Human T-bet Governs Innate and Innate-like Adaptive IFN-γ Immunity against Mycobacteria

Mendelian susceptibility to mycobacterial disease: recent discoveries

(2020) Jacinta Bustamante   HUMAN GENETICS

Lethal Infectious Diseases as Inborn Errors of Immunity: Toward a Synthesis of the Germ and Genetic Theories

(2020) Jean-Laurent Casanova et al.   Annual Review of Pathology-Mechanisms of Disease

Improved transplant survival and long-term disease outcome in children with MHC class II deficiency

(2020) Su Han Lum et al.   BLOOD

The human genetic determinism of life-threatening infectious diseases: genetic heterogeneity and physiological homogeneity?

(2020) Jean-Laurent Casanova et al.   HUMAN GENETICS

Inherited human IFN-γ deficiency underlies mycobacterial disease

(2020) Gaspard Kerner et al.   JOURNAL OF CLINICAL INVESTIGATION

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Multibatch Cytometry Data Integration for Optimal Immunophenotyping

(2020) Masato Ogishi et al.   JOURNAL OF IMMUNOLOGY

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Somatic genetic rescue in Mendelian haematopoietic diseases

(2019) Patrick Revy et al.   NATURE REVIEWS GENETICS

Circulating CXCR3+ Tfh cells positively correlate with neutralizing antibody responses in HCV-infected patients

(2019) Jian Zhang et al.   Scientific Reports

The biology and functional importance of MAIT cells

(2019) Dale I. Godfrey et al.   NATURE IMMUNOLOGY

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

Hematopoietic Cell Transplantation for MHC Class II Deficiency

(2019) Su Han Lum et al.   Frontiers in Pediatrics

PopViz: a webserver for visualizing minor allele frequencies and damage prediction scores of human genetic variations

(2018) Peng Zhang et al.   BIOINFORMATICS

Human Th9 differentiation is dependent upon STAT3 to restrain STAT1-mediated inhibition

(2018) Yuan Zhang et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Butyrophilin3A proteins and Vγ9Vδ2 T cell activation

(2018) Siyi Gu et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Human genetics of infectious diseases: Unique insights into immunological redundancy

(2018) Jean-Laurent Casanova et al.   SEMINARS IN IMMUNOLOGY

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

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

Clinical, Immunological, and Molecular Findings in Five Patients with Major Histocompatibility Complex Class II Deficiency from India

(2018) Jahnavi Aluri et al.   Frontiers in Immunology

Mendelian susceptibility to mycobacterial disease: 2014-2018 update

(2018) Jérémie Rosain et al.   IMMUNOLOGY AND CELL BIOLOGY

Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency

(2018) Nicholas Hernandez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Disruption of an antimycobacterial circuit between dendritic and helper T cells in human SPPL2a deficiency

(2018) Xiao-Fei Kong et al.   NATURE IMMUNOLOGY

Human Sox4 facilitates the development of CXCL13-producing helper T cells in inflammatory environments

(2018) Hiroyuki Yoshitomi et al.   Nature Communications

T-bet controls intestinal mucosa immune responses via repression of type 2 innate lymphoid cell function

(2018) N. Garrido-Mesa et al.   Mucosal Immunology

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Transcription Factor T-bet Limits Amplification of Type I IFN Transcriptome and Circuitry in T Helper 1 Cells

(2017) Shigeru Iwata et al.   IMMUNITY

Inherited GINS1 deficiency underlies growth retardation along with neutropenia and NK cell deficiency

(2017) Julien Cottineau et al.   JOURNAL OF CLINICAL INVESTIGATION

Human immunity against EBV—lessons from the clinic

(2017) Stuart G. Tangye et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Stability and function of regulatory T cells expressing the transcription factor T-bet

(2017) Andrew G. Levine et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Mucosal-Associated Invariant T Cells: New Insights into Antigen Recognition and Activation

(2017) Xingxing Xiao et al.   Frontiers in Immunology

Detection of genome-edited mutant clones by a simple competition-based PCR method

(2017) Takeshi Harayama et al.   PLoS One

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Dual T cell– and B cell–intrinsic deficiency in humans with biallelicRLTPRmutations

(2016) Yi Wang et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Induction of Th1-Biased T Follicular Helper (Tfh) Cells in Lymphoid Tissues during Chronic Simian Immunodeficiency Virus Infection Defines Functionally Distinct Germinal Center Tfh Cells

(2016) Vijayakumar Velu et al.   JOURNAL OF IMMUNOLOGY

Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery

(2016) Eric M Scott et al.   NATURE GENETICS

The mutation significance cutoff: gene-level thresholds for variant predictions

(2016) Yuval Itan et al.   NATURE METHODS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

