Maternal cecal microbiota transfer rescues early-life antibiotic-induced enhancement of type 1 diabetes in mice

Histone H3K27me3 demethylases regulate human Th17 cell development and effector functions by impacting on metabolism

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Maternal gut microbiota in pregnancy influences offspring metabolic phenotype in mice

(2020) Ikuo Kimura et al.   SCIENCE

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study

(2020) Katri Korpela et al.   CELL

Association of Infant Antibiotic Exposure With Childhood Health Outcomes

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A Novel Sparse Compositional Technique Reveals Microbial Perturbations

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Increased intron retention is a post-transcriptional signature associated with progressive aging and Alzheimer’s disease

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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

The Interaction Between Two Worlds: MicroRNAs and Toll-Like Receptors

(2019) Recep Bayraktar et al.   Frontiers in Immunology

Fatty acid metabolism in the host and commensal bacteria for the control of intestinal immune responses and diseases

(2019) Koji Hosomi et al.   Gut Microbes

AIDE: annotation-assisted isoform discovery with high precision

(2019) Wei Vivian Li et al.   GENOME RESEARCH

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(2019) James T. Morton et al.   NATURE METHODS

Microbial bile acid metabolites modulate gut RORγ+ regulatory T cell homeostasis

(2019) Xinyang Song et al.   NATURE

Fetal and early life antibiotics exposure and very early onset inflammatory bowel disease: a population-based study

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Functions and Signaling Pathways of Amino Acids in Intestinal Inflammation

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Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

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Stereotypic Immune System Development in Newborn Children

(2018) Axel Olin et al.   CELL

Loss of HDAC6 alters gut microbiota and worsens obesity

(2018) Arnon D. Lieber et al.   FASEB JOURNAL

Early-life exposure to gut microbiota from disease protected mice does not impact disease outcome in type 1 diabetes susceptible NOD mice

(2018) Jane A. Mullaney et al.   IMMUNOLOGY AND CELL BIOLOGY

Impact of Retinoic Acid on Immune Cells and Inflammatory Diseases

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Antibiotic-induced acceleration of type 1 diabetes alters maturation of innate intestinal immunity

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Bile Acids Activated Receptors Regulate Innate Immunity

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Antibiotic and acid-suppression medications during early childhood are associated with obesity

(2018) Christopher M Stark et al.   GUT

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

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(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

Role of CD44 in Regulating TLR2 Activation of Human Macrophages and Downstream Expression of Proinflammatory Cytokines

(2017) Marwa Qadri et al.   JOURNAL OF IMMUNOLOGY

Sulfate-reducing bacteria stimulate gut immune responses and contribute to inflammation in experimental colitis

(2017) Vanessa Ribeiro Figliuolo et al.   LIFE SCIENCES

The Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics

(2017) Lindsay K. Pino et al.   MASS SPECTROMETRY REVIEWS

A single-cell survey of the small intestinal epithelium

(2017) Adam L. Haber et al.   NATURE

Alternative splicing: A thermometer controlling gene expression

(2017) Linda Koch   NATURE REVIEWS GENETICS

The MetaCyc database of metabolic pathways and enzymes

(2017) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Antibiotics, gut microbiota, environment in early life and type 1 diabetes

(2017) Youjia Hu et al.   PHARMACOLOGICAL RESEARCH

Regulation of intestinal permeability: The role of proteases

(2017) Hanne Van Spaendonk et al.   WORLD JOURNAL OF GASTROENTEROLOGY

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

(2017) Victoria E. Ruiz et al.   Nature Communications

The TMAO-Producing Enzyme Flavin-Containing Monooxygenase 3 Regulates Obesity and the Beiging of White Adipose Tissue

(2017) Rebecca C. Schugar et al.   Cell Reports

Association Between Early-Life Antibiotic Use and the Risk of Islet or Celiac Disease Autoimmunity

(2017) Kaisa M. Kemppainen et al.   JAMA Pediatrics

Early-Life Host–Microbiome Interphase: The Key Frontier for Immune Development

(2017) Nelly Amenyogbe et al.   Frontiers in Pediatrics

Uncoupling of mucosal gene regulation, mRNA splicing and adherent microbiota signatures in inflammatory bowel disease

(2016) Robert Häsler et al.   GUT

Protease inhibition as new therapeutic strategy for GI diseases

(2016) Nathalie Vergnolle   GUT

Accurate quantification of mouse mitochondrial DNA without co-amplification of nuclear mitochondrial insertion sequences

(2016) Afshan N. Malik et al.   MITOCHONDRION

Diet-Microbiota Interactions Mediate Global Epigenetic Programming in Multiple Host Tissues

(2016) Kimberly A. Krautkramer et al.   MOLECULAR CELL

MicroRNA-143 targets CD44 to inhibit breast cancer progression and stem cell-like properties

(2016) ZHUANGQING YANG et al.   Molecular Medicine Reports

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

The right gut microbes help infants grow

(2016) E. Pennisi   SCIENCE

How colonization by microbiota in early life shapes the immune system

(2016) Thomas Gensollen et al.   SCIENCE

A sentinel goblet cell guards the colonic crypt by triggering Nlrp6-dependent Muc2 secretion

(2016) G. M. H. Birchenough et al.   SCIENCE

Oscillospira : a Central, Enigmatic Component of the Human Gut Microbiota

(2016) Tom Konikoff et al.   TRENDS IN MICROBIOLOGY

Elucidating MicroRNA Regulatory Networks Using Transcriptional, Post-transcriptional, and Histone Modification Measurements

