Liver Immune Profiling Reveals Pathogenesis and Therapeutics for Biliary Atresia

Gasdermin E suppresses tumour growth by activating anti-tumour immunity

(2020) Zhibin Zhang et al.   NATURE

Granzyme A from cytotoxic lymphocytes cleaves GSDMB to trigger pyroptosis in target cells

(2020) Zhiwei Zhou et al.   SCIENCE

Role of AGAP2 in the profibrogenic effects induced by TGFβ in LX-2 hepatic stellate cells

(2019) Amaia Navarro-Corcuera et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH

Intratumoral Tcf1+PD-1+CD8+ T Cells with Stem-like Properties Promote Tumor Control in Response to Vaccination and Checkpoint Blockade Immunotherapy

(2019) Imran Siddiqui et al.   IMMUNITY

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

New players in the gene regulatory network controlling late B cell differentiation

(2019) Simon N Willis et al.   CURRENT OPINION IN IMMUNOLOGY

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Discovery of a CD10-negative B-progenitor in human fetal life identifies unique ontogeny-related developmental programs

(2019) Sorcha O’Byrne et al.   BLOOD

Bile acid metabolites control TH17 and Treg cell differentiation

(2019) Saiyu Hang et al.   NATURE

Recovering Gene Interactions from Single-Cell Data Using Data Diffusion

(2018) David van Dijk et al.   CELL

S1PR5 is essential for human natural killer cell migration toward sphingosine-1 phosphate

(2018) Annabelle Drouillard et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

C1q restrains autoimmunity and viral infection by regulating CD8+T cell metabolism

(2018) Guang Sheng Ling et al.   SCIENCE

Autoimmune liver disease-related autoantibodies in patients with biliary atresia

(2018) Shu-Yin Pang et al.   WORLD JOURNAL OF GASTROENTEROLOGY

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Incidence of Biliary Atresia and Timing of Hepatoportoenterostomy in the United States

(2017) Perri C. Hopkins et al.   JOURNAL OF PEDIATRICS

T memory stem cells in health and disease

(2017) Luca Gattinoni et al.   NATURE MEDICINE

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Hepatic Hilar Lymph Node Reactivity at Kasai Portoenterostomy for Biliary Atresia: Correlations With Age, Outcome, and Histology of Proximal Biliary Remnant

(2017) KE Bove et al.   PEDIATRIC AND DEVELOPMENTAL PATHOLOGY

Cystatin F Affects Natural Killer Cell Cytotoxicity

(2017) Milica Perišić Nanut et al.   Frontiers in Immunology

CD4 CTL, a Cytotoxic Subset of CD4+ T Cells, Their Differentiation and Function

(2017) Arata Takeuchi et al.   Frontiers in Immunology

Stromal cell-derived factor-1 (SDF-1) as a target in liver diseases

(2016) Anke Liepelt et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Bile Acids Control Inflammation and Metabolic Disorder through Inhibition of NLRP3 Inflammasome

(2016) Chuansheng Guo et al.   IMMUNITY

The Chemokine Receptor CX3CR1 Defines Three Antigen-Experienced CD8 T Cell Subsets with Distinct Roles in Immune Surveillance and Homeostasis

(2016) Carmen Gerlach et al.   IMMUNITY

Chitinase 3-Like 1 (Chil1) Regulates Survival and Macrophage-Mediated Interleukin-1β and Tumor Necrosis Factor Alpha during Pseudomonas aeruginosa Pneumonia

(2016) Chad R. Marion et al.   INFECTION AND IMMUNITY

Biliary atresia: A comprehensive review

(2016) Bhanumathi Lakshminarayanan et al.   JOURNAL OF AUTOIMMUNITY

An Atypical Splenic B Cell Progenitor Population Supports Antibody Production duringPlasmodiumInfection in Mice

(2016) Debopam Ghosh et al.   JOURNAL OF IMMUNOLOGY

Biliary atresia: Indications and timing of liver transplantation and optimization of pretransplant care

(2016) Shikha S. Sundaram et al.   LIVER TRANSPLANTATION

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Role of Natural Autoantibodies and Natural IgM Anti-Leucocyte Autoantibodies in Health and Disease

(2016) Peter Isaac Lobo   Frontiers in Immunology

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Polyfunctional, Pathogenic CD161+Th17 Lineage Cells Are Resistant to Regulatory T Cell–Mediated Suppression in the Context of Autoimmunity

(2015) Sharee A. Basdeo et al.   JOURNAL OF IMMUNOLOGY

The phosphatase DUSP2 controls the activity of the transcription activator STAT3 and regulates TH17 differentiation