Singular role for T-BET+CXCR3+regulatory T cells in protection from autoimmune diabetes

(2016) Tze Guan Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Quantitative Analysis of Complexity of Human Pathogen-Specific CD4 T Cell Responses in Healthy M. tuberculosis Infected South Africans

(2016) Cecilia S. Lindestam Arlehamn et al.   PLoS Pathogens

FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

(2015) Sofie Van Gassen et al.   CYTOMETRY PART A

β2-Microglobulin deficiency causes a complex immunodeficiency of the innate and adaptive immune system

(2015) Ömür Ardeniz et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Monogenic mutations differentially affect the quantity and quality of T follicular helper cells in patients with human primary immunodeficiencies

(2015) Cindy S. Ma et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Diverse Roles for T-bet in the Effector Responses Required for Resistance to Infection

(2015) Gretchen Harms Pritchard et al.   JOURNAL OF IMMUNOLOGY

T-bet Is Required for the Rapid Clearance of Attenuated Rabies Virus from Central Nervous System Tissue

(2015) Aurore Lebrun et al.   JOURNAL OF IMMUNOLOGY

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Human genetic basis of interindividual variability in the course of infection

(2015) Jean-Laurent Casanova   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The human gene damage index as a gene-level approach to prioritizing exome variants

(2015) Yuval Itan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Severe infectious diseases of childhood as monogenic inborn errors of immunity

(2015) Jean-Laurent Casanova   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive serological profiling of human populations using a synthetic human virome

(2015) G. J. Xu et al.   SCIENCE

Impairment of immunity to Candida and Mycobacterium in humans with bi-allelic RORC mutations

(2015) S. Okada et al.   SCIENCE

The Intolerance of Regulatory Sequence to Genetic Variation Predicts Gene Dosage Sensitivity

(2015) Slavé Petrovski et al.   PLoS Genetics

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

γδT Cells: First Line of Defense and Beyond

(2014) Yueh-hsiu Chien et al.   Annual Review of Immunology

HGCS: an online tool for prioritizing disease-causing gene variants by biological distance

(2014) Yuval Itan et al.   BMC GENOMICS

MHC class I and II deficiencies

(2014) Suheir Hanna et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Major Histocompatibility Complex Class II Deficiency Complicated by Mycobacterium avium Complex in a Boy of Mixed Ethnicity

(2014) Dimana Dimitrova et al.   JOURNAL OF CLINICAL IMMUNOLOGY

Guidelines for genetic studies in single patients: lessons from primary immunodeficiencies

(2014) Jean-Laurent Casanova et al.   JOURNAL OF EXPERIMENTAL MEDICINE

T-bet and Eomes instruct the development of two distinct natural killer cell lineages in the liver and in the bone marrow

(2014) Cécile Daussy et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Role of Th1/Th17 Balance Regulated by T-bet in a Mouse Model of Mycobacterium avium Complex Disease

(2014) M. Matsuyama et al.   JOURNAL OF IMMUNOLOGY

Human intracellular ISG15 prevents interferon-α/β over-amplification and auto-inflammation

(2014) Xianqin Zhang et al.   NATURE

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Motif-based analysis of large nucleotide data sets using MEME-ChIP

(2014) Wenxiu Ma et al.   Nature Protocols

Functional heterogeneity of human memory CD4+ T cell clones primed by pathogens or vaccines

(2014) S. Becattini et al.   SCIENCE

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data

(2014) Thomas S. Carroll et al.   Frontiers in Genetics

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

(2013) Y. Liao et al.   BIOINFORMATICS

Lysine 313 of T-box Is Crucial for Modulation of Protein Stability, DNA Binding, and Threonine Phosphorylation of T-bet

(2013) E. J. Jang et al.   JOURNAL OF IMMUNOLOGY

Genome-Wide Regulatory Analysis Reveals That T-bet Controls Th17 Lineage Differentiation through Direct Suppression of IRF4

(2013) M. R. Gokmen et al.   JOURNAL OF IMMUNOLOGY

The Transcription Factor T-bet Regulates Parasitemia and Promotes Pathogenesis during Plasmodium berghei ANKA Murine Malaria

(2013) M. S. Oakley et al.   JOURNAL OF IMMUNOLOGY

viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia

(2013) El-ad David Amir et al.   NATURE BIOTECHNOLOGY

The transcription factor T-bet is essential for the development of NKp46+ innate lymphocytes via the Notch pathway

(2013) Lucille C Rankin et al.   NATURE IMMUNOLOGY

Butyrophilin 3A1 binds phosphorylated antigens and stimulates human γδ T cells

(2013) Stefano Vavassori et al.   NATURE IMMUNOLOGY

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

The human gene connectome as a map of short cuts for morbid allele discovery

(2013) Y. Itan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Key implication of CD277/butyrophilin-3 (BTN3A) in cellular stress sensing by a major human    T-cell subset

