Identification of environmental factors that promote intestinal inflammation

Gut-licensed IFNγ+ NK cells drive LAMP1+TRAIL+ anti-inflammatory astrocytes

(2021) Liliana M. Sanmarco et al.   NATURE

Self-tunable engineered yeast probiotics for the treatment of inflammatory bowel disease

(2021) Benjamin M. Scott et al.   NATURE MEDICINE

Environmentally-relevant exposure to diethylhexyl phthalate (DEHP) alters regulation of double-strand break formation and crossover designation leading to germline dysfunction in Caenorhabditis elegans

(2020) Luciann Cuenca et al.   PLoS Genetics

The Aryl Hydrocarbon Receptor (AHR) as a Potential Target for the Control of Intestinal Inflammation: Insights from an Immune and Bacteria Sensor Receptor

(2020) Larissa Pernomian et al.   CLINICAL REVIEWS IN ALLERGY & IMMUNOLOGY

JAK–STAT pathway targeting for the treatment of inflammatory bowel disease

(2020) Azucena Salas et al.   Nature Reviews Gastroenterology & Hepatology

Sutterella Species, IgA-degrading Bacteria in Ulcerative Colitis

(2020) Nadeem O. Kaakoush   TRENDS IN MICROBIOLOGY

Peroxisome Proliferator-Activated Receptors: Experimental Targeting for the Treatment of Inflammatory Bowel Diseases

(2020) Juan Decara et al.   Frontiers in Pharmacology

Heterogeneity and clonal relationships of adaptive immune cells in ulcerative colitis revealed by single-cell analyses

(2020) Brigid S. Boland et al.   Science Immunology

Single-Cell Sequencing of Developing Human Gut Reveals Transcriptional Links to Childhood Crohn’s Disease

(2020) Rasa Elmentaite et al.   DEVELOPMENTAL CELL

Environmental Control of Astrocyte Pathogenic Activities in CNS Inflammation

(2019) Michael A. Wheeler et al.   CELL

Tumour Necrosis Factor Alpha in Intestinal Homeostasis and Gut Related Diseases

(2019) Barbara Ruder et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

NetworkAnalyst 3.0: a visual analytics platform for comprehensive gene expression profiling and meta-analysis

(2019) Guangyan Zhou et al.   NUCLEIC ACIDS RESEARCH

Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data

(2019) Samuel L. Wolock et al.   Cell Systems

Risk Assessment on Benzene Exposure among Gasoline Station Workers

(2019) Chaiklieng et al.   International Journal of Environmental Research and Public Health

Divergent Roles for the IL-1 Family in Gastrointestinal Homeostasis and Inflammation

(2019) Craig P. McEntee et al.   Frontiers in Immunology

Single-Cell Analysis of Crohn’s Disease Lesions Identifies a Pathogenic Cellular Module Associated with Resistance to Anti-TNF Therapy

(2019) Jerome C. Martin et al.   CELL

The role of the p-value in the multitesting problem

(2019) P. Martínez-Camblor et al.   JOURNAL OF APPLIED STATISTICS

The microbiota regulate neuronal function and fear extinction learning

(2019) Coco Chu et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Dietary and Microbial Oxazoles Induce Intestinal Inflammation by Modulating Aryl Hydrocarbon Receptor Responses

(2018) Shankar S. Iyer et al.   CELL

Microglial control of astrocytes in response to microbial metabolites

(2018) Veit Rothhammer et al.   NATURE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

PANTHER version 14: more genomes, a new PANTHER GO-slim and improvements in enrichment analysis tools

(2018) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

(2017)   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Rapid changes in epidemiology of inflammatory bowel disease

(2017) Michael A Kamm   LANCET

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

Feedback control of AHR signalling regulates intestinal immunity

(2017) Chris Schiering et al.   NATURE

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

ToxCast Chemical Landscape: Paving the Road to 21st Century Toxicology

(2016) Ann M. Richard et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Identification of an atypical monocyte and committed progenitor involved in fibrosis

(2016) Takashi Satoh et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Type I interferons and microbial metabolites of tryptophan modulate astrocyte activity and central nervous system inflammation via the aryl hydrocarbon receptor

