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

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

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

Chromosomal Contact Permits Transcription between Coregulated Genes

(2013) Stephanie Fanucchi et al.   CELL

Extensive polymerase pausing during Drosophila axis patterning enables high-level and pliable transcription

(2013) A. Saunders et al.   GENES & DEVELOPMENT

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

ArchTEx: accurate extraction and visualization of next-generation sequence data

(2012) William K. M. Lai et al.   BIOINFORMATICS

A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History

(2012) Guillaume Junion et al.   CELL

Controlling Long-Range Genomic Interactions at a Native Locus by Targeted Tethering of a Looping Factor

(2012) Wulan Deng et al.   CELL

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

(2012) Tom Sexton et al.   CELL

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

Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development

(2012) Stefan Bonn et al.   NATURE GENETICS

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

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

Cell type–specific chromatin immunoprecipitation from multicellular complex samples using BiTS-ChIP

(2012) Stefan Bonn et al.   Nature Protocols

FlyBase: improvements to the bibliography

(2012) Steven J. Marygold et al.   NUCLEIC ACIDS RESEARCH

Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression

(2012) Bjoern Gaertner et al.   Cell Reports

Predicting Spatial and Temporal Gene Expression Using an Integrative Model of Transcription Factor Occupancy and Chromatin State

(2012) Bartek Wilczynski et al.   PLoS Computational Biology

Polycomb-Dependent Regulatory Contacts between Distant Hox Loci in Drosophila

(2011) Frédéric Bantignies et al.   CELL

A Regulatory Archipelago Controls Hox Genes Transcription in Digits

(2011) Thomas Montavon et al.   CELL

RNA sequencing reveals two major classes of gene expression levels in metazoan cells

(2011) D. Hebenstreit et al.   Molecular Systems Biology

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

The Dynamic Architecture of Hox Gene Clusters

(2011) D. Noordermeer et al.   SCIENCE

Interactions among Polycomb Domains Are Guided by Chromosome Architecture

(2011) Bas Tolhuis et al.   PLoS Genetics

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

The transmembrane receptor Uncoordinated5 (Unc5) is essential for heart lumen formation in Drosophila melanogaster

(2010) Stefanie Albrecht et al.   DEVELOPMENTAL BIOLOGY

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

REDfly v3.0: toward a comprehensive database of transcriptional regulatory elements in Drosophila

(2010) S. M. Gallo et al.   NUCLEIC ACIDS RESEARCH

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Stalled Hox promoters as chromosomal boundaries

(2009) V. S. Chopra et al.   GENES & DEVELOPMENT

Combinatorial binding predicts spatio-temporal cis-regulatory activity

(2009) Robert P. Zinzen et al.   NATURE

Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells

(2009) Stefan Schoenfelder et al.   NATURE GENETICS

Transcription Regulation Through Promoter-Proximal Pausing of RNA Polymerase II

(2008) L. J. Core et al.   SCIENCE