(2015) Dan Lu et al.   NATURE IMMUNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Pathogenesis of biliary atresia: defining biology to understand clinical phenotypes

(2015) Akihiro Asai et al.   Nature Reviews Gastroenterology & Hepatology

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

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

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

Functional classification of memory CD8+ T cells by CX3CR1 expression

(2015) Jan P. Böttcher et al.   Nature Communications

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

TGR5 reduces macrophage migration through mTOR-induced C/EBPβ differential translation

(2014) Alessia Perino et al.   JOURNAL OF CLINICAL INVESTIGATION

The Soluble Leukocyte-Associated Ig-Like Receptor (LAIR)-2 Antagonizes the Collagen/LAIR-1 Inhibitory Immune Interaction

(2014) R. J. Lebbink et al.   JOURNAL OF IMMUNOLOGY

Serglycin: At the Crossroad of Inflammation and Malignancy

(2014) Angeliki Korpetinou et al.   Frontiers in Oncology

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

Bile acids PKA-dependently induce a switch of the IL-10/IL-12 ratio and reduce proinflammatory capability of human macrophages

(2013) Katrin Haselow et al.   JOURNAL OF LEUKOCYTE BIOLOGY

Rotavirus particles in the extrahepatic bile duct in experimental biliary atresia

(2013) Christina Oetzmann von Sochaczewski et al.   JOURNAL OF PEDIATRIC SURGERY

Chitinase 3-like 1 Regulates Cellular and Tissue Responses via IL-13 Receptor α2

(2013) Chuan Hua He et al.   Cell Reports

CD4+CD161+ T Lymphocytes Infiltrate Crohn’s Disease-Associated Perianal Fistulas and Are Reduced by Anti-TNF-a Local Therapy

(2012) Laura Maggi et al.   INTERNATIONAL ARCHIVES OF ALLERGY AND IMMUNOLOGY

Aiolos promotes TH17 differentiation by directly silencing Il2 expression

(2012) Francisco J Quintana et al.   NATURE IMMUNOLOGY

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The G-Protein-coupled bile acid receptor, Gpbar1 (TGR5), negatively regulates hepatic inflammatory response through antagonizing nuclear factor kappa light-chain enhancer of activated B cells (NF-κB) in mice

(2011) Yan-Dong Wang et al.   HEPATOLOGY

Interleukin-32: A new proinflammatory cytokine involved in hepatitis C virus-related liver inflammation and fibrosis

(2011) Alexander R. Moschen et al.   HEPATOLOGY

Fate mapping of IL-17-producing T cells in inflammatory responses

(2011) Keiji Hirota et al.   NATURE IMMUNOLOGY

G protein-coupled receptor 56 and collagen III, a receptor-ligand pair, regulates cortical development and lamination

(2011) R. Luo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biliary Atresia: Will Blocking Inflammation Tame the Disease?

(2010) Kazuhiko Bessho et al.   Annual Review of Medicine

α-Enolase Autoantibodies Cross-Reactive to Viral Proteins in a Mouse Model of Biliary Atresia

(2010) Brandy R. Lu et al.   GASTROENTEROLOGY

The fractalkine receptor CX3CR1 protects against liver fibrosis by controlling differentiation and survival of infiltrating hepatic monocytes

(2010) Karlin Raja Karlmark et al.   HEPATOLOGY

NADPH Oxidase Deficiency Regulates Th Lineage Commitment and Modulates Autoimmunity

(2010) H. M. Tse et al.   JOURNAL OF IMMUNOLOGY

A human B-cell interactome identifies MYB and FOXM1 as master regulators of proliferation in germinal centers

(2010) Celine Lefebvre et al.   Molecular Systems Biology

Preferential recruitment of interferon-γ-expressing TH17 cells in multiple sclerosis

(2009) Hania Kebir et al.   ANNALS OF NEUROLOGY

CX3CL1/fractalkine shedding by human hepatic stellate cells: contribution to chronic inflammation in the liver

(2009) Katia Bourd-Boittin et al.   JOURNAL OF CELLULAR AND MOLECULAR MEDICINE

Circulating and gut-resident human Th17 cells express CD161 and promote intestinal inflammation

(2009) Melanie A. Kleinschek et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Biliary atresia

(2009) Jane L Hartley et al.   LANCET

Expression and function of the bile acid receptor TGR5 in Kupffer cells

(2008) Verena Keitel et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

B lymphocytes: how they develop and function

(2008) T. W. LeBien et al.   BLOOD