Population and single-cell genomics reveal theAiredependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

CGAT: computational genomics analysis toolkit

(2014) D. Sims et al.   BIOINFORMATICS

Expression of Aire and the Early Wave of Apoptosis in Spermatogenesis

(2014) C. E. Schaller et al.   JOURNAL OF IMMUNOLOGY

Elephant shark genome provides unique insights into gnathostome evolution

(2014) Byrappa Venkatesh et al.   NATURE

The transcriptional regulator Aire coopts the repressive ATF7ip-MBD1 complex for the induction of immunotolerance

(2014) Michael Waterfield et al.   NATURE IMMUNOLOGY

Polycomb complexes in stem cells and embryonic development

(2013) L. Aloia et al.   DEVELOPMENT

Serial progression of cortical and medullary thymic epithelial microenvironments

(2013) Nuno L. Alves et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicing

(2013) G. K. Marinov et al.   GENOME RESEARCH

The Mechanism of Tissue-Restricted Antigen Gene Expression by AIRE

(2013) K. Zumer et al.   JOURNAL OF IMMUNOLOGY

Autoimmune Gastro-Pancreatitis with Anti-Protein Disulfide Isomerase-Associated 2 Autoantibody in Aire-Deficient BALB/cAnN Mice

(2013) Hironori Kurisaki et al.   PLoS One

Aire's plant homeodomain(PHD)-2 is critical for induction of immunological tolerance

(2013) S. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Murine thymic selection quantified using a unique method to capture deleted T cells

(2013) G. L. Stritesky et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BPIFB1 Is a Lung-Specific Autoantigen Associated with Interstitial Lung Disease

(2013) A. K. Shum et al.   Science Translational Medicine

Transcriptome sequencing of neonatal thymic epithelial cells

(2013) Charles St-Pierre et al.   Scientific Reports

Plasmacytoid Dendritic Cells Transport Peripheral Antigens to the Thymus to Promote Central Tolerance

(2012) Husein Hadeiba et al.   IMMUNITY

MicroRNAs Control the Maintenance of Thymic Epithelia and Their Competence for T Lineage Commitment and Thymocyte Selection

(2012) S. Zuklys et al.   JOURNAL OF IMMUNOLOGY

Unmodified Histone H3K4 and DNA-Dependent Protein Kinase Recruit Autoimmune Regulator to Target Genes

(2012) K. Zumer et al.   MOLECULAR AND CELLULAR BIOLOGY

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

AIRE-PHD fingers are structural hubs to maintain the integrity of chromatin-associated interactome

(2012) Massimiliano Gaetani et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Aire Promotes the Self-Renewal of Embryonic Stem Cells Through Lin28

(2012) Gu Bin et al.   STEM CELLS AND DEVELOPMENT

Thymic epithelial cells: working class heroes for T cell development and repertoire selection

(2012) Graham Anderson et al.   TRENDS IN IMMUNOLOGY

T-Cell Tolerance: Central and Peripheral

(2012) Y. Xing et al.   Cold Spring Harbor Perspectives in Biology

An encyclopedia of mouse DNA elements (Mouse ENCODE)

(2012) et al.   GENOME BIOLOGY

AIRE1A might be involved in cyclin B2 degradation in testicular lysates

(2011) M. Brahmaraju et al.   Biochemistry and Cell Biology

CHD6 chromatin remodeler is a negative modulator of influenza virus replication that relocates to inactive chromatin upon infection

(2011) Roberto Alfonso et al.   CELLULAR MICROBIOLOGY

Plant Homeodomain (PHD) Fingers of CHD4 Are Histone H3-binding Modules with Preference for Unmodified H3K4 and Methylated H3K9

(2011) Robyn E. Mansfield et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq

(2011) Mazhar Adli et al.   Nature Protocols

Fast and SNP-tolerant detection of complex variants and splicing in short reads

(2010) T. D. Wu et al.   BIOINFORMATICS

Aire's Partners in the Molecular Control of Immunological Tolerance

(2010) Jakub Abramson et al.   CELL

How thymic antigen presenting cells sample the body's self-antigens

(2010) Jens Derbinski et al.   CURRENT OPINION IN IMMUNOLOGY

Thymus-specific serine protease contributes to the diversification of the functional endogenous CD4 T cell receptor repertoire

(2010) Christophe Viret et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Epigenetic regulation of promiscuous gene expression in thymic medullary epithelial cells

(2010) L.-O. Tykocinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global relevance of Aire binding to hypomethylated lysine-4 of histone-3

(2010) A. S. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Aire

(2009) Diane Mathis et al.   Annual Review of Immunology

Binding of the CHD4 PHD2 finger to histone H3 is modulated by covalent modifications

(2009) Catherine A. Musselman et al.   BIOCHEMICAL JOURNAL

qvality: non-parametric estimation of q-values and posterior error probabilities

(2009) Lukas Käll et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Clearing the AIRE: On the Pathophysiological Basis of the Autoimmune Polyendocrinopathy Syndrome Type-1

(2009) Noriko Shikama et al.   ENDOCRINOLOGY AND METABOLISM CLINICS OF NORTH AMERICA

AIRE activated tissue specific genes have histone modifications associated with inactive chromatin

(2009) Tõnis Org et al.   HUMAN MOLECULAR GENETICS

Structure and Site-Specific Recognition of Histone H3 by the PHD Finger of Human Autoimmune Regulator

(2009) Suvobrata Chakravarty et al.   STRUCTURE

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

The autoimmune regulator PHD finger binds to non-methylated histone H3K4 to activate gene expression

(2008) Tõnis Org et al.   EMBO REPORTS

Autoantigen-Specific Interactions with CD4+ Thymocytes Control Mature Medullary Thymic Epithelial Cell Cellularity

(2008) Magali Irla et al.   IMMUNITY

Clonal deletion of thymocytes can occur in the cortex with no involvement of the medulla

(2008) Tom M. McCaughtry et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Ectopic expression of peripheral-tissue antigens in the thymic epithelium: Probabilistic, monoallelic, misinitiated

(2008) J. Villasenor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aire employs a histone-binding module to mediate immunological tolerance, linking chromatin regulation with organ-specific autoimmunity

(2008) A. S. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differentiation of regulatory Foxp3+ T cells in the thymic cortex

(2008) A. Liston et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Promiscuous gene expression patterns in single medullary thymic epithelial cells argue for a stochastic mechanism

(2008) J. Derbinski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells

(2008) J. M. Gardner et al.   SCIENCE

TSCOT + Thymic Epithelial Cell-Mediated Sensitive CD4 Tolerance by Direct Presentation

(2008) Sejin Ahn et al.   PLOS BIOLOGY

Role of PHD fingers and COOH-terminal 30 amino acids in AIRE transactivation activity

(2007) Alessandra Meloni et al.   MOLECULAR IMMUNOLOGY