Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming

EBF2 transcriptionally regulates brown adipogenesis via the histone reader DPF3 and the BAF chromatin remodeling complex

(2017) Suzanne N. Shapira et al.   GENES & DEVELOPMENT

A dynamic interplay of enhancer elements regulates Klf4 expression in naïve pluripotency

(2017) Liangqi Xie et al.   GENES & DEVELOPMENT

A Stringent Systems Approach Uncovers Gene-Specific Mechanisms Regulating Inflammation

(2016) Ann-Jay Tong et al.   CELL

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Chromatin programming by developmentally regulated transcription factors: lessons from the study of haematopoietic stem cell specification and differentiation

(2016) Nadine Obier et al.   FEBS LETTERS

Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming

(2016) Sören Boller et al.   IMMUNITY

Single-cell analysis of mixed-lineage states leading to a binary cell fate choice

(2016) Andre Olsson et al.   NATURE

Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment

(2016) Hao Yuan Kueh et al.   NATURE IMMUNOLOGY

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Tissue-specific DNA demethylation is required for proper B-cell differentiation and function

(2016) Shari Orlanski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

(2015) A. Pataskar et al.   EMBO JOURNAL

The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth

(2015) Claudia Bossen et al.   NATURE IMMUNOLOGY

New roles for DNA cytosine modification, eRNA, anchors, and superanchors in developing B cell progenitors

(2015) Christopher Benner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional Control of Early T and B Cell Developmental Choices

(2014) Ellen V. Rothenberg   Annual Review of Immunology

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

The regulatory network of B-cell differentiation: a focused view of early B-cell factor 1 function

(2014) Sören Boller et al.   IMMUNOLOGICAL REVIEWS

EBF1 Is Essential for B-Lineage Priming and Establishment of a Transcription Factor Network in Common Lymphoid Progenitors

(2014) S. Zandi et al.   JOURNAL OF IMMUNOLOGY

Coregulation of Transcription Factor Binding and Nucleosome Occupancy through DNA Features of Mammalian Enhancers

(2014) Iros Barozzi et al.   MOLECULAR CELL

The establishment of B versus T cell identity

(2014) Kazuko Miyazaki et al.   TRENDS IN IMMUNOLOGY

Transcriptional Repression of Gata3 Is Essential for Early B Cell Commitment

(2013) Anupam Banerjee et al.   IMMUNITY

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells

(2013) Robert Nechanitzky et al.   NATURE IMMUNOLOGY

Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data

(2013) Jason Piper et al.   NUCLEIC ACIDS RESEARCH

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Foxp3 Exploits a Pre-Existent Enhancer Landscape for Regulatory T Cell Lineage Specification

(2012) Robert M. Samstein et al.   CELL

DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina

(2012) Joseph M. Zullo et al.   CELL

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis

(2012) Roger Revilla-i-Domingo et al.   EMBO JOURNAL

The SWI/SNF-like BAF Complex Is Essential for Early B Cell Development

(2012) J. Choi et al.   JOURNAL OF IMMUNOLOGY

Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

(2012) Yin C Lin et al.   NATURE IMMUNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate

(2012) R. Mansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lineage Regulators Direct BMP and Wnt Pathways to Cell-Specific Programs during Differentiation and Regeneration

(2011) Eirini Trompouki et al.   CELL

Multilineage Priming of Enhancer Repertoires Precedes Commitment to the B and Myeloid Cell Lineages in Hematopoietic Progenitors

(2011) Elinore M. Mercer et al.   IMMUNITY

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges et al.   MOLECULAR CELL

Early B Cell Factor 1 Regulates B Cell Gene Networks by Activation, Repression, and Transcription- Independent Poising of Chromatin

(2010) Thomas Treiber et al.   IMMUNITY

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

(2010) Yin C Lin et al.   NATURE IMMUNOLOGY

An Early T Cell Lineage Commitment Checkpoint Dependent on the Transcription Factor Bcl11b

(2010) L. Li et al.   SCIENCE

An Essential Developmental Checkpoint for Production of the T Cell Lineage

(2010) T. Ikawa et al.   SCIENCE

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ly6d marks the earliest stage of B-cell specification and identifies the branchpoint between B-cell and T-cell development

(2009) M. A. Inlay et al.   GENES & DEVELOPMENT

Opposing effects of SWI/SNF and Mi-2/NuRD chromatin remodeling complexes on epigenetic reprogramming by EBF and Pax5

(2009) H. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptional repression mediated by repositioning of genes to the nuclear lamina

(2008) K. L. Reddy et al.   NATURE

Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros

(2008) Damien Reynaud et al.   NATURE IMMUNOLOGY

Distinct functions for the transcription factor Foxo1 at various stages of B cell differentiation

(2008) Hart S Dengler et al.   NATURE IMMUNOLOGY

Transcription factor EBF restricts alternative lineage options and promotes B cell fate commitment independently of Pax5

(2008) Jagan M R Pongubala et al.   NATURE IMMUNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY