GutLogo: Agent-based modeling framework to investigate spatial and temporal dynamics in the gut microbiome

Protective Effects of Bifidobacterial Strains Against Toxigenic Clostridium difficile

(2018) Yanxia Wei et al.   Frontiers in Microbiology

Effect of flow and peristaltic mixing on bacterial growth in a gut-like channel

(2016) Jonas Cremer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

Agent Based Modeling of Human Gut Microbiome Interactions and Perturbations

(2016) Tatiana Shashkova et al.   PLoS One

The gut microbiome in health and in disease

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

An agent-based modeling framework for evaluating hypotheses on risks for developing autism: Effects of the gut microbial environment

(2015) Bronson Weston et al.   MEDICAL HYPOTHESES

Morpheus: a user-friendly modeling environment for multiscale and multicellular systems biology

(2014) Jörn Starruß et al.   BIOINFORMATICS

Efficient Modeling and Simulation of Bacteria-Based Nanonetworks with BNSim

(2014) Guopeng Wei et al.   IEEE JOURNAL ON SELECTED AREAS IN COMMUNICATIONS

MALDI-TOF Identification of the Human Gut Microbiome in People with and without Diarrhea in Senegal

(2014) Bissoume Samb-Ba et al.   PLoS One

Comparison of brush and biopsy sampling methods of the ileal pouch for assessment of mucosa-associated microbiota of human subjects

(2014) Susan M Huse et al.   Microbiome

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Prebiotic-non-digestible oligosaccharides preference of probiotic bifidobacteria and antimicrobial activity against Clostridium difficile

(2012) Kanthi Kiran Kondepudi et al.   ANAEROBE

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

(2012) Jose C. Clemente et al.   CELL

Hypothesis for a systems connectivity model of autism spectrum disorder pathogenesis: Links to gut bacteria, oxidative stress, and intestinal permeability

(2012) Colin A. Heberling et al.   MEDICAL HYPOTHESES

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

BSim: An Agent-Based Tool for Modeling Bacterial Populations in Systems and Synthetic Biology

(2012) Thomas E. Gorochowski et al.   PLoS One

State of the art; microbiology in health and disease. Intestinal bacterial flora in autism

(2011) Sydney M. Finegold   ANAEROBE

Desulfovibrio species are potentially important in regressive autism

(2011) Sydney M. Finegold   MEDICAL HYPOTHESES

Genomic Insights into Bifidobacteria

(2010) J.-H. Lee et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Detailed Simulations of Cell Biology with Smoldyn 2.1

(2010) Steven S. Andrews et al.   PLoS Computational Biology

Coculture Fermentations of Bifidobacterium Species and Bacteroides thetaiotaomicron Reveal a Mechanistic Insight into the Prebiotic Effect of Inulin-Type Fructans

(2009) G. Falony et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Bacterial growth and motility in sub-micron constrictions

(2009) J. Mannik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Growth of infant faecal bifidobacteria and clostridia on prebiotic oligosaccharides in in vitro conditions

(2008) Vojtěch Rada et al.   ANAEROBE