Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

MIG: Multi-Image Genome viewer

(2013) S. J. McGowan et al.   BIOINFORMATICS

Using GBrowse 2.0 to visualize and share next-generation sequence data

(2013) L. D. Stein   BRIEFINGS IN BIOINFORMATICS

ImpairedIn VitroErythropoiesis following Deletion of theScl(Tal1) +40 Enhancer Is Largely Compensated forIn Vivodespite a Significant Reduction in Expression

(2013) Rita Ferreira et al.   MOLECULAR AND CELLULAR BIOLOGY

Multiplexed chromosome conformation capture sequencing for rapid genome-scale high-resolution detection of long-range chromatin interactions

(2013) Ralph Stadhouders et al.   Nature Protocols

Enhancers: five essential questions

(2013) Len A. Pennacchio et al.   NATURE REVIEWS GENETICS

GATA-1 genome-wide occupancy associates with distinct epigenetic profiles in mouse fetal liver erythropoiesis

(2013) Giorgio L. Papadopoulos et al.   NUCLEIC ACIDS RESEARCH

High-resolution analysis of cis-acting regulatory networks at the  -globin locus

(2013) J. R. Hughes et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Causes and Consequences of Chromatin Variation between Inbred Mice

(2013) Mona Hosseini et al.   PLoS Genetics

Methods for Identifying Higher-Order Chromatin Structure

(2012) Samin A. Sajan et al.   Annual Review of Genomics and Human Genetics

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome

(2012) Andrea H. Horakova et al.   HUMAN MOLECULAR GENETICS

3C-based technologies to study the shape of the genome

(2012) Wouter de Laat et al.   METHODS

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The long-range interaction landscape of gene promoters

(2012) Amartya Sanyal 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

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Enhancers and silencers: an integrated and simple model for their function

(2012) Petros Kolovos et al.   Epigenetics & Chromatin

Chapter 11: Genome-Wide Association Studies

(2012) William S. Bush et al.   PLoS Computational Biology

Identification of Distal cis-Regulatory Elements at Mouse Mitoferrin Loci Using Zebrafish Transgenesis

(2011) J. D. Amigo et al.   MOLECULAR AND CELLULAR BIOLOGY

HIF1  synergizes with glucocorticoids to promote BFU-E progenitor self-renewal

(2010) J. Flygare et al.   BLOOD

A global role for KLF1 in erythropoiesis revealed by ChIP-seq in primary erythroid cells

(2010) M. R. Tallack et al.   GENOME RESEARCH

Genome-wide identification of TAL1's functional targets: Insights into its mechanisms of action in primary erythroid cells

(2010) M. T. Kassouf et al.   GENOME RESEARCH

USF and NF-E2 Cooperate to Regulate the Recruitment and Activity of RNA Polymerase II in the β-Globin Gene Locus

(2010) Zhuo Zhou et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias 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

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Whole exome capture in solution with 3 Gbp of data

(2010) Matthew N Bainbridge et al.   GENOME BIOLOGY

Chromosome looping at the human  -globin locus is mediated via the major upstream regulatory element (HS -40)

(2009) D. Vernimmen et al.   BLOOD

Adventitious changes in long-range gene expression caused by polymorphic structural variation and promoter competition

(2009) K. M. Lower et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Progress and challenges in genome-wide association studies in humans

(2008) Peter Donnelly   NATURE

High-resolution circular chromosome conformation capture assay

(2008) Anita Göndör et al.   Nature Protocols