Mapping the microbial interactome: Statistical and experimental approaches for microbiome network inference

Microbial communities as dynamical systems

(2018) Didier Gonze et al.   CURRENT OPINION IN MICROBIOLOGY

Extended local similarity analysis (eLSA) reveals unique associations between bacterial community structure and odor emission during pig carcasses decomposition

(2018) Bo-Min Ki et al.   JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH PART A-TOXIC/HAZARDOUS SUBSTANCES & ENVIRONMENTAL ENGINEERING

Gut microbiome and depression: what we know and what we need to know

(2018) Gal Winter et al.   REVIEWS IN THE NEUROSCIENCES

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

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

Fungi stabilize connectivity in the lung and skin microbial ecosystems

(2018) Laura Tipton et al.   Microbiome

The influence of ethnicity and geography on human gut microbiome composition

(2018) Christopher A. Gaulke et al.   NATURE MEDICINE

Klebsiella oxytoca expands in cancer cachexia and acts as a gut pathobiont contributing to intestinal dysfunction

(2018) Sarah A. Pötgens et al.   Scientific Reports

A microbial signature for Crohn's disease

(2017) Victoria Pascal et al.   GUT

Fundamental limitations of network reconstruction from temporal data

(2017) Marco Tulio Angulo et al.   Journal of the Royal Society Interface

MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data

(2017) Achal Dhariwal et al.   NUCLEIC ACIDS RESEARCH

The Gut Microbiota and Autism Spectrum Disorders

(2017) Qinrui Li et al.   Frontiers in Cellular Neuroscience

Mapping the ecological networks of microbial communities

(2017) Yandong Xiao et al.   Nature Communications

Global metabolic interaction network of the human gut microbiota for context-specific community-scale analysis

(2017) Jaeyun Sung et al.   Nature Communications

Randomised controlled trial of Lactobacillus rhamnosus (LGG) versus placebo in children presenting to the emergency department with acute gastroenteritis: the PECARN probiotic study protocol

(2017) David Schnadower et al.   BMJ Open

MPLasso: Inferring microbial association networks using prior microbial knowledge

(2017) Chieh Lo et al.   PLoS Computational Biology

A Bayesian method for detecting pairwise associations in compositional data

(2017) Emma Schwager et al.   PLoS Computational Biology

Two dynamic regimes in the human gut microbiome

(2017) Sean M. Gibbons et al.   PLoS Computational Biology

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

(2017) Babak Momeni et al.   eLife

Gut Dysbiosis in Animals Due to Environmental Chemical Exposures

(2017) Cheryl S. Rosenfeld   Frontiers in Cellular and Infection Microbiology

Individual signatures and environmental factors shape skin microbiota in healthy dogs

(2017) Anna Cuscó et al.   Microbiome

Microbiota Transfer Therapy alters gut ecosystem and improves gastrointestinal and autism symptoms: an open-label study

(2017) Dae-Wook Kang et al.   Microbiome

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures

(2017) Zehra Esra Ilhan et al.   mSphere

Compositional data analysis of the microbiome: fundamentals, tools, and challenges

(2016) Matthew C.B. Tsilimigras et al.   ANNALS OF EPIDEMIOLOGY

MetaMIS: a metagenomic microbial interaction simulator based on microbial community profiles

(2016) Grace Tzun-Wen Shaw et al.   BMC BIOINFORMATICS

Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease

(2016) Timothy R. Sampson et al.   CELL

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

(2016) Sophie Weiss et al.   ISME Journal

Acetate mediates a microbiome–brain–β-cell axis to promote metabolic syndrome

(2016) Rachel J. Perry et al.   NATURE

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

A microfluidics-based in vitro model of the gastrointestinal human–microbe interface

(2016) Pranjul Shah et al.   Nature Communications

Fecal Microbiota Transplantation and Its Usage in Neuropsychiatric Disorders

(2016) Alper Evrensel et al.   Clinical Psychopharmacology and Neuroscience

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

(2016) Cecilia Noecker et al.   mSystems

Piphillin: Improved Prediction of Metagenomic Content by Direct Inference from Human Microbiomes

(2016) Shoko Iwai et al.   PLoS One

Tax4Fun: predicting functional profiles from metagenomic 16S rRNA data: Fig. 1.

