Absence of canonical marks of active chromatin in developmentally regulated genes

The transcription factor Nerfin-1 prevents reversion of neurons into neural stem cells

(2015) Francesca Froldi et al.   GENES & DEVELOPMENT

Chromatin-Driven Behavior of Topologically Associating Domains

(2015) Filippo Ciabrelli et al.   JOURNAL OF MOLECULAR BIOLOGY

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

Uncoupling Transcription from Covalent Histone Modification

(2014) Hesheng Zhang et al.   PLoS Genetics

The heat shock response: A case study of chromatin dynamics in gene regulation

(2013) Sheila S. Teves et al.   Biochemistry and Cell Biology

GAGA factor repression of transcription is a rare event but the negative regulation of Trl is conserved in Drosophila species

(2013) David Piñeyro et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Transcription-generated torsional stress destabilizes nucleosomes

(2013) Sheila S Teves et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Holo-TFIID controls the magnitude of a transcription burst and fine-tuning of transcription

(2013) K. L. Pennington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

(2013) Kai Chen et al.   eLife

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Transcription in the Absence of Histone H3.2 and H3K4 Methylation

(2012) Martina Hödl et al.   CURRENT BIOLOGY

Polycomb: a paradigm for genome organization from one to three dimensions

(2012) Anna Delest et al.   CURRENT OPINION IN CELL BIOLOGY

HOT DNAs: a novel class of developmental enhancers

(2012) E. Farley et al.   GENES & DEVELOPMENT

Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact

(2012) Joshua C. Black et al.   MOLECULAR CELL

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Understanding the language of Lys36 methylation at histone H3

(2012) Eric J. Wagner et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Fast Computation and Applications of Genome Mappability

(2012) Thomas Derrien et al.   PLoS One

Poised RNA Polymerase II Changes over Developmental Time and Prepares Genes for Future Expression

(2012) Bjoern Gaertner et al.   Cell Reports

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

A cis-regulatory map of the Drosophila genome

(2011) Nicolas Nègre et al.   NATURE

Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36

(2011) Sérgio Fernandes de Almeida et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells

(2010) Guillaume J. Filion et al.   CELL

Dynamic regulation of alternative splicing and chromatin structure in Drosophila gonads revealed by RNA-seq

(2010) Qiang Gan et al.   CELL RESEARCH

Developmental gene regulation in the era of genomics

(2010) Julia Zeitlinger et al.   DEVELOPMENTAL BIOLOGY

A spatial and temporal map of C. elegans gene expression

(2010) W. C. Spencer et al.   GENOME RESEARCH

The transcriptional diversity of 25 Drosophila cell lines

(2010) L. Cherbas et al.   GENOME RESEARCH

Genome-wide analysis of promoter architecture in Drosophila melanogaster

(2010) R. A. Hoskins et al.   GENOME RESEARCH

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

The developmental transcriptome of Drosophila melanogaster

(2010) Brenton R. Graveley et al.   NATURE

A paired-end sequencing strategy to map the complex landscape of transcription initiation

(2010) Ting Ni et al.   NATURE METHODS

FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system

(2010) Lihua Julie Zhu et al.   NUCLEIC ACIDS RESEARCH

The Insulator Protein SU(HW) Fine-Tunes Nuclear Lamina Interactions of the Drosophila Genome

(2010) Joke G. van Bemmel et al.   PLoS One

Histone modification levels are predictive for gene expression

(2010) R. Karlic et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

Regulation of Alternative Splicing by Histone Modifications

(2010) R. F. Luco et al.   SCIENCE

Regulation of gene expression via the core promoter and the basal transcriptional machinery

(2009) Tamar Juven-Gershon et al.   DEVELOPMENTAL BIOLOGY

Nucleosome positioning as a determinant of exon recognition

(2009) Hagen Tilgner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin organization marks exon-intron structure

(2009) Schraga Schwartz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

DNA methylation and the functional organization of the nuclear compartment

(2009) Jesús Espada et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

(2009) Elizabeth A Rach et al.   GENOME BIOLOGY

The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation

(2008) E. Wingender   BRIEFINGS IN BIOINFORMATICS

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE

FlyBase: enhancing Drosophila Gene Ontology annotations

(2008) S. Tweedie et al.   NUCLEIC ACIDS RESEARCH