ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm

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

(2018) Jenna E. Haines et al.   PLoS Genetics

The cis-regulatory dynamics of embryonic development at single-cell resolution

(2018) Darren A. Cusanovich et al.   NATURE

Dense Bicoid hubs accentuate binding along the morphogen gradient

(2017) Mustafa Mir et al.   GENES & DEVELOPMENT

A Fully Synthetic Transcriptional Platform for a Multicellular Eukaryote

(2017) Justin Crocker et al.   Cell Reports

Concentration dependent chromatin states induced by the bicoid morphogen gradient

(2017) Colleen E Hannon et al.   eLife

Chromatin profiling ofDrosophilaCNS subpopulations identifies active transcriptional enhancers

(2016) Joseph C. Pearson et al.   DEVELOPMENT

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

(2016) Nina Koenecke et al.   GENOME RESEARCH

FlyBase at 25: looking to the future

(2016) L. Sian Gramates et al.   NUCLEIC ACIDS RESEARCH

Acetylation Mimics Within a Single Nucleosome Alter Local DNA Accessibility In Compacted Nucleosome Arrays

(2016) Laxmi N. Mishra et al.   Scientific Reports

Distinct Roles of Histone H3 and H2A Tails in Nucleosome Stability

(2016) Zhenhai Li et al.   Scientific Reports

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

(2016) Shelby A Blythe et al.   eLife

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

(2015) Yujia Sun et al.   GENOME RESEARCH

Structured nucleosome fingerprints enable high-resolution mapping of chromatin architecture within regulatory regions

(2015) Alicia N. Schep et al.   GENOME RESEARCH

Zelda Potentiates Morphogen Activity by Increasing Chromatin Accessibility

(2014) Sun Melody Foo et al.   CURRENT BIOLOGY

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

(2014) Xiao-Yong Li et al.   eLife

Control of Drosophila embryo patterning by transcriptional co-regulators

(2013) Mattias Mannervik   EXPERIMENTAL CELL RESEARCH

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

Mechanisms by which transcription factors gain access to target sequence elements in chromatin

(2012) Michael J Guertin et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

(2012) R. Satija et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Cell type–specific genomics of Drosophila neurons

(2012) Gilbert L. Henry et al.   NUCLEIC ACIDS RESEARCH

DNA regions bound at low occupancy by transcription factors do not drive patterned reporter gene expression in Drosophila

(2012) W. W. Fisher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Long- and Short-Range Transcriptional Repressors Induce Distinct Chromatin States on Repressed Genes

(2011) Li M. Li et al.   CURRENT BIOLOGY

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

The gap gene network

(2010) Johannes Jaeger   CELLULAR AND MOLECULAR LIFE SCIENCES

Transcriptional Enhancers in Animal Development and Evolution

(2010) Mike Levine   CURRENT BIOLOGY

Chromatin signatures of the Drosophila replication program

(2010) M. L. Eaton et al.   GENOME RESEARCH

Deciphering a transcriptional regulatory code: modeling short-range repression in the Drosophila embryo

(2010) Walid D Fakhouri et al.   Molecular Systems Biology

The INTACT method for cell type–specific gene expression and chromatin profiling in Arabidopsis thaliana

(2010) Roger B Deal et al.   Nature Protocols

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

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

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

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

Quantitative Analysis of the Drosophila Segmentation Regulatory Network Using Pattern Generating Potentials

(2010) Majid Kazemian et al.   PLOS BIOLOGY

Thermodynamics-Based Models of Transcriptional Regulation by Enhancers: The Roles of Synergistic Activation, Cooperative Binding and Short-Range Repression

(2010) Xin He et al.   PLoS Computational Biology

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

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

Predicting expression patterns from regulatory sequence in Drosophila segmentation

(2008) Eran Segal et al.   NATURE

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

(2008) Hsiao-Lan Liang et al.   NATURE

A One Pot, One Step, Precision Cloning Method with High Throughput Capability

(2008) Carola Engler et al.   PLoS One

Tools for neuroanatomy and neurogenetics in Drosophila

(2008) B. D. Pfeiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Characterization of the Drosophila segment determination morphome

(2007) Svetlana Surkova et al.   DEVELOPMENTAL BIOLOGY