(2015) Kathrin P. Aßhauer et al.   BIOINFORMATICS

CCLasso: correlation inference for compositional data through Lasso

(2015) Huaying Fang et al.   BIOINFORMATICS

Investigating microbial co-occurrence patterns based on metagenomic compositional data

(2015) Yuguang Ban et al.   BIOINFORMATICS

The gut microbiota and Type 1 Diabetes

(2015) Elke Gülden et al.   CLINICAL IMMUNOLOGY

Rhythmicity of the intestinal microbiota is regulated by gender and the host circadian clock

(2015) Xue Liang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fecal microbiota transplantation broadening its application beyond intestinal disorders

(2015) Meng-Que Xu   WORLD JOURNAL OF GASTROENTEROLOGY

Sparse and Compositionally Robust Inference of Microbial Ecological Networks

(2015) Zachary D. Kurtz et al.   PLoS Computational Biology

Social networks predict gut microbiome composition in wild baboons

(2015) Jenny Tung et al.   eLife

Microbiome, Metagenomics, and High-Dimensional Compositional Data Analysis

(2015) Hongzhe Li   Annual Review of Statistics and Its Application

Probiotics in the prevention of eczema: a randomised controlled trial

(2014) S. J. Allen et al.   ARCHIVES OF DISEASE IN CHILDHOOD

Methods for time series analysis of RNA-seq data with application to human Th17 cell differentiation

(2014) Tarmo Äijö et al.   BIOINFORMATICS

The dynamic microbiome

(2014) Georg K. Gerber   FEBS LETTERS

Towards Predictive Models of the Human Gut Microbiome

(2014) Vanni Bucci et al.   JOURNAL OF MOLECULAR BIOLOGY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

The gut microbiota, bacterial metabolites and colorectal cancer

(2014) Petra Louis et al.   NATURE REVIEWS MICROBIOLOGY

Identifying Keystone Species in the Human Gut Microbiome from Metagenomic Timeseries Using Sparse Linear Regression

(2014) Charles K. Fisher et al.   PLoS One

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of emergency department probiotic treatment of pediatric gastroenteritis: study protocol for the PROGUT (Probiotic Regimen for Outpatient Gastroenteritis Utility of Treatment) randomized controlled trial

(2014) Stephen B Freedman et al.   Trials

Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition

(2014) Mihai Pop et al.   GENOME BIOLOGY

Variable selection for sparse Dirichlet-multinomial regression with an application to microbiome data analysis

(2013) Jun Chen et al.   Annals of Applied Statistics

Exploring host-microbiota interactions in animal models and humans

(2013) A. D. Kostic et al.   GENES & DEVELOPMENT

Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome

(2013) Jonna Jalanka-Tuovinen et al.   GUT

Lactobacilli and bifidobacteria in the prevention of antibiotic-associated diarrhoea and Clostridium difficile diarrhoea in older inpatients (PLACIDE): a randomised, double-blind, placebo-controlled, multicentre trial

(2013) Stephen J Allen et al.   LANCET

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Causal inference with multiple time series: principles and problems

(2013) M. Eichler   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

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

The Gut Microbiome: A New Frontier in Autism Research

(2013) Jennifer G. Mulle et al.   Current Psychiatry Reports

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

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

Efficient statistical significance approximation for local similarity analysis of high-throughput time series data

(2012) Li C. Xia et al.   BIOINFORMATICS

Molecular ecological network analyses

(2012) Ye Deng et al.   BMC BIOINFORMATICS

The microbiome as a human organ

(2012) F. Baquero et al.   CLINICAL MICROBIOLOGY AND INFECTION

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

Studying and modelling dynamic biological processes using time-series gene expression data

(2012) Ziv Bar-Joseph et al.   NATURE REVIEWS GENETICS

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Multivariate Approach for Studying Interactions between Environmental Variables and Microbial Communities

(2012) Xinhui Wang et al.   PLoS One

Interkingdom metabolic transformations captured by microbial imaging mass spectrometry

(2012) W. J. Moree et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting Causality in Complex Ecosystems

(2012) G. Sugihara et al.   SCIENCE

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Inferring Dynamic Signatures of Microbes in Complex Host Ecosystems

(2012) Georg K. Gerber et al.   PLoS Computational Biology

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon

(2011) Dallas R. Donohoe et al.   Cell Metabolism

Microbial metabolic exchange—the chemotype-to-phenotype link

(2011) Vanessa V Phelan et al.   Nature Chemical Biology

Detecting Novel Associations in Large Data Sets

(2011) D. N. Reshef et al.   SCIENCE

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Erratum: Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice

(2010) Chenhong Zhang et al.   ISME Journal

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

Advantages and limitations of current network inference methods

(2010) Riet De Smet et al.   NATURE REVIEWS MICROBIOLOGY

The Human Intestinal Microbiome: A New Frontier of Human Biology

(2009) M. Hattori et al.   DNA RESEARCH

Network inference and network response identification: moving genome-scale data to the next level of biological discovery

(2009) Diogo F. T. Veiga et al.   Molecular BioSystems

Applications of genome-scale metabolic reconstructions

(2009) Matthew A Oberhardt et al.   Molecular Systems Biology

Commercial Ripening Starter Microorganisms Inoculated into Cheese Milk Do Not Successfully Establish Themselves in the Resident Microbial Ripening Consortia of a South German Red Smear Cheese

(2008) S. Goerges et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterizing mixed microbial population dynamics using time-series analysis

(2008) Pål Trosvik et al.   ISME Journal

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE