Single-cell transcriptome analysis reveals coordinated ectopic gene-expression patterns in medullary thymic epithelial cells

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Regulatory T cells generated early in life play a distinct role in maintaining self-tolerance

(2015) S. Yang et al.   SCIENCE

Homeodomain-Interacting Protein Kinase 2, a Novel Autoimmune Regulator Interaction Partner, Modulates Promiscuous Gene Expression in Medullary Thymic Epithelial Cells

(2015) Kristin Rattay et al.   JOURNAL OF IMMUNOLOGY

Misinitiation of intrathymicMART-1transcription and biased TCR usage explain the high frequency of MART-1-specific T cells

(2014) Sheena Pinto et al.   EUROPEAN JOURNAL OF IMMUNOLOGY

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

(2014) Stephen N. Sansom et al.   GENOME RESEARCH

Distinct Contributions of Aire and Antigen-Presenting-Cell Subsets to the Generation of Self-Tolerance in the Thymus

(2014) Justin S.A. Perry et al.   IMMUNITY

A promoter-level mammalian expression atlas

(2014)   NATURE

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

(2014) Michael Waterfield et al.   NATURE IMMUNOLOGY

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

(2013) Yusuke Ohnishi et al.   NATURE CELL BIOLOGY

Accounting for technical noise in single-cell RNA-seq experiments

(2013) Philip Brennecke et al.   NATURE METHODS

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

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Overlapping gene coexpression patterns in human medullary thymic epithelial cells generate self-antigen diversity

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

Aire-Dependent Thymic Development of Tumor-Associated Regulatory T Cells

(2013) S. Malchow et al.   SCIENCE

Transcriptome sequencing of neonatal thymic epithelial cells

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

Regional Activation of the Cancer Genome by Long-Range Epigenetic Remodeling

(2012) Saul A. Bert et al.   CANCER CELL

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Highly multiplexed and strand-specific single-cell RNA 5′ end sequencing

(2012) Saiful Islam et al.   Nature Protocols

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Aire unleashes stalled RNA polymerase to induce ectopic gene expression in thymic epithelial cells

(2011) M. Giraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Aire's Partners in the Molecular Control of Immunological Tolerance

(2010) Jakub Abramson et al.   CELL

RNA-Seq analysis to capture the transcriptome landscape of a single cell

(2010) Fuchou Tang et al.   Nature Protocols

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

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Aire

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

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

The impact of negative selection on thymocyte migration in the medulla

(2009) Marie Le Borgne et al.   NATURE IMMUNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS

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

(2008) Tõnis Org et al.   EMBO REPORTS

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

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