CATaDa reveals global remodelling of chromatin accessibility during stem cell differentiation in vivo

Systemic and local cues drive neural stem cell niche remodelling during neurogenesis in Drosophila

(2018) Pauline Spéder et al.   eLife

Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates

(2017) Moritz Mall et al.   NATURE

Single-cell sequencing reveals dissociation-induced gene expression in tissue subpopulations

(2017) Susanne C van den Brink et al.   NATURE METHODS

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

(2017) Seth W. Cheetham et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin state changes during neural development revealed by in vivo cell-type specific profiling

(2017) Owen J. Marshall et al.   Nature Communications

RNA-DamID reveals cell-type-specific binding of roX RNAs at chromatin-entry sites

(2017) Seth W. Cheetham et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comprehensive Characterization of the Complex lola Locus Reveals a Novel Role in the Octopaminergic Pathway via Tyramine Beta-Hydroxylase Regulation

(2017) Nadja Dinges et al.   Cell Reports

Mapping cell type-specific transcriptional enhancers using high affinity, lineage-specific Ep300 bioChIP-seq

(2017) Pingzhu Zhou et al.   eLife

Chromatin profiling ofDrosophilaCNS subpopulations identifies active transcriptional enhancers

(2016) Joseph C. Pearson et al.   DEVELOPMENT

Cell-type-specific profiling of protein–DNA interactions without cell isolation using targeted DamID with next-generation sequencing

(2016) Owen J Marshall et al.   Nature Protocols

Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo

(2016) Mark A. Le Gros et al.   Cell Reports

damidseq_pipeline: an automated pipeline for processing DamID sequencing datasets: Fig. 1.

(2015) Owen J. Marshall et al.   BIOINFORMATICS

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

ChIP bias as a function of cross-linking time

(2015) Laura Baranello et al.   CHROMOSOME RESEARCH

Intestinal stem cell proliferation and epithelial homeostasis in the adult Drosophila midgut

(2015) Máté Nászai et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples

(2015) Wenfei Jin et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Plug-and-Play Genetic Access to Drosophila Cell Types using Exchangeable Exon Cassettes

(2015) Fengqiu Diao et al.   Cell Reports

EGFR/Ras Signaling Controls Drosophila Intestinal Stem Cell Proliferation via Capicua-Regulated Genes

(2015) Yinhua Jin et al.   PLoS Genetics

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Dam it's good! DamID profiling of protein-DNA interactions

(2015) Gabriel N. Aughey et al.   Wiley Interdisciplinary Reviews-Developmental Biology

Dedifferentiation of Neurons Precedes Tumor Formation in lola Mutants

(2014) Tony D. Southall et al.   DEVELOPMENTAL CELL

Escargotmaintains stemness and suppresses differentiation inDrosophilaintestinal stem cells

(2014) Jerome Korzelius et al.   EMBO JOURNAL

Genome-scale functional characterization of Drosophila developmental enhancers in vivo

(2014) Evgeny Z. Kvon et al.   NATURE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Wnt/Catenin Signaling in Adult Stem Cell Physiology and Disease

(2014) Alexander Ring et al.   Stem Cell Reviews and Reports

Chromatin accessibility: a window into the genome

(2014) Maria Tsompana et al.   Epigenetics & Chromatin

A GAL4 Driver Resource for Developmental and Behavioral Studies on the Larval CNS of Drosophila

(2014) Hsing-Hsi Li et al.   Cell Reports

Integration of UPRER and Oxidative Stress Signaling in the Control of Intestinal Stem Cell Proliferation

(2014) Lifen Wang et al.   PLoS Genetics

Cell-Type-Specific Profiling of Gene Expression and Chromatin Binding without Cell Isolation: Assaying RNA Pol II Occupancy in Neural Stem Cells

(2013) Tony D. Southall 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

Enhancers: five essential questions

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

Drosophila neuroblasts: a model for stem cell biology

(2012) C. C. F. Homem et al.   DEVELOPMENT

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

A GAL4-Driver Line Resource for Drosophila Neurobiology

(2012) Arnim Jenett et al.   Cell Reports

Intestinal stem cells in the adult Drosophila midgut

(2011) Huaqi Jiang et al.   EXPERIMENTAL CELL RESEARCH

Open chromatin in pluripotency and reprogramming

(2010) Alexandre Gaspar-Maia et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cytokine/Jak/Stat Signaling Mediates Regeneration and Homeostasis in the Drosophila Midgut

(2009) Huaqi Jiang et al.   CELL

Neural stem cell transcriptional networks highlight genes essential for nervous system development

(2009) Tony D Southall et al.   EMBO JOURNAL

MEME SUITE: tools for motif discovery and searching

(2009) T. L. Bailey et al.   NUCLEIC ACIDS RESEARCH