‘NetShift’: a methodology for understanding ‘driver microbes’ from healthy and disease microbiome datasets

Structure and co-occurrence patterns in microbial communities under acute environmental stress reveal ecological factors fostering resilience

(2018) Dinka Mandakovic et al.   Scientific Reports

‘TIME’: A Web Application for Obtaining Insights into Microbial Ecology Using Longitudinal Microbiome Data

(2018) Krishanu D. Baksi et al.   Frontiers in Microbiology

EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies

(2017) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

Combined use of network inference tools identifies ecologically meaningful bacterial associations in a paddy soil

(2017) Honggui Wang et al.   SOIL BIOLOGY & BIOCHEMISTRY

CompNet: a GUI based tool for comparison of multiple biological interaction networks

(2016) Bhusan K. Kuntal et al.   BMC BIOINFORMATICS

A method for automated pathogenic content estimation with application to rheumatoid arthritis

(2016) Xiaoyuan Zhou et al.   BMC Systems Biology

Exercise-induced stress behavior, gut-microbiota-brain axis and diet: a systematic review for athletes

(2016) Allison Clark et al.   Journal of the International Society of Sports Nutrition

From gut dysbiosis to altered brain function and mental illness: mechanisms and pathways

(2016) G B Rogers et al.   MOLECULAR PSYCHIATRY

Xenobiotic Metabolism and Gut Microbiomes

(2016) Anubhav Das et al.   PLoS One

Allergic Patients with Long-Term Asthma Display Low Levels of Bifidobacterium adolescentis

(2016) Arancha Hevia et al.   PLoS One

The H-index of a network node and its relation to degree and coreness

(2016) Linyuan Lü et al.   Nature Communications

Global investigation of composition and interaction networks in gut microbiomes of individuals belonging to diverse geographies and age-groups

(2016) Deepak Yadav et al.   Gut Pathogens

Intestinal Short Chain Fatty Acids and their Link with Diet and Human Health

(2016) David Ríos-Covián et al.   Frontiers in Microbiology

Porphyromonas gingivalis: An Overview of Periodontopathic Pathogen below the Gum Line

(2016) Kah Yan How et al.   Frontiers in Microbiology

Preliminary analysis of salivary microbiome and their potential roles in oral lichen planus

(2016) Kun Wang et al.   Scientific Reports

A Comparative Analysis of Community Detection Algorithms on Artificial Networks

(2016) Zhao Yang et al.   Scientific Reports

Resistant Microbial Cooccurrence Patterns Inferred by Network Topology

(2015) Sari Peura et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Proper evaluation of alignment-free network comparison methods

(2015) Ömer Nebil Yaveroğlu et al.   BIOINFORMATICS

Coaggregation and biofilm growth of Granulicatella spp. with Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans

(2015) Maribasappa Karched et al.   BMC MICROBIOLOGY

Microbiota in Allergy and Asthma and the Emerging Relationship with the Gut Microbiome

(2015) Kei E. Fujimura et al.   Cell Host & Microbe

The role of the gut microbiome in the healthy adult status

(2015) Valeria D’Argenio et al.   CLINICA CHIMICA ACTA

The gut microbiome in health and in disease

(2015) Andrew B. Shreiner et al.   CURRENT OPINION IN GASTROENTEROLOGY

Fusobacterium nucleatum: a commensal-turned pathogen

(2015) Yiping W Han   CURRENT OPINION IN MICROBIOLOGY

Gut/brain axis and the microbiota

(2015) Emeran A. Mayer et al.   JOURNAL OF CLINICAL INVESTIGATION

The oral microbiome in human immunodeficiency virus (HIV)-positive individuals

(2015) James O. Kistler et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Role of the normal gut microbiota

(2015) Sai Manasa Jandhyala   WORLD JOURNAL OF GASTROENTEROLOGY

Cross-biome comparison of microbial association networks

(2015) Karoline Faust et al.   Frontiers in Microbiology

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

Inflammatory Bowel Disease as a Model for Translating the Microbiome

(2014) Curtis Huttenhower et al.   IMMUNITY

Diet, microbiota and autoimmune diseases

(2014) SM Vieira et al.   LUPUS

Gut Microbiomes of Indian Children of Varying Nutritional Status

(2014) Tarini Shankar Ghosh et al.   PLoS One

The Human Microbiome: From Symbiosis to Pathogenesis

(2013) Emiley A. Eloe-Fadrosh et al.   Annual Review of Medicine

MIMO: an efficient tool for molecular interaction maps overlap

(2013) Pietro Lena et al.   BMC BIOINFORMATICS

Community-Analyzer: A platform for visualizing and comparing microbial community structure across microbiomes

(2013) Bhusan K. Kuntal et al.   GENOMICS

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome

(2013) Dan Knights et al.   GUT

Translating the human microbiome

(2013) James Brown et al.   NATURE BIOTECHNOLOGY

Metabolic modeling of species interaction in the human microbiome elucidates community-level assembly rules

(2013) R. Levy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

House dust exposure mediates gut microbiome Lactobacillus enrichment and airway immune defense against allergens and virus infection

(2013) K. E. Fujimura et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Commensal Clostridia: leading players in the maintenance of gut homeostasis

(2013) Loris R Lopetuso et al.   Gut Pathogens

Quantitative Profiling of Gut Microbiota of Children With Diarrhea-Predominant Irritable Bowel Syndrome

(2012) Laura Rigsbee et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

Intestinal Commensal Microbes as Immune Modulators

(2012) Ivaylo I. Ivanov et al.   Cell Host & Microbe

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Granulicatella infection: diagnosis and management

(2012) J. S. Cargill et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Levels ofSelenomonasspecies in generalized aggressive periodontitis

(2012) L. F. H. Gonçalves et al.   JOURNAL OF PERIODONTAL RESEARCH

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

(2012) Junjie Qin et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Periodontal disease in HIV/AIDS

(2012) Mark I. Ryder et al.   PERIODONTOLOGY 2000

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Metagenome of the gut of a malnourished child

(2011) Sourav Gupta et al.   Gut Pathogens

Using graph theory to analyze biological networks

(2011) Georgios A Pavlopoulos et al.   BioData Mining

Human Microbiome and HIV/AIDS

(2011) Deepak Saxena et al.   Current HIV/AIDS Reports

Homeostasis and Inflammation in the Intestine

(2010) Wendy S. Garrett et al.   CELL

Perspective: Alpha-Bugs, Their Microbial Partners, and the Link to Colon Cancer

(2010) Cynthia L. Sears et al.   JOURNAL OF INFECTIOUS DISEASES

Enhanced modularity-based community detection by random walk network preprocessing

(2010) Darong Lai et al.   PHYSICAL REVIEW E

The core gut microbiome, energy balance and obesity

(2009) Peter J. Turnbaugh et al.   JOURNAL OF PHYSIOLOGY-LONDON

The role of microbiota in infectious disease

(2008) Bärbel Stecher et al.   TRENDS IN MICROBIOLOGY