Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila

Hsp90 Globally Targets Paused RNA Polymerase to Regulate Gene Expression in Response to Environmental Stimuli

(2012) Ritwick Sawarkar et al.   CELL

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

(2012) Tom Sexton et al.   CELL

Nature and function of insulator protein binding sites in the Drosophila genome

(2012) Y. B. Schwartz et al.   GENOME RESEARCH

Df31 Protein and snoRNAs Maintain Accessible Higher-Order Structures of Chromatin

(2012) Thomas Schubert et al.   MOLECULAR CELL

Rrp6 is recruited to transcribed genes and accompanies the spliced mRNA to the nuclear pore

(2012) V. Hessle et al.   RNA

Defining the Status of RNA Polymerase at Promoters

(2012) Leighton J. Core et al.   Cell Reports

Tissue-Specific Regulation of Chromatin Insulator Function

(2012) Leah H. Matzat et al.   PLoS Genetics

abd-A Regulation by the iab-8 Noncoding RNA

(2012) Maheshwar Gummalla et al.   PLoS Genetics

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function

(2011) N. Moshkovich et al.   GENES & DEVELOPMENT

The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements

(2011) Constance Richter et al.   NATURE CELL BIOLOGY

DNA Topoisomerase II Modulates Insulator Function in Drosophila

(2011) Edward Ramos et al.   PLoS One

Antisense RNA polymerase II divergent transcripts are P-TEFb dependent and substrates for the RNA exosome

(2011) R. A. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

(2011) Elizabeth A. Rach et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mediation of CTCF transcriptional insulation by DEAD-box RNA-binding protein p68 and steroid receptor RNA activator SRA

(2010) H. Yao et al.   GENES & DEVELOPMENT

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

(2010) Ting Ni et al.   NATURE METHODS

Mechanisms of nuclear mRNA quality control

(2010) Milo B. Fasken et al.   RNA Biology

Genome-wide analysis reveals distinct substrate specificities of Rrp6, Dis3, and core exosome subunits

(2010) D. L. Kiss et al.   RNA

The exozyme model: A continuum of functionally distinct complexes

(2010) D. L. Kiss et al.   RNA

HP1 Recruitment in the Absence of Argonaute Proteins in Drosophila

(2010) Nellie Moshkovich et al.   PLoS Genetics

Alternative Epigenetic Chromatin States of Polycomb Target Genes

(2010) Yuri B. Schwartz et al.   PLoS Genetics

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Yeast Exosome Functions as a Macromolecular Cage to Channel RNA Substrates for Degradation

(2009) Fabien Bonneau et al.   CELL

Active promoters and insulators are marked by the centrosomal protein 190

(2009) Marek Bartkuhn et al.   EMBO JOURNAL

Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions

(2009) A. M. Bushey et al.   GENES & DEVELOPMENT

Genome-Wide Mapping of Boundary Element-Associated Factor (BEAF) Binding Sites in Drosophila melanogaster Links BEAF to Transcription

(2009) N. Jiang et al.   MOLECULAR AND CELLULAR BIOLOGY

The Exosome Associates Cotranscriptionally with the Nascent Pre-mRNP through Interactions with Heterogeneous Nuclear Ribonucleoproteins

(2009) Viktoria Hessle et al.   MOLECULAR BIOLOGY OF THE CELL

Bidirectional promoters generate pervasive transcription in yeast

(2009) Zhenyu Xu et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila

(2009) Delphine Fagegaltier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Structural organization of the RNA-degrading exosome

(2008) Esben Lorentzen et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

MicroRNAs in the Drosophila bithorax complex

(2008) W. Bender   GENES & DEVELOPMENT

Functionally distinct regulatory RNAs generated by bidirectional transcription and processing of microRNA loci

(2008) D. M. Tyler et al.   GENES & DEVELOPMENT

Functional Interaction between the Fab-7 and Fab-8 Boundaries and the Upstream Promoter Region in the Drosophila Abd-B Gene

(2008) O. Kyrchanova et al.   MOLECULAR AND CELLULAR BIOLOGY

NELF and GAGA Factor Are Linked to Promoter-Proximal Pausing at Many Genes in Drosophila

(2008) C. Lee et al.   MOLECULAR AND CELLULAR BIOLOGY

Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells

(2008) Yoshinori Kawamura et al.   NATURE

An endogenous small interfering RNA pathway in Drosophila

(2008) Benjamin Czech et al.   NATURE

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

RNA Exosome Depletion Reveals Transcription Upstream of Active Human Promoters

(2008) Pascal Preker et al.   SCIENCE

Endogenous siRNAs Derived from Transposons and mRNAs in Drosophila Somatic Cells

(2008) M. Ghildiyal et al.   SCIENCE

BEAF Regulates Cell-Cycle Genes through the Controlled Deposition of H3K9 Methylation Marks into Its Conserved Dual-Core Binding Sites

(2008) Eldon Emberly et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY