Species-specific enhancement of enterohemorrhagic E. coli pathogenesis mediated by microbiome metabolites

Organ-on-Chip Recapitulates Thrombosis Induced by an anti-CD154 Monoclonal Antibody: Translational Potential of Advanced Microengineered Systems

(2018) Riccardo Barrile et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Chemotaxis of Escherichia coli to major hormones and polyamines present in human gut

(2018) Joana G. Lopes et al.   ISME Journal

Have you tried spermine? A rapid and cost-effective method to eliminate dextran sodium sulfate inhibition of PCR and RT-PCR

(2018) Łukasz Krych et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Modeling radiation injury-induced cell death and countermeasure drug responses in a human Gut-on-a-Chip

(2018) Sasan Jalili-Firoozinezhad et al.   Cell Death & Disease

Understanding the prebiotic potential of different dietary fibers using an in vitro continuous adult fermentation model (PolyFermS)

(2018) Sophie A. Poeker et al.   Scientific Reports

Cytokine Tuning of Intestinal Epithelial Function

(2018) Caroline Andrews et al.   Frontiers in Immunology

A Gut Commensal-Produced Metabolite Mediates Colonization Resistance to Salmonella Infection

(2018) Amanda Jacobson et al.   Cell Host & Microbe

Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids

(2018) Magdalena Kasendra et al.   Scientific Reports

TrackMate: An open and extensible platform for single-particle tracking

(2017) Jean-Yves Tinevez et al.   METHODS

Moving beyond microbiome-wide associations to causal microbe identification

(2017) Neeraj K. Surana et al.   NATURE

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Enterohemorrhagic Escherichia coli pathogenesis: role of Long polar fimbriae in Peyer’s patches interactions

(2017) Charlotte Cordonnier et al.   Scientific Reports

Transcriptional control of motility enables directional movement of Escherichia coli in a signal gradient

(2017) Jayamary Divya Ravichandar et al.   Scientific Reports

A microfluidic chip based model for the study of full thickness human intestinal tissue using dual flow

(2016) A. Dawson et al.   Biomicrofluidics

Reverse Engineering Human Pathophysiology with Organs-on-Chips

(2016) Donald E. Ingber   CELL

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Catabolite and Oxygen Regulation of Enterohemorrhagic Escherichia coli Virulence

(2016) Kimberly M. Carlson-Banning et al.   mBio

The Reciprocal Interactions between Polyphenols and Gut Microbiota and Effects on Bioaccessibility

(2016) Tugba Ozdal et al.   Nutrients

Matched-Comparative Modeling of Normal and Diseased Human Airway Responses Using a Microengineered Breathing Lung Chip

(2016) Kambez H. Benam et al.   Cell Systems

An isotope-labeled chemical derivatization method for the quantitation of short-chain fatty acids in human feces by liquid chromatography–tandem mass spectrometry

(2015) Jun Han et al.   ANALYTICA CHIMICA ACTA

Integrated multi-scale strategies to investigate nutritional compounds and their effect on the gut microbiota

(2015) Christophe Lacroix et al.   CURRENT OPINION IN BIOTECHNOLOGY

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Effect of enterohaemorrhagicEscherichia coliO157:H7-specific enterohaemolysin on interleukin-1βproduction differs between human and mouse macrophages due to the different sensitivity of NLRP3 activation

(2015) Yu-Li Cheng et al.   IMMUNOLOGY

No Vacancy: How Beneficial Microbes Cooperate with Immunity To Provide Colonization Resistance to Pathogens

(2015) Martina Sassone-Corsi et al.   JOURNAL OF IMMUNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Design and Investigation of PolyFermS In Vitro Continuous Fermentation Models Inoculated with Immobilized Fecal Microbiota Mimicking the Elderly Colon

(2015) Sophie Fehlbaum et al.   PLoS One

Contributions of microbiome and mechanical deformation to intestinal bacterial overgrowth and inflammation in a human gut-on-a-chip

(2015) Hyun Jung Kim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of an enhanced human gastrointestinal epithelial culture system to facilitate patient-based assays

(2014) Kelli L VanDussen et al.   GUT

Enterohemorrhagic Escherichia coli Colonization of Human Colonic EpitheliumIn VitroandEx Vivo

(2014) Steven B. Lewis et al.   INFECTION AND IMMUNITY

The intestinal epithelium is an integral component of a communications network

(2014) Martin F. Kagnoff   JOURNAL OF CLINICAL INVESTIGATION

Modeling the mitochondrial cardiomyopathy of Barth syndrome with induced pluripotent stem cell and heart-on-chip technologies

(2014) Gang Wang et al.   NATURE MEDICINE

In Vitro Continuous Fermentation Model (PolyFermS) of the Swine Proximal Colon for Simultaneous Testing on the Same Gut Microbiota

(2014) Sabine A. Tanner et al.   PLoS One

Prediction and quantification of bioactive microbiota metabolites in the mouse gut

(2014) Gautham V. Sridharan et al.   Nature Communications

A targeted metabolomic protocol for short-chain fatty acids and branched-chain amino acids

(2013) Xiaojiao Zheng et al.   Metabolomics

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Novel Polyfermentor Intestinal Model (PolyFermS) for Controlled Ecological Studies: Validation and Effect of pH

(2013) Annina Zihler Berner et al.   PLoS One

Growing Self-Organizing Mini-Guts from a Single Intestinal Stem Cell: Mechanism and Applications

(2013) T. Sato et al.   SCIENCE

Why interleukin-10 supplementation does not work in Crohn’s disease patients

(2013) Gareth J Marlow   WORLD JOURNAL OF GASTROENTEROLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

Cytokine profiles of patients with enterohemorrhagic Escherichia coli O111-induced hemolytic-uremic syndrome

(2012) Masaki Shimizu et al.   CYTOKINE

Novel Repressor of Escherichia coli O157:H7 Motility Encoded in the Putative Fimbrial Cluster OI-1

(2012) S. E. Allison et al.   JOURNAL OF BACTERIOLOGY

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

A Human Disease Model of Drug Toxicity–Induced Pulmonary Edema in a Lung-on-a-Chip Microdevice

(2012) Dongeun Huh et al.   Science Translational Medicine

Inhibition of Escherichia coli CFT073fliCExpression and Motility by Cranberry Materials

(2011) Gabriela Hidalgo et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization

(2011) Raffaella Di Cagno et al.   BMC MICROBIOLOGY

Mouse Models ofEscherichia coliO157:H7 Infection and Shiga Toxin Injection

(2011) Krystle L. Mohawk et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Colloids in a bacterial bath: simulations and experiments

(2011) Chantal Valeriani et al.   Soft Matter

Shiga Toxin Interaction with Human Intestinal Epithelium

(2011) Stephanie Schüller   Toxins

Activation of Motility by Sensing Short-Chain Fatty Acids via Two Steps in a Flagellar Gene Regulatory Cascade in EnterohemorrhagicEscherichia coli

(2010) Toru Tobe et al.   INFECTION AND IMMUNITY

Regulation of virulence by butyrate sensing in enterohaemorrhagic Escherichia coli

(2009) N. Nakanishi et al.   MICROBIOLOGY-SGM

Sequence variants in IL10, ARPC2 and multiple other loci contribute to ulcerative colitis susceptibility

(2008) Andre Franke et al.   NATURE GENETICS