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

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

(2013) Daniel J. McKay et al.   DEVELOPMENTAL CELL

In Drosophila, RhoGEF2 cooperates with activated Ras in tumorigenesis through a pathway involving Rho1-Rok-Myosin-II and JNK signalling

(2013) P. Khoo et al.   Disease Models & Mechanisms

Evidence for Tissue-Specific JAK/STAT Target Genes in Drosophila Optic Lobe Development

(2013) H. Wang et al.   GENETICS

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

FlyBase 102—advanced approaches to interrogating FlyBase

(2013) Susan E. St. Pierre et al.   NUCLEIC ACIDS RESEARCH

The BTB-zinc Finger Transcription Factor Abrupt Acts as an Epithelial Oncogene in Drosophila melanogaster through Maintaining a Progenitor-like Cell State

(2013) Nezaket Turkel et al.   PLoS Genetics

The actin cross-linker Filamin/Cheerio mediates tumor malignancy downstream of JNK signaling

(2012) E. Kulshammer et al.   JOURNAL OF CELL SCIENCE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

A Survey of 6,300 Genomic Fragments for cis-Regulatory Activity in the Imaginal Discs of Drosophila melanogaster

(2012) Aurélie Jory et al.   Cell Reports

A GAL4-Driver Line Resource for Drosophila Neurobiology

(2012) Arnim Jenett et al.   Cell Reports

Retinal differentiation in Drosophila

(2012) Jessica E. Treisman   Wiley Interdisciplinary Reviews-Developmental Biology

Loss of the Drosophila cell polarity regulator Scribbled promotes epithelial tissue overgrowth and cooperation with oncogenic Ras-Raf through impaired Hippo pathway signaling

(2011) Karen Doggett et al.   BMC DEVELOPMENTAL BIOLOGY

Differential activities of the Drosophila JAK/STAT pathway ligands Upd, Upd2 and Upd3

(2011) Victoria M. Wright et al.   CELLULAR SIGNALLING

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

(2011) L. Song et al.   GENOME RESEARCH

RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets

(2011) Morgane Thomas-Chollier et al.   NUCLEIC ACIDS RESEARCH

STAT Is an Essential Activator of the Zygotic Genome in the Early Drosophila Embryo

(2011) Amy Tsurumi et al.   PLoS Genetics

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Activation of JNK signaling links lgl mutations to disruption of the cell polarity and epithelial organization in Drosophila imaginal discs

(2010) Mingwei Zhu et al.   CELL RESEARCH

Size matters: The contribution of cell proliferation to the progression of the specification Drosophila eye gene regulatory network

(2010) Gabriele Amore et al.   DEVELOPMENTAL BIOLOGY

Characterization of a dominant-active STAT that promotes tumorigenesis in Drosophila

(2010) Laura A. Ekas et al.   DEVELOPMENTAL BIOLOGY

chinmo Is a Functional Effector of the JAK/STAT Pathway that Regulates Eye Development, Tumor Formation, and Stem Cell Self-Renewal in Drosophila

(2010) Maria Sol Flaherty et al.   DEVELOPMENTAL CELL

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

(2010) A. P. Boyle et al.   GENOME RESEARCH

Interaction between Ras V12 and scribbled clones induces tumour growth and invasion

(2010) Ming Wu et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

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

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

Ectopic Expression of Germline Genes Drives Malignant Brain Tumor Growth in Drosophila

(2010) A. Janic et al.   SCIENCE

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

(2010) Andrew Adey et al.   GENOME BIOLOGY

CEAS: cis-regulatory element annotation system

(2009) Hyunjin Shin et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Genome-wide expression profiling in theDrosophilaeye reveals unexpected repression of notch signaling by the JAK/STAT pathway

(2009) Maria Sol Flaherty et al.   DEVELOPMENTAL DYNAMICS

The TEAD/TEF Family of Transcription Factor Scalloped Mediates Hippo Signaling in Organ Size Control

(2008) Lei Zhang et al.   DEVELOPMENTAL CELL

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

(2008) Hsiao-Lan Liang et al.   NATURE