(2016) Sara J.C. Gosline et al.   Cell Reports

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

(2016) Amy Langdon et al.   Genome Medicine

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice

(2016) Alexandra E. Livanos et al.   Nature Microbiology

Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms, and Outlook

(2015) Colleen R. Kelly et al.   GASTROENTEROLOGY

Antimicrobial Defense of the Intestine

(2015) Sohini Mukherjee et al.   IMMUNITY

Prolonged antibiotic treatment induces a diabetogenic intestinal microbiome that accelerates diabetes in NOD mice

(2015) Kirsty Brown et al.   ISME Journal

Maternal Antibiotic Treatment Protects Offspring from Diabetes Development in Nonobese Diabetic Mice by Generation of Tolerogenic APCs

(2015) Youjia Hu et al.   JOURNAL OF IMMUNOLOGY

Reg3g overexpression promotes β cell regeneration and induces immune tolerance in nonobese-diabetic mouse model

(2015) Fei Xia et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Quantification of SAHA-Dependent Changes in Histone Modifications Using Data-Independent Acquisition Mass Spectrometry

(2015) Kimberly A. Krautkramer et al.   JOURNAL OF PROTEOME RESEARCH

Role of the gastrointestinal ecosystem in the development of type 1 diabetes

(2015) Joseph G Daft et al.   PEDIATRIC DIABETES

Impact of Early-Life Exposures on Immune Maturation and Susceptibility to Disease

(2015) Eva S. Gollwitzer et al.   TRENDS IN IMMUNOLOGY

The infant microbiome development: mom matters

(2015) Noel T. Mueller et al.   TRENDS IN MOLECULAR MEDICINE

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(2015) Yingming Zhao et al.   Cold Spring Harbor Perspectives in Biology

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

(2015) Yael R. Nobel et al.   Nature Communications

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Antibiotics in Early Life Alter the Gut Microbiome and Increase Disease Incidence in a Spontaneous Mouse Model of Autoimmune Insulin-Dependent Diabetes

(2015) Sophie Candon et al.   PLoS One

A Nano Ultra-Performance Liquid Chromatography–High Resolution Mass Spectrometry Approach for Global Metabolomic Profiling and Case Study on Drug-Resistant Multiple Myeloma

(2014) Drew R. Jones et al.   ANALYTICAL CHEMISTRY

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

Regulation of alternative splicing of CD44 in cancer

(2014) Lubomir Prochazka et al.   CELLULAR SIGNALLING

Evaluating the Role of Epigenetic Histone Modifications in the Metabolic Memory of Type 1 Diabetes

(2014) Feng Miao et al.   DIABETES

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

A method for high purity intestinal epithelial cell culture from adult human and murine tissues for the investigation of innate immune function

(2014) Christina L. Graves et al.   JOURNAL OF IMMUNOLOGICAL METHODS

CD44 Suppresses TLR-Mediated Inflammation

(2014) H. Kawana et al.   JOURNAL OF IMMUNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Autoantibody Induction by DNA-Containing Immune Complexes Requires HMGB1 with the TLR2/MicroRNA-155 Pathway

(2013) Z. Wen et al.   JOURNAL OF IMMUNOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The regulation of toll-like receptor 2 by miR-143 suppresses the invasion and migration of a subset of human colorectal carcinoma cells

(2013) Haiyan Guo et al.   Molecular Cancer

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Duodenal Infusion of Donor Feces for Recurrent Clostridium difficile

(2013) Els van Nood et al.   NEW ENGLAND JOURNAL OF MEDICINE

Increase of Faecal Tryptic Activity Relates to Changes in the Intestinal Microbiome: Analysis of Crohn's Disease with a Multidisciplinary Platform

(2013) Tore Midtvedt et al.   PLoS One

The immune modifying effects of amino acids on gut-associated lymphoid tissue

(2013) Megan R Ruth et al.   Journal of Animal Science and Biotechnology

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Does the gut microbiota have a role in type 1 diabetes? Early evidence from humans and animal models of the disease

(2012) M. A. Atkinson et al.   DIABETOLOGIA

Innate immune signalling at the intestinal epithelium in homeostasis and disease

(2012) Johanna Pott et al.   EMBO REPORTS

Microbiota conservation and BMI signatures in adult monozygotic twins

(2012) Sebastian Tims et al.   ISME Journal

Analysis of the combined action of miR-143 and miR-145 on oncogenic pathways in colorectal cancer cells reveals a coordinate program of gene repression

(2012) A Pagliuca et al.   ONCOGENE

18S rRNA is a reliable normalisation gene for real time PCR based on influenza virus infected cells

(2012) Suresh V Kuchipudi et al.   Virology Journal

Development of the Human Gastrointestinal Microbiota and Insights From High-Throughput Sequencing

(2011) Maria Gloria Dominguez-Bello et al.   GASTROENTEROLOGY

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

The role of innate immune pathways in type 1 diabetes pathogenesis

(2011) Steven C Pino et al.   Current Opinion in Endocrinology Diabetes and Obesity

Skyline: an open source document editor for creating and analyzing targeted proteomics experiments

(2010) Brendan MacLean et al.   BIOINFORMATICS

MicroRNAs Control Intestinal Epithelial Differentiation, Architecture, and Barrier Function

(2010) Lindsay B. McKenna et al.   GASTROENTEROLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Alternative Splicing Markers for Breast Cancer

(2008) J. P. Venables et al.   CANCER RESEARCH

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

(2008) Li Wen et al.   NATURE