Wapl repression by Pax5 promotes V gene recombination by Igh loop extrusion

Absolute quantification of cohesin, CTCF and their regulators in human cells

(2019) Johann Holzmann et al.   eLife

The fundamental role of chromatin loop extrusion in physiological V(D)J recombination

(2019) Yu Zhang et al.   NATURE

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

CTCF-Binding Elements Mediate Accessibility of RAG Substrates During Chromatin Scanning

(2018) Suvi Jain et al.   CELL

Unbiased quantification of immunoglobulin diversity at the DNA level with VDJ-seq

(2018) Peter Chovanec et al.   Nature Protocols

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Multifunctional role of the transcription factor Blimp-1 in coordinating plasma cell differentiation

(2016) Martina Minnich et al.   NATURE IMMUNOLOGY

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Chromosomal Loop Domains Direct the Recombination of Antigen Receptor Genes

(2015) Jiazhi Hu et al.   CELL

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering

(2013) Hui Yang et al.   CELL

Mechanisms of Programmed DNA Lesions and Genomic Instability in the Immune System

(2013) Frederick W. Alt et al.   CELL

Flexible Long-Range Loops in the VH Gene Region of the Igh Locus Facilitate the Generation of a Diverse Antibody Repertoire

(2013) Jasna Medvedovic et al.   IMMUNITY

Wapl is an essential regulator of chromatin structure and chromosome segregation

(2013) Antonio Tedeschi et al.   NATURE

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

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples

(2012) Günter P. Wagner et al.   THEORY IN BIOSCIENCES

MEME-ChIP: motif analysis of large DNA datasets

(2011) Philip Machanick et al.   BIOINFORMATICS

The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells

(2011) Shane McManus et al.   EMBO JOURNAL

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

PeakAnalyzer: Genome-wide annotation of chromatin binding and modification loci

(2010) Mali Salmon-Divon et al.   BMC BIOINFORMATICS

The In Vivo Pattern of Binding of RAG1 and RAG2 to Antigen Receptor Loci

(2010) Yanhong Ji et al.   CELL

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Dre recombinase, like Cre, is a highly efficient site-specific recombinase in E. coli, mammalian cells and mice

(2009) K. Anastassiadis et al.   Disease Models & Mechanisms

Floxin, a resource for genetically engineering mouse ESCs

(2009) Veena Singla et al.   NATURE METHODS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Cohesins Functionally Associate with CTCF on Mammalian Chromosome Arms

(2008) Vania Parelho et al.   CELL

The 3D Structure of the Immunoglobulin Heavy-Chain Locus: Implications for Long-Range Genomic Interactions

(2008) Suchit Jhunjhunwala et al.   CELL

Cohesin mediates transcriptional insulation by CCCTC-binding factor

(2008) Kerstin S. Wendt et al.   NATURE

BAC TransgeneOmics: a high-throughput method for exploration of protein function in mammals

(2008) Ina Poser et al.   NATURE METHODS