Disrupting the three-dimensional regulatory topology of thePitx1locus results in overtly normal development

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

Shhand ZRS enhancer colocalisation is specific to the zone of polarising activity

(2016) Iain Williamson et al.   DEVELOPMENT

Characterization of hundreds of regulatory landscapes in developing limbs reveals two regimes of chromatin folding

(2016) Guillaume Andrey et al.   GENOME RESEARCH

FourCSeq: analysis of 4C sequencing data

(2015) Felix A. Klein et al.   BIOINFORMATICS

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

Enhancer loops appear stable during development and are associated with paused polymerase

(2014) Yad Ghavi-Helm et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

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

(2013) Hui Yang et al.   CELL

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

The genomic landscape of cohesin-associated chromatin interactions

(2013) L. E. DeMare et al.   GENOME RESEARCH

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

(2012) Justin Cotney et al.   GENOME RESEARCH

Analysis of long-range chromatin interactions using Chromosome Conformation Capture

(2012) Natalia Naumova et al.   METHODS

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal et al.   NATURE

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

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

Pitx1 haploinsufficiency causes clubfoot in humans and a clubfoot-like phenotype in mice

(2011) D. M. Alvarado et al.   HUMAN MOLECULAR GENETICS

Genomics of Long-Range Regulatory Elements

(2010) James P. Noonan et al.   Annual Review of Genomics and Human Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Shadow Enhancers Foster Robustness of Drosophila Gastrulation

(2010) Michael W. Perry et al.   CURRENT BIOLOGY

Distinct enhancers at the Pax3 locus can function redundantly to regulate neural tube and neural crest expressions

(2010) Karl R. Degenhardt et al.   DEVELOPMENTAL BIOLOGY

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

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

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Adaptive Evolution of Pelvic Reduction in Sticklebacks by Recurrent Deletion of a Pitx1 Enhancer

(2009) Y. F. Chan et al.   SCIENCE

Chromosomal Dynamics at the Shh Locus: Limb Bud-Specific Differential Regulation of Competence and Active Transcription

(2008) Takanori Amano et al.   DEVELOPMENTAL CELL

Shadow Enhancers as a Source of Evolutionary Novelty

(2008) J.-W. Hong et al.   SCIENCE

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY