Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations

Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico

(2015) Almut Heinken et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Systems biology of host-microbe metabolomics

(2015) Almut Heinken et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Is eating behavior manipulated by the gastrointestinal microbiota? Evolutionary pressures and potential mechanisms

(2014) Joe Alcock et al.   BIOESSAYS

Modeling the effects of commonly used drugs on human metabolism

(2014) Swagatika Sahoo et al.   FEBS Journal

Short-Term Effect of Antibiotics on Human Gut Microbiota

(2014) Suchita Panda et al.   PLoS One

Positive Feedback Promotes Oscillations in Negative Feedback Loops

(2014) Bharath Ananthasubramaniam et al.   PLoS One

Trophic coherence determines food-web stability

(2014) Samuel Johnson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Adiposity, gut microbiota and faecal short chain fatty acids are linked in adult humans

(2014) J Fernandes et al.   Nutrition & Diabetes

Investigation of Inflammation and Tissue Patterning in the Gut Using a Spatially Explicit General-Purpose Model of Enteric Tissue (SEGMEnT)

(2014) Chase Cockrell et al.   PLoS Computational Biology

The role of bacteriocins as selfish genetic elements

(2013) R. F. Inglis et al.   Biology Letters

The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism

(2013) Gijs den Besten et al.   JOURNAL OF LIPID RESEARCH

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

Mathematical modeling of primary succession of murine intestinal microbiota

(2013) S. Marino et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

Ecological Modeling from Time-Series Inference: Insight into Dynamics and Stability of Intestinal Microbiota

(2013) Richard R. Stein et al.   PLoS Computational Biology

Seasonal restructuring of the ground squirrel gut microbiota over the annual hibernation cycle

(2012) Hannah V. Carey et al.   AMERICAN JOURNAL OF PHYSIOLOGY-REGULATORY INTEGRATIVE AND COMPARATIVE PHYSIOLOGY

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

(2012) Omry Koren et al.   CELL

How to assemble a beneficial microbiome in three easy steps

(2012) István Scheuring et al.   ECOLOGY LETTERS

Early life antibiotic-driven changes in microbiota enhance susceptibility to allergic asthma

(2012) Shannon L Russell et al.   EMBO REPORTS

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Quorum Sensing and Bacterial Social Interactions in Biofilms

(2012) Yung-Hua Li et al.   SENSORS

The Evolution of Mutualism in Gut Microbiota Via Host Epithelial Selection

(2012) Jonas Schluter et al.   PLOS BIOLOGY

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Social Interaction, Noise and Antibiotic-Mediated Switches in the Intestinal Microbiota

(2012) Vanni Bucci et al.   PLoS Computational Biology

The Evolution of Bacteriocin Production in Bacterial Biofilms

(2011) Vanni Bucci et al.   AMERICAN NATURALIST

Infection Control in the Multidrug-Resistant Era: Tending the Human Microbiome

(2011) P. K. Tosh et al.   CLINICAL INFECTIOUS DISEASES

Antibiotics and the resistant microbiome

(2011) Morten OA Sommer et al.   CURRENT OPINION IN MICROBIOLOGY

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Crosstalk between B lymphocytes, microbiota and the intestinal epithelium governs immunity versus metabolism in the gut

(2011) Natalia Shulzhenko et al.   NATURE MEDICINE

A Metaproteomic Approach to Study Human-Microbial Ecosystems at the Mucosal Luminal Interface

(2011) Xiaoxiao Li et al.   PLoS One

Dynamics in the mixed microbial concourse

(2010) E. H. Wintermute et al.   GENES & DEVELOPMENT

Transcriptomic Analyses of Xylan Degradation byPrevotella bryantiiand Insights into Energy Acquisition by Xylanolytic Bacteroidetes

(2010) Dylan Dodd et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Evolutionary game theory: Theoretical concepts and applications to microbial communities

(2010) Erwin Frey   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

QseC Mediates Salmonella enterica Serovar Typhimurium Virulence In Vitro and In Vivo

(2009) C. G. Moreira et al.   INFECTION AND IMMUNITY

Reproducible Community Dynamics of the Gastrointestinal Microbiota following Antibiotic Perturbation

(2009) D. A. Antonopoulos et al.   INFECTION AND IMMUNITY

Snowdrift game dynamics and facultative cheating in yeast

(2009) Jeff Gore et al.   NATURE

Microbiota and SCFA in Lean and Overweight Healthy Subjects

(2009) Andreas Schwiertz et al.   Obesity

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotic-Induced Perturbations of the Intestinal Microbiota Alter Host Susceptibility to Enteric Infection

(2008) I. Sekirov et al.   INFECTION AND IMMUNITY

Molecular analysis of the gut microbiota of identical twins with Crohn's disease

(2008) Johan Dicksved et al.   ISME Journal

A comparison of homologous recombination rates in bacteria and archaea

(2008) Michiel Vos et al.   ISME Journal

Introduction of an agent-based multi-scale modular architecture for dynamic knowledge representation of acute inflammation

(2008) Gary An   Theoretical Biology and Medical Modelling