(2012) C. Harly et al.   BLOOD

RIPPLY3 is a retinoic acid-inducible repressor required for setting the borders of the pre-placodal ectoderm

(2012) A. Janesick et al.   DEVELOPMENT

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

The Transcription Factor T-bet Regulates Intestinal Inflammation Mediated by Interleukin-7 Receptor+ Innate Lymphoid Cells

(2012) Nick Powell et al.   IMMUNITY

MCM4 mutation causes adrenal failure, short stature, and natural killer cell deficiency in humans

(2012) Claire R. Hughes et al.   JOURNAL OF CLINICAL INVESTIGATION

Recessive mutations inMCM4/PRKDCcause a novel syndrome involving a primary immunodeficiency and a disorder of DNA repair

(2012) Jillian P Casey et al.   JOURNAL OF MEDICAL GENETICS

MR1 presents microbial vitamin B metabolites to MAIT cells

(2012) Lars Kjer-Nielsen et al.   NATURE

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Mycobacterial Disease and Impaired IFN-  Immunity in Humans with Inherited ISG15 Deficiency

(2012) D. Bogunovic et al.   SCIENCE

T-bet and GATA3 orchestrate Th1 and Th2 differentiation through lineage-specific targeting of distal regulatory elements

(2012) Aditi Kanhere et al.   Nature Communications

Annexin A1 and the regulation of innate and adaptive immunity

(2012) Felicity N. E. Gavins et al.   Frontiers in Immunology

The Role of XCR1 and its Ligand XCL1 in Antigen Cross-Presentation by Murine and Human Dendritic Cells

(2012) Richard A. Kroczek et al.   Frontiers in Immunology

CXCR3 in T cell function

(2011) Joanna R. Groom et al.   EXPERIMENTAL CELL RESEARCH

Mutation in the TCRα subunit constant gene (TRAC) leads to a human immunodeficiency disorder characterized by a lack of TCRαβ+ T cells

(2011) Neil V. Morgan et al.   JOURNAL OF CLINICAL INVESTIGATION

In vitro differentiation of human macrophages with enhanced antimycobacterial activity

(2011) Guillaume Vogt et al.   JOURNAL OF CLINICAL INVESTIGATION

Gain-of-function humanSTAT1mutations impair IL-17 immunity and underlie chronic mucocutaneous candidiasis

(2011) Luyan Liu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Transcription factor T-bet represses expression of the inhibitory receptor PD-1 and sustains virus-specific CD8+ T cell responses during chronic infection

(2011) Charlly Kao et al.   NATURE IMMUNOLOGY

IRF8Mutations and Human Dendritic-Cell Immunodeficiency

(2011) Sophie Hambleton et al.   NEW ENGLAND JOURNAL OF MEDICINE

Differentiation of Effector CD4 T Cell Populations

(2010) Jinfang Zhu et al.   Annual Review of Immunology

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Molecular mechanisms by which T-bet regulates T-helper cell commitment

(2010) Sara A. Miller et al.   IMMUNOLOGICAL REVIEWS

T-bet represses TH17 differentiation by preventing Runx1-mediated activation of the gene encoding RORγt

(2010) Vanja Lazarevic et al.   NATURE IMMUNOLOGY

CD56 negative NK cells: origin, function, and role in chronic viral disease

(2010) Niklas K. Björkström et al.   TRENDS IN IMMUNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Antisense-mediated exon skipping to correct IL-12Rβ1 deficiency in T cells

(2009) Esther van de Vosse et al.   BLOOD

The role of the Th1 transcription factor T-bet in a mouse model of immune-mediated bone-marrow failure

(2009) Y. Tang et al.   BLOOD

The Wiskott-Aldrich syndrome protein is required for iNKT cell maturation and function

(2009) Michela Locci et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Human naive and memory CD4+T cell repertoires specific for naturally processed antigens analyzed using libraries of amplified T cells

(2009) Rebekka Geiger et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The transcription factor T-bet controls regulatory T cell homeostasis and function during type 1 inflammation

(2009) Meghan A Koch et al.   NATURE IMMUNOLOGY

The transcription factors T-bet and GATA-3 control alternative pathways of T-cell differentiation through a shared set of target genes

(2009) R. G. Jenner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unprecedented diversity of genotypic revertants in lymphocytes of a patient with Wiskott-Aldrich syndrome

(2008) B. R. Davis et al.   BLOOD

Signal Transducer and Activator of Transcription 4 Is Required for the Transcription Factor T-bet to Promote T Helper 1 Cell-Fate Determination

(2008) Vivian T. Thieu et al.   IMMUNITY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY