Effects of Gene Dose, Chromatin, and Network Topology on Expression in Drosophila melanogaster

No current evidence for widespread dosage compensation in S. cerevisiae

(2016) Eduardo M Torres et al.   eLife

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution

(2016) Audrey P Gasch et al.   eLife

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Dosage Compensation inDrosophila

(2015) John C. Lucchesi et al.   Cold Spring Harbor Perspectives in Biology

Long-Range Chromatin Interactions

(2015) Job Dekker et al.   Cold Spring Harbor Perspectives in Biology

X Chromosome and Autosome Dosage Responses in Drosophila melanogaster Heads

(2015) Z.-X. Chen et al.   G3-Genes Genomes Genetics

Sex Bias and Maternal Contribution to Gene Expression Divergence in Drosophila Blastoderm Embryos

(2015) Mathilde Paris et al.   PLoS Genetics

Dosage compensation can buffer copy-number variation in wild yeast

(2015) James Hose et al.   eLife

Sex Differences in Drosophila melanogaster Heterochromatin Are Regulated by Non-Sex Specific Factors

(2015) Manasi S. Apte et al.   PLoS One

Sex- and Tissue-Specific Functions of Drosophila Doublesex Transcription Factor Target Genes

(2014) Emily Clough et al.   DEVELOPMENTAL CELL

Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells

(2014) Shanrong Zhao et al.   PLoS One

Autophagy inDrosophila: From Historical Studies to Current Knowledge

(2014) Nitha C. Mulakkal et al.   Biomed Research International

DNA copy number evolution in Drosophila cell lines

(2014) Hangnoh Lee et al.   GENOME BIOLOGY

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

Transcriptional effects of gene dose reduction

(2014) Zhen-Xia Chen et al.   Biology of Sex Differences

Chromatin insulators and long-distance interactions inDrosophila

(2013) Olga Kyrchanova et al.   FEBS LETTERS

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

(2013) S. C. R. Elgin et al.   Cold Spring Harbor Perspectives in Biology

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

Rearrangements of 2.5 Kilobases of Noncoding DNA from the Drosophila even-skipped Locus Define Predictive Rules of Genomic cis-Regulatory Logic

(2013) Ah-Ram Kim et al.   PLoS Genetics

RNA-seq and microarray complement each other in transcriptome profiling

(2012) Sunitha Kogenaru et al.   BMC GENOMICS

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

(2012) Tom Sexton et al.   CELL

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Buffering and proteolysis are induced by segmental monosomy in Drosophila melanogaster

(2012) Lina E. Lundberg et al.   NUCLEIC ACIDS RESEARCH

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Synthetic Spike-in Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing

(2012) Justin M. Zook et al.   PLoS One

Gene balance hypothesis: Connecting issues of dosage sensitivity across biological disciplines

(2012) J. A. Birchler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A GAL4-Driver Line Resource for Drosophila Neurobiology

(2012) Arnim Jenett et al.   Cell Reports

Mediation of Drosophila autosomal dosage effects and compensation by network interactions

(2012) John H Malone et al.   GENOME BIOLOGY

The generation of chromosomal deletions to provide extensive coverage and subdivision of the Drosophila melanogaster genome

(2012) R Kimberley Cook et al.   GENOME BIOLOGY

Microarrays, deep sequencing and the true measure of the transcriptome

(2011) John H Malone et al.   BMC BIOLOGY

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

Buffering and the evolution of chromosome-wide gene regulation

(2011) Per Stenberg et al.   CHROMOSOMA

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

(2011) A. Schlattl et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

The Characterisation of Three Types of Genes that Overlie Copy Number Variable Regions

(2011) Cara Woodwark et al.   PLoS One

A Low-Cost Library Construction Protocol and Data Analysis Pipeline for Illumina-Based Strand-Specific Multiplex RNA-Seq

(2011) Lin Wang et al.   PLoS One

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

(2011) Susan E. Lott et al.   PLOS BIOLOGY

BioNet: an R-Package for the functional analysis of biological networks

(2010) D. Beisser et al.   BIOINFORMATICS

Identification of Aneuploidy-Tolerating Mutations

(2010) Eduardo M. Torres et al.   CELL

An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man

(2010) Timothy Ravasi et al.   CELL

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

(2010) Guillaume J. Filion et al.   CELL

Proteomic analysis reveals CCT is a target of Fragile X mental retardation protein regulation in Drosophila

(2010) Kate Monzo et al.   DEVELOPMENTAL BIOLOGY

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

(2010) Benjamin Schuster-Böckler et al.   PLoS One

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

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

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

Neighbourhood Continuity Is Not Required for Correct Testis Gene Expression in Drosophila

(2010) Lisa A. Meadows et al.   PLOS BIOLOGY

Expression in Aneuploid Drosophila S2 Cells

(2010) Yu Zhang et al.   PLOS BIOLOGY

A Comprehensive Map of Insulator Elements for the Drosophila Genome

(2010) Nicolas Nègre et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists

(2009) Eran Eden et al.   BMC BIOINFORMATICS

Widespread Transcriptional Autosomal Dosage Compensation in Drosophila Correlates with Gene Expression Level

(2009) Ashley A. McAnally et al.   Genome Biology and Evolution

Buffering of Segmental and Chromosomal Aneuploidies in Drosophila melanogaster

(2009) Per Stenberg et al.   PLoS Genetics

Gene networks in Drosophila melanogaster: integrating experimental data to predict gene function

(2009) James C Costello et al.   GENOME BIOLOGY

Metabolism and regulation of canonical histone mRNAs: life without a poly(A) tail

(2008) William F. Marzluff et al.   NATURE REVIEWS GENETICS