Aire controls gene expression in the thymic epithelium with ordered stochasticity

Promiscuous mRNA splicing under the control of AIRE in medullary thymic epithelial cells

(2014) Peter Keane et al.   BIOINFORMATICS

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

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

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

(2014) Michael Waterfield et al.   NATURE IMMUNOLOGY

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

An RNAi screen for Aire cofactors reveals a role for Hnrnpl in polymerase release and Aire-activated ectopic transcription

(2014) M. Giraud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Quantitative assessment of single-cell RNA-sequencing methods

(2013) Angela R Wu et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

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

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

(2012) Massimiliano Gaetani et al.   NUCLEIC ACIDS RESEARCH

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

Aire regulates the transfer of antigen from mTECs to dendritic cells for induction of thymic tolerance

(2011) F.-X. Hubert et al.   BLOOD

Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation

(2011) Rui Zhao et al.   NATURE CELL BIOLOGY

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

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

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

(2009) Tõnis Org et al.   HUMAN MOLECULAR GENETICS

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

The impact of negative selection on thymocyte migration in the medulla

(2009) Marie Le Borgne et al.   NATURE IMMUNOLOGY

Regulated Fluctuations in Nanog Expression Mediate Cell Fate Decisions in Embryonic Stem Cells

(2009) Tibor Kalmar et al.   PLOS BIOLOGY

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

(2008) Tõnis Org et al.   EMBO REPORTS

The variable immunological self: Genetic variation and nongenetic noise in Aire-regulated transcription

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

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

Deletional Tolerance Mediated by Extrathymic Aire-Expressing Cells

(2008) J. M. Gardner et al.   SCIENCE