Distinct microbial and immune niches of the human colon

Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches

(2019) Svetoslav Chakarov et al.   SCIENCE

Single-Cell Transcriptomics of Regulatory T Cells Reveals Trajectories of Tissue Adaptation

(2019) Ricardo J. Miragaia et al.   IMMUNITY

Anti-commensal IgG Drives Intestinal Inflammation and Type 17 Immunity in Ulcerative Colitis

(2019) Tomas Castro-Dopico et al.   IMMUNITY

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

BBKNN: fast batch alignment of single cell transcriptomes

(2019) Krzysztof Polański et al.   BIOINFORMATICS

Plasma cell output from germinal centers is regulated by signals from Tfh and stromal cells

(2018) Yang Zhang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Lamin A/C augments Th1 differentiation and response against vaccinia virus and Leishmania major

(2018) Raquel Toribio-Fernández et al.   Cell Death & Disease

Effector T Helper Cell Subsets in Inflammatory Bowel Diseases

(2018) Tanbeena Imam et al.   Frontiers in Immunology

Combined Influence of B-Cell Receptor Rearrangement and Somatic Hypermutation on B-Cell Class-Switch Fate in Health and in Chronic Lymphocytic Leukemia

(2018) Velislava N. Petrova et al.   Frontiers in Immunology

Human retinoic acid–regulated CD161+ regulatory T cells support wound repair in intestinal mucosa

(2018) Giovanni A. M. Povoleri et al.   NATURE IMMUNOLOGY

Cells with Treg-specific FOXP3 demethylation but low CD25 are prevalent in autoimmunity

(2017) Ricardo C. Ferreira et al.   JOURNAL OF AUTOIMMUNITY

Characterization of the B Cell Receptor Repertoire in the Intestinal Mucosa and of Tumor-Infiltrating Lymphocytes in Colorectal Adenoma and Carcinoma

(2017) Wei Zhang et al.   JOURNAL OF IMMUNOLOGY

An atlas of B-cell clonal distribution in the human body

(2017) Wenzhao Meng et al.   NATURE BIOTECHNOLOGY

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

Human Tissue-Resident Memory T Cells Are Defined by Core Transcriptional and Functional Signatures in Lymphoid and Mucosal Sites

(2017) Brahma V. Kumar et al.   Cell Reports

Dynamics of the human gut microbiome in inflammatory bowel disease

(2017) Jonas Halfvarson et al.   Nature Microbiology

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Highly specific blockade of CCR5 inhibits leukocyte trafficking and reduces mucosal inflammation in murine colitis

(2016) Andrea Mencarelli et al.   Scientific Reports

Change-O: a toolkit for analyzing large-scale B cell immunoglobulin repertoire sequencing data: Table 1.

(2015) Namita T. Gupta et al.   BIOINFORMATICS

tcR: an R package for T cell receptor repertoire advanced data analysis

(2015) Vadim I. Nazarov et al.   BMC BIOINFORMATICS

Th17 Cell Induction by Adhesion of Microbes to Intestinal Epithelial Cells

(2015) Koji Atarashi et al.   CELL

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Gut biogeography of the bacterial microbiota

(2015) Gregory P. Donaldson et al.   NATURE REVIEWS MICROBIOLOGY

Th17 cells give rise to Th1 cells that are required for the pathogenesis of colitis

(2015) Stacey N. Harbour et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

pRESTO: a toolkit for processing high-throughput sequencing raw reads of lymphocyte receptor repertoires

(2014) Jason A. Vander Heiden et al.   BIOINFORMATICS

The alarmin IL-33 promotes regulatory T-cell function in the intestine

(2014) Chris Schiering et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

IgBLAST: an immunoglobulin variable domain sequence analysis tool

(2013) Jian Ye et al.   NUCLEIC ACIDS RESEARCH

Plasticity of Foxp3+ T Cells Reflects Promiscuous Foxp3 Expression in Conventional T Cells but Not Reprogramming of Regulatory T Cells

(2012) Takahisa Miyao et al.   IMMUNITY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Bifidobacterial surface-exopolysaccharide facilitates commensal-host interaction through immune modulation and pathogen protection

(2012) S. Fanning et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Specializations of Intestinal Dendritic Cell and Macrophage Subsets That Control Th17 and Regulatory T Cell Responses Are Dependent on the T Cell/APC Ratio, Source of Mouse Strain, and Regional Localization

(2011) T. L. Denning et al.   JOURNAL OF IMMUNOLOGY

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Circulating human B and plasma cells. Age-associated changes in counts and detailed characterization of circulating normal CD138- and CD138+ plasma cells

(2010) A. Caraux et al.   HAEMATOLOGICA

Function of Mucosa-Associated Lymphoid Tissue in Antibody Formation

(2010) Per Brandtzaeg   IMMUNOLOGICAL INVESTIGATIONS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Loss of FOXP3 expression in natural human CD4+CD25+regulatory T cells upon repetitivein vitrostimulation

(2009) Petra Hoffmann et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

Requirement for Lymphoid Tissue-Inducer Cells in Isolated Follicle Formation and T Cell-Independent Immunoglobulin A Generation in the Gut

(2008) Masayuki Tsuji et al.   IMMUNITY

Differentiation and homing of IgA-secreting cells

(2008) J R Mora et al.   Mucosal Immunology

Transcription factor KLF2 regulates the migration of naive T cells by restricting chemokine receptor expression patterns

(2008) Eric Sebzda et al.   NATURE IMMUNOLOGY