Modelling microbiome recovery after antibiotics using a stability landscape framework

Multiple stable states in microbial communities explained by the stable marriage problem

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Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Stan: A Probabilistic Programming Language

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The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

The antibiotic course has had its day

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The antibiotic course has had its day

(2017) Martin J Llewelyn et al.   BMJ-British Medical Journal

Lotka-Volterra pairwise modeling fails to capture diverse pairwise microbial interactions

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Diversity is the question, not the answer

(2016) Ashley Shade   ISME Journal

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Individuality, Stability, and Variability of the Plaque Microbiome

(2016) Daniel R. Utter et al.   Frontiers in Microbiology

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The ecology of the microbiome: Networks, competition, and stability

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Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

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Antibiotics and the gut microbiota

(2014) Sheetal R. Modi et al.   JOURNAL OF CLINICAL INVESTIGATION

Towards Predictive Models of the Human Gut Microbiome

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Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

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Host lifestyle affects human microbiota on daily timescales

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The Long-Term Stability of the Human Gut Microbiota

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

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

The human microbiome: ecosystem resilience and health

(2012) David A Relman   NUTRITION REVIEWS

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

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

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

Microbiota-Targeted Therapies: An Ecological Perspective

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The emerging medical ecology of the human gut microbiome

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

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Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis

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Antimicrobial Stewardship

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Experimental species removal alters ecological dynamics in a natural ecosystem

(2010) J. Timothy Wootton   ECOLOGY

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

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The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

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