Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Diverse and pervasive subcellular distributions for both coding and long noncoding RNAs

(2016) Ronit Wilk et al.   GENES & DEVELOPMENT

Drosophilapoised enhancers are generated during tissue patterning with the help of repression

(2016) Nina Koenecke et al.   GENOME RESEARCH

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

The eukaryotic promoter database in its 30th year: focus on non-vertebrate organisms

(2016) René Dreos et al.   NUCLEIC ACIDS RESEARCH

GAGA factor, a positive regulator of global gene expression, modulates transcriptional pausing and organization of upstream nucleosomes

(2016) Shih-Ying Tsai et al.   Epigenetics & Chromatin

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

Zygotic Genome Activation Triggers the DNA Replication Checkpoint at the Midblastula Transition

(2015) Shelby A. Blythe et al.   CELL

Zelda overcomes the high intrinsic nucleosome barrier at enhancers duringDrosophilazygotic genome activation

(2015) Yujia Sun et al.   GENOME RESEARCH

Zelda is differentially required for chromatin accessibility, transcription factor binding, and gene expression in the earlyDrosophilaembryo

(2015) Katharine N. Schulz et al.   GENOME RESEARCH

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in Drosophila

(2014) Z. Xu et al.   GENES & DEVELOPMENT

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

The Eukaryotic Promoter Database: expansion of EPDnew and new promoter analysis tools

(2014) René Dreos et al.   NUCLEIC ACIDS RESEARCH

Transcriptional repressors: multifaceted regulators of gene expression

(2013) N. Reynolds et al.   DEVELOPMENT

The Embryonic Linker Histone H1 Variant of Drosophila, dBigH1, Regulates Zygotic Genome Activation

(2013) Salvador Pérez-Montero et al.   DEVELOPMENTAL CELL

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

An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo

(2013) Zehra Ali-Murthy et al.   PLoS Genetics

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

(2013) Kai Chen et al.   eLife

Spatial expression of transcription factors in Drosophila embryonic organ development

(2013) Ann S Hammonds et al.   GENOME BIOLOGY

A System of Repressor Gradients Spatially Organizes the Boundaries of Bicoid-Dependent Target Genes

(2012) Hongtao Chen et al.   CELL

Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer

(2011) P. Struffi et al.   DEVELOPMENT

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Multiple enhancers ensure precision of gap gene-expression patterns in the Drosophila embryo

(2011) M. W. Perry et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

(2011) Susan E. Lott et al.   PLOS BIOLOGY

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

(2011) Chung-Yi Nien et al.   PLoS Genetics

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

(2011) Melissa M. Harrison et al.   PLoS Genetics

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

(2011) Xiao-Yong Li et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

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

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

Binding Site Turnover Produces Pervasive Quantitative Changes in Transcription Factor Binding between Closely Related Drosophila Species

(2010) Robert K. Bradley et al.   PLOS BIOLOGY

The maternal-to-zygotic transition: a play in two acts

(2009) W. Tadros et al.   DEVELOPMENT

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions

(2009) Stewart MacArthur et al.   GENOME BIOLOGY

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

(2008) Hsiao-Lan Liang et al.   NATURE

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

(2008) Xiao-yong Li et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY