Pioneer-like factor GAF cooperates with PBAP (SWI/SNF) and NURF (ISWI) to regulate transcription

Structure of nucleosome-bound human BAF complex

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Structure of SWI/SNF chromatin remodeller RSC bound to a nucleosome

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The emergence of genome architecture and zygotic genome activation

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Profiling of Pluripotency Factors in Single Cells and Early Embryos

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OUP accepted manuscript

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Pioneer transcription factors shape the epigenetic landscape

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Targeted in situ genome-wide profiling with high efficiency for low cell numbers

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Molecular mechanisms driving transcriptional stress responses

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The UCSC Genome Browser database: 2019 update

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FlyBase 2.0: the next generation

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UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

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Genome-wide search for Zelda-like chromatin signatures identifies GAF as a pioneer factor in early fly development

(2017) Arbel Moshe et al.   Epigenetics & Chromatin

The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

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An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

The GAGA factor regulatory network: Identification of GAGA factor associated proteins

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Complex heatmaps reveal patterns and correlations in multidimensional genomic data

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Genomic Nucleosome Organization Reconstituted with Pure Proteins

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Pioneer transcription factors, chromatin dynamics, and cell fate control

(2016) Kenneth S Zaret et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Transcription factors GAF and HSF act at distinct regulatory steps to modulate stress-induced gene activation

(2016) Fabiana M. Duarte et al.   GENES & DEVELOPMENT

Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq)

(2016) Dig Bijay Mahat et al.   Nature Protocols

Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators

(2016) So Yeon Kwon et al.   PLoS Genetics

The Release 6 reference sequence of theDrosophila melanogastergenome

(2015) Roger A. Hoskins et al.   GENOME RESEARCH

GAGA Factor Maintains Nucleosome-Free Regions and Has a Role in RNA Polymerase II Recruitment to Promoters

(2015) Nicholas J. Fuda et al.   PLoS Genetics

Chromatin Immunoprecipitation Indirect Peaks Highlight Long-Range Interactions of Insulator Proteins and Pol II Pausing

(2014) Jun Liang et al.   MOLECULAR CELL

deepTools: a flexible platform for exploring deep-sequencing data

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Distinct mechanisms of transcriptional pausing orchestrated by GAGA factor and M1BP, a novel transcription factor

(2013) Jian Li et al.   EMBO JOURNAL

Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing

(2013) H. Kwak et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

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The PBAP remodeling complex is required for histone H3.3 replacement at chromatin boundaries and for boundary functions

(2012) T. Nakayama et al.   DEVELOPMENT

The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species

(2012) J. Yang et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

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Pausing of RNA Polymerase II Disrupts DNA-Specified Nucleosome Organization to Enable Precise Gene Regulation

(2010) Daniel A. Gilchrist et al.   CELL

Model-based Analysis of ChIP-Seq (MACS)

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