Enhancer redundancy provides phenotypic robustness in mammalian development

Composition and dosage of a multipartite enhancer cluster control developmental expression of Ihh (Indian hedgehog)

(2017) Anja J Will et al.   NATURE GENETICS

Limb development: a paradigm of gene regulation

(2017) Florence Petit et al.   NATURE REVIEWS GENETICS

Progressive Loss of Function in a Limb Enhancer during Snake Evolution

(2016) Evgeny Z. Kvon et al.   CELL

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Shadow Enhancers Are Pervasive Features of Developmental Regulatory Networks

(2016) Enrico Cannavò et al.   CURRENT BIOLOGY

A unique stylopod patterning mechanism byShox2-controlled osteogenesis

(2016) Wenduo Ye 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

Cis-regulatory architecture of a brain signaling center predates the origin of chordates

(2016) Yao Yao et al.   NATURE GENETICS

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Systematic mapping of functional enhancer–promoter connections with CRISPR interference

(2016) Charles P. Fulco et al.   SCIENCE

Genome-wide compendium and functional assessment of in vivo heart enhancers

(2016) Diane E. Dickel et al.   Nature Communications

The Gene Regulatory Network of Lens Induction Is Wired through Meis-Dependent Shadow Enhancers of Pax6

(2016) Barbora Antosova et al.   PLoS Genetics

Using combined evidence from replicates to evaluate ChIP-seq peaks

(2015) Vahid Jalili et al.   BIOINFORMATICS

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

(2015) Darío G. Lupiáñez et al.   CELL

Epigenomic Signatures of Neuronal Diversity in the Mammalian Brain

(2015) Alisa Mo et al.   NEURON

Mouse genome database 2016

(2015) Carol J. Bult et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

Partially Redundant Enhancers Cooperatively Maintain Mammalian Pomc Expression Above a Critical Functional Threshold

(2015) Daniel D. Lam et al.   PLoS Genetics

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

(2014) S. Anders et al.   BIOINFORMATICS

A Gli silencer is required for robust repression of gremlin in the vertebrate limb bud

(2014) Qiang Li et al.   DEVELOPMENT

HAND2 Targets Define a Network of Transcriptional Regulators that Compartmentalize the Early Limb Bud Mesenchyme

(2014) Marco Osterwalder et al.   DEVELOPMENTAL CELL

Identification of Novel Craniofacial Regulatory Domains Located far Upstream ofSOX9and Disrupted in Pierre Robin Sequence

(2014) Christopher T. Gordon et al.   HUMAN MUTATION

Generating genetically modified mice using CRISPR/Cas-mediated genome engineering

(2014) Hui Yang et al.   Nature Protocols

Gene Ontology Consortium: going forward

(2014)   NUCLEIC ACIDS RESEARCH

CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing

(2014) Tessa G. Montague et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Hui Yang et al.   CELL

A High-Resolution Enhancer Atlas of the Developing Telencephalon

(2013) Axel Visel et al.   CELL

Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development

(2013) Alex S. Nord et al.   CELL

An Integrated Holo-Enhancer Unit Defines Tissue and Gene Specificity of the Fgf8 Regulatory Landscape

(2013) Mirna Marinić et al.   DEVELOPMENTAL CELL

Comparative transgenic analysis of enhancers from the human SHOX and mouse Shox2 genomic regions

(2013) J. M. Rosin et al.   HUMAN MOLECULAR GENETICS

Fine Tuning of Craniofacial Morphology by Distant-Acting Enhancers

(2013) C. Attanasio et al.   SCIENCE

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

(2013) Daehwan Kim et al.   GENOME BIOLOGY

GLI3 Constrains Digit Number by Controlling Both Progenitor Proliferation and BMP-Dependent Exit to Chondrogenesis

(2012) Javier Lopez-Rios et al.   DEVELOPMENTAL CELL

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Cis-regulatory control of corticospinal system development and evolution

(2012) Sungbo Shim et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Shadow enhancers: Frequently asked questions about distributed cis-regulatory information and enhancer redundancy

(2011) Scott Barolo   BIOESSAYS

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

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

Phenotypic robustness conferred by apparently redundant transcriptional enhancers

(2010) Nicolás Frankel et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Sall genes regulate region-specific morphogenesis in the mouse limb by modulating Hox activities

(2009) Y. Kawakami et al.   DEVELOPMENT

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Vertebrate limb bud development: moving towards integrative analysis of organogenesis

(2009) Rolf Zeller et al.   NATURE REVIEWS GENETICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs

(2008) D. B. Menke et al.   DEVELOPMENT

Analyzing real-time PCR data by the comparative CT method

(2008) Thomas D Schmittgen et al.   Nature Protocols

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