Damage-responsive elements in Drosophila regeneration

Assessing sufficiency and necessity of enhancer activities for gene expression and the mechanisms of transcription activation

(2018) Rui R. Catarino et al.   GENES & DEVELOPMENT

The degree of enhancer or promoter activity is reflected by the levels and directionality of eRNA transcription

(2018) Olga Mikhaylichenko et al.   GENES & DEVELOPMENT

Dual functionality of cis -regulatory elements as developmental enhancers and Polycomb response elements

(2017) Jelena Erceg et al.   GENES & DEVELOPMENT

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

Clustering of Drosophila housekeeping promoters facilitates their expression

(2017) Marc Corrales et al.   GENOME RESEARCH

Correlation Does Not Imply Causation: Histone Methyltransferases, but Not Histone Methylation, SET the Stage for Enhancer Activation

(2017) Tim Pollex et al.   MOLECULAR CELL

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

(2017) Kristel M. Dorighi et al.   MOLECULAR CELL

Chromatin States in Mouse Sperm Correlate with Embryonic and Adult Regulatory Landscapes

(2017) Yoon Hee Jung et al.   Cell Reports

The Drosophila Duox maturation factor is a key component of a positive feedback loop that sustains regeneration signaling

(2017) Sumbul Jawed Khan et al.   PLoS Genetics

Three-Dimensional Genome Organization and Function in Drosophila

(2017) Yuri B. Schwartz et al.   GENETICS

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Suppression of the SWI/SNF Component Arid1a Promotes Mammalian Regeneration

(2016) Xuxu Sun et al.   Cell Stem Cell

Extracellular Reactive Oxygen Species Drive Apoptosis-Induced Proliferation via Drosophila Macrophages

(2016) Caitlin E. Fogarty et al.   CURRENT BIOLOGY

The three-dimensional genome: principles and roles of long-distance interactions

(2016) M Jordan Rowley et al.   CURRENT OPINION IN CELL BIOLOGY

The early wound signals

(2016) Philipp Niethammer   CURRENT OPINION IN GENETICS & DEVELOPMENT

Arrested development: coordinating regeneration with development and growth in Drosophila melanogaster

(2016) Jacob S Jaszczak et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Complexcis-regulatory landscape of the insulin receptor gene underlies the broad expression of a central signaling regulator

(2016) Yiliang Wei et al.   DEVELOPMENT

Modulation of tissue repair by regeneration enhancer elements

(2016) Junsu Kang et al.   NATURE

OUP accepted manuscript

(2016)   NUCLEIC ACIDS RESEARCH

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Localized epigenetic silencing of a damage-activated WNT enhancer limits regeneration in mature Drosophila imaginal discs

(2016) Robin E Harris et al.   eLife

Analysis of the dynamic co-expression network of heart regeneration in the zebrafish

(2016) Sophie Rodius et al.   Scientific Reports

Absence of canonical marks of active chromatin in developmentally regulated genes

(2015) Sílvia Pérez-Lluch et al.   NATURE GENETICS

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

DuringDrosophiladisc regeneration, JAK/STAT coordinates cell proliferation with Dilp8-mediated developmental delay

(2015) Tomonori Katsuyama et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ROS-Induced JNK and p38 Signaling Is Required for Unpaired Cytokine Activation during Drosophila Regeneration

(2015) Paula Santabárbara-Ruiz et al.   PLoS Genetics

Establishment of a Developmental Compartment Requires Interactions between Three Synergistic Cis-regulatory Modules

(2015) Dimitri Bieli 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

bwtool: a tool for bigWig files

(2014) Andy Pohl et al.   BIOINFORMATICS

Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution

(2014) Cosmas D Arnold et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Deep conservation of wrist and digit enhancers in fish

(2014) Andrew R. Gehrke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calcium Flashes Orchestrate the Wound Inflammatory Response through DUOX Activation and Hydrogen Peroxide Release

(2013) William Razzell et al.   CURRENT BIOLOGY

Cell fate respecification and cell division orientation drive intercalary regeneration in Drosophila wing discs

(2013) A. Repiso et al.   DEVELOPMENT

A Common Set of DNA Regulatory Elements Shapes Drosophila Appendages

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

Modification of Enhancer Chromatin: What, How, and Why?

(2013) Eliezer Calo et al.   MOLECULAR CELL

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Sustained production of ROS triggers compensatory proliferation and is required for regeneration to proceed

(2013) Carole Gauron et al.   Scientific Reports

Regeneration and Transdetermination in Drosophila Imaginal Discs

(2012) Melanie I. Worley et al.   Annual Review of Genetics

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

The GEM mapper: fast, accurate and versatile alignment by filtration

(2012) Santiago Marco-Sola et al.   NATURE METHODS

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

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

Limb Regeneration: A New Development?

(2011) Eugen Nacu et al.   Annual Review of Cell and Developmental Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The Cellular Basis for Animal Regeneration

(2011) Elly M. Tanaka et al.   DEVELOPMENTAL CELL

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

High conservation of transcription factor binding and evidence for combinatorial regulation across six Drosophila species

(2011) Qiye He et al.   NATURE GENETICS

Genome-wide chromatin occupancy analysis reveals a role for ASH2 in transcriptional pausing

(2011) Sílvia Pérez-Lluch et al.   NUCLEIC ACIDS RESEARCH

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Imaginal discs: Renaissance of a model for regenerative biology

(2010) Cora Bergantiños et al.   BIOESSAYS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Gene expression following induction of regeneration in Drosophila wing imaginal discs. Expression profile of regenerating wing discs

(2010) Enrique Blanco et al.   BMC DEVELOPMENTAL BIOLOGY

Cell death-induced regeneration in wing imaginal discs requires JNK signalling

(2010) C. Bergantinos et al.   DEVELOPMENT

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

CROC: finding chromosomal clusters in eukaryotic genomes

(2009) M. Pignatelli et al.   BIOINFORMATICS

Regenerative Growth in Drosophila Imaginal Discs Is Regulated by Wingless and Myc

(2009) Rachel K. Smith-Bolton et al.   DEVELOPMENTAL CELL

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Coexpression, coregulation, and cofunctionality of neighboring genes in eukaryotic genomes

(2007) Pawel Michalak   GENOMICS