(2016) Veit Rothhammer et al.   NATURE MEDICINE

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands

(2016) Bruno Lamas et al.   NATURE MEDICINE

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease

(2016) H. Chu et al.   SCIENCE

Tolerogenic nanoparticles inhibit T cell–mediated autoimmunity through SOCS2

(2016) Ada Yeste et al.   Science Signaling

System-wide Analysis of the T Cell Response

(2016) Ruxandra Covacu et al.   Cell Reports

AHR Activation Is Protective against Colitis Driven by T Cells in Humanized Mice

(2016) Jeremy A. Goettel et al.   Cell Reports

Tolerogenic nanoparticles inhibit T cell–mediated autoimmunity through SOCS2

(2016) Ada Yeste et al.   Science Signaling

Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome

(2015) Benoit Chassaing et al.   NATURE

Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys

(2015) William Walters et al.   mSystems

Identification of Cinnabarinic Acid as a Novel Endogenous Aryl Hydrocarbon Receptor Ligand That Drives IL-22 Production

(2014) Margaret M. Lowe et al.   PLoS One

NF-κB: roles and regulation in different CD4+T-cell subsets

(2013) Hyunju Oh et al.   IMMUNOLOGICAL REVIEWS

Dynamic regulatory network controlling TH17 cell differentiation

(2013) Nir Yosef et al.   NATURE

IL-27 acts on DCs to suppress the T cell response and autoimmunity by inducing expression of the immunoregulatory molecule CD39

(2013) Ivan D Mascanfroni et al.   NATURE IMMUNOLOGY

Notch2-dependent classical dendritic cells orchestrate intestinal immunity to attaching-and-effacing bacterial pathogens

(2013) Ansuman T Satpathy et al.   NATURE IMMUNOLOGY

NF-κB control of T cell development

(2013) Steve Gerondakis et al.   NATURE IMMUNOLOGY

AhR signalling and dioxin toxicity

(2013) Olivier Sorg   TOXICOLOGY LETTERS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Zebrafish screen identifies novel compound with selective toxicity against leukemia

(2012) S. Ridges et al.   BLOOD

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Expression of the zinc finger transcription factor zDC (Zbtb46, Btbd4) defines the classical dendritic cell lineage

(2012) Matthew M. Meredith et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Human T cell expansion and experimental autoimmune encephalomyelitis inhibited by Lenaldekar, a small molecule discovered in a zebrafish screen

(2012) Matthew F. Cusick et al.   JOURNAL OF NEUROIMMUNOLOGY

A High-Throughput Chromatin Immunoprecipitation Approach Reveals Principles of Dynamic Gene Regulation in Mammals

(2012) Manuel Garber et al.   MOLECULAR CELL

Host–microbe interactions have shaped the genetic architecture of inflammatory bowel disease

(2012) Luke Jostins et al.   NATURE

Whole-organism screening for gluconeogenesis identifies activators of fasting metabolism

(2012) Philipp Gut et al.   Nature Chemical Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The Th17 immune response is controlled by the Rel–RORγ–RORγT transcriptional axis

(2011) Qingguo Ruan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

DHODH modulates transcriptional elongation in the neural crest and melanoma

(2011) Richard Mark White et al.   NATURE

Modular Utilization of Distal cis-Regulatory Elements Controls Ifng Gene Expression in T Cells Activated by Distinct Stimuli

(2010) Anand Balasubramani et al.   IMMUNITY

In vivo analysis of gut function and disease changes in a zebrafish larvae model of inflammatory bowel disease

(2010) Angeleen Fleming et al.   INFLAMMATORY BOWEL DISEASES

UniFrac: an effective distance metric for microbial community comparison

(2010) Catherine Lozupone et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Adaptive Autoimmunity and Foxp3-Based Immunoregulation in Zebrafish

(2010) Francisco J. Quintana et al.   PLoS One

Microtubule-mediated NF-κB activation in the TNF-α signaling pathway

(2009) Robert W. Jackman et al.   EXPERIMENTAL CELL RESEARCH

Predicting new molecular targets for known drugs

(2009) Michael J. Keiser et al.   NATURE

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS