE (2016)

Article Biochemical Research Methods

DADA2: High-resolution sample inference from Illumina amplicon data

Benjamin J. Callahan et al.

NATURE METHODS (2016)

Review Microbiology

Metagenome-wide association studies: fine-mining the microbiome

Jun Wang et al.

NATURE REVIEWS MICROBIOLOGY (2016)

Review Medicine, General & Internal

The Human Intestinal Microbiome in Health and Disease

Susan V. Lynch et al.

NEW ENGLAND JOURNAL OF MEDICINE (2016)

Article Gastroenterology & Hepatology

Dysfunctional gut microbiota and relative co-abundance network in infantile eczema

Heping Wang et al.

Gut Pathogens (2016)

Article Genetics & Heredity

Strain-level dissection of the contribution of the gut microbiome to human metabolic disease

Chenhong Zhang et al.

GENOME MEDICINE (2016)

Article Biochemical Research Methods

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation

Roie Levy et al.

BMC BIOINFORMATICS (2015)

Article Forestry

A guild-based approach to assessing the influence of beech forest structure on bird communities

Rosario Balestrieri et al.

FOREST ECOLOGY AND MANAGEMENT (2015)

Article Biotechnology & Applied Microbiology

Comparative genomics of the Bifidobacterium breve taxon

Francesca Bottacini et al.

BMC GENOMICS (2014)

Article Biochemistry & Molecular Biology

Meta-analyses of human gut microbes associated with obesity and IBD

William A. Walters et al.

FEBS LETTERS (2014)

Article Food Science & Technology

Impact of Kamut® Khorasan on gut microbiota and metabolome in healthy volunteers

Danielle Taneyo Saa et al.

FOOD RESEARCH INTERNATIONAL (2014)

Article Mathematics, Interdisciplinary Applications

Ward's Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward's Criterion?

Fionn Murtagh et al.

JOURNAL OF CLASSIFICATION (2014)

Article Multidisciplinary Sciences

Diet rapidly and reproducibly alters the human gut microbiome

Lawrence A. David et al.

NATURE (2014)

Article Multidisciplinary Sciences

Alterations of the human gut microbiome in liver cirrhosis

Nan Qin et al.

NATURE (2014)

Article Biotechnology & Applied Microbiology

An integrated catalog of reference genes in the human gut microbiome

Junhua Li et al.

NATURE BIOTECHNOLOGY (2014)

Article Biotechnology & Applied Microbiology

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

H. Bjorn Nielsen et al.

NATURE BIOTECHNOLOGY (2014)

Article Gastroenterology & Hepatology

Inflammation and colorectal cancer, when microbiota-host mutualism breaks

Marco Candela et al.

WORLD JOURNAL OF GASTROENTEROLOGY (2014)

Article Multidisciplinary Sciences

Gut metagenome in European women with normal, impaired and diabetic glucose control

Fredrik H. Karlsson et al.

NATURE (2013)

Article Biochemical Research Methods

UPARSE: highly accurate OTU sequences from microbial amplicon reads

Robert C. Edgar

NATURE METHODS (2013)

Review Microbiology

The gut microbiota and obesity: from correlation to causality

Liping Zhao

NATURE REVIEWS MICROBIOLOGY (2013)

Article Multidisciplinary Sciences

Structural modulation of gut microbiota in life-long calorie-restricted mice

Chenhong Zhang et al.

NATURE COMMUNICATIONS (2013)

Review Biochemistry & Molecular Biology

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

Jose C. Clemente et al.

Article Multidisciplinary Sciences

Gut microbiota composition correlates with diet and health in the elderly

Marcus J. Claesson et al.

NATURE (2012)

Article Multidisciplinary Sciences

Structure, function and diversity of the healthy human microbiome

Curtis Huttenhower et al.

NATURE (2012)

Review Microbiology

Microbial interactions: from networks to models

Karoline Faust et al.

NATURE REVIEWS MICROBIOLOGY (2012)

Article Biochemical Research Methods

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

Sahar Abubucker et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

Inferring Correlation Networks from Genomic Survey Data

Jonathan Friedman et al.

PLOS COMPUTATIONAL BIOLOGY (2012)

Article Biochemical Research Methods

SmashCommunity: a metagenomic annotation and analysis tool

Manimozhiyan Arumugam et al.

BIOINFORMATICS (2010)

Review Biotechnology & Applied Microbiology

Assembly algorithms for next-generation sequencing data

Jason R. Miller et al.

GENOMICS (2010)

Article Multidisciplinary Sciences

A human gut microbial gene catalogue established by metagenomic sequencing

Junjie Qin et al.

NATURE (2010)

Article Biochemistry & Molecular Biology

Ab initio gene identification in metagenomic sequences

Wenhan Zhu et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Endocrinology & Metabolism

Microbiota and SCFA in Lean and Overweight Healthy Subjects

Andreas Schwiertz et al.

OBESITY (2010)

Article Multidisciplinary Sciences

A core gut microbiome in obese and lean twins

Peter J. Turnbaugh et al.

NATURE (2009)

Article Endocrinology & Metabolism

Human colonic microbiota associated with diet, obesity and weight loss

S. H. Duncan et al.

INTERNATIONAL JOURNAL OF OBESITY (2008)

Article Biotechnology & Applied Microbiology

Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy

Qiong Wang et al.

APPLIED AND ENVIRONMENTAL MICROBIOLOGY (2007)

Article Microbiology

DNA-DNA hybridization values and their relationship to whole-genome sequence similarities

Johan Goris et al.

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY (2007)

Article Multidisciplinary Sciences

Reducing the dimensionality of data with neural networks

G. E. Hinton et al.

SCIENCE (2006)

Article Biochemical Research Methods

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences

Weizhong Li et al.

BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

Obesity alters gut microbial ecology

RE Ley et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2005)

Article Multidisciplinary Sciences

Singular value decomposition for genome-wide expression data processing and modeling

O Alter et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2000)

Article Biochemistry & Molecular Biology

KEGG: Kyoto Encyclopedia of Genes and Genomes

M Kanehisa et al.

NUCLEIC ACIDS RESEARCH (2000)