Comprehensively Profiling the Chromatin Architecture of Tissue Restricted Antigen Expression in Thymic Epithelial Cells Over Development

Rapid chromatin repression by Aire provides precise control of immune tolerance

(2018) Andrew S. Koh et al.   NATURE IMMUNOLOGY

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

DNA breaks and chromatin structural changes enhance the transcription of autoimmune regulator target genes

(2017) Mithu Guha et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Prdm1 Regulates Thymic Epithelial Function To Prevent Autoimmunity

(2017) Natalie A. Roberts et al.   JOURNAL OF IMMUNOLOGY

A benchmark of gene expression tissue-specificity metrics

(2016) Nadezda Kryuchkova-Mostacci et al.   BRIEFINGS IN BIOINFORMATICS

Transcriptional programs that control expression of the autoimmune regulator gene Aire

(2016) Yonatan Herzig et al.   NATURE IMMUNOLOGY

Fezf2 Orchestrates a Thymic Program of Self-Antigen Expression for Immune Tolerance

(2015) Hiroyuki Takaba et al.   CELL

Adult thymic epithelial cell (TEC) progenitors and TEC stem cells: Models and mechanisms for TEC development and maintenance

(2015) Yoko Hamazaki   EUROPEAN JOURNAL OF IMMUNOLOGY

Dominant Mutations in the Autoimmune Regulator AIRE Are Associated with Common Organ-Specific Autoimmune Diseases

(2015) Bergithe E. Oftedal et al.   IMMUNITY

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Aire controls gene expression in the thymic epithelium with ordered stochasticity

(2015) Matthew Meredith et al.   NATURE IMMUNOLOGY

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

(2015) Philip Brennecke et al.   NATURE IMMUNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger 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

An Overview of the Intrathymic Intricacies of T Cell Development

(2014) D. K. Shah et al.   JOURNAL OF IMMUNOLOGY

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

Remodeling of the Enhancer Landscape during Macrophage Activation Is Coupled to Enhancer Transcription

(2013) Minna U. Kaikkonen et al.   MOLECULAR CELL

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

Aire-expressing thymic medullary epithelial cells originate from  5t-expressing progenitor cells

(2013) I. Ohigashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Post-Aire Maturation of Thymic Medullary Epithelial Cells Involves Selective Expression of Keratinocyte-Specific Autoantigens

(2012) Xiaoping Wang et al.   Frontiers in Immunology

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Skint-1 Identifies a Common Molecular Mechanism for the Development of Interferon-γ-Secreting versus Interleukin-17-Secreting γδ T Cells

(2011) Gleb Turchinovich et al.   IMMUNITY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads

(2010) G. Lunter et al.   GENOME RESEARCH

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY