Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid

Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans

(2016) Maxwell Kramer et al.   GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Untangling the Contributions of Sex-Specific Gene Regulation and X-Chromosome Dosage to Sex-Biased Gene Expression in Caenorhabditis elegans

(2016) Maxwell Kramer et al.   GENETICS

The X Chromosome of Hemipteran Insects: Conservation, Dosage Compensation and Sex-Biased Expression

(2015) Arka Pal et al.   Genome Biology and Evolution

Complete Dosage Compensation inAnopheles stephensiand the Evolution of Sex-Biased Genes in Mosquitoes

(2015) Xiaofang Jiang et al.   Genome Biology and Evolution

Partial Dosage Compensation in Strepsiptera, a Sister Group of Beetles

(2015) Shivani Mahajan et al.   Genome Biology and Evolution

Gene Networks in the Wild: Identifying Transcriptional Modules that Mediate Coral Resistance to Experimental Heat Stress

(2015) Noah H. Rose et al.   Genome Biology and Evolution

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Dosage Compensation in Mammals

(2015) Neil Brockdorff et al.   Cold Spring Harbor Perspectives in Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Sex-Biased Gene Expression and Evolution of the X Chromosome in Nematodes

(2014) S. E. Albritton et al.   GENETICS

Complete Dosage Compensation and Sex-Biased Gene Expression in the Moth Manduca sexta

(2014) Gilbert Smith et al.   Genome Biology and Evolution

Addendum: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2014) Jeremy M Simon et al.   Nature Protocols

Evolutionary conservation of long non-coding RNAs; sequence, structure, function

(2013) Per Johnsson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

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

Genome expression control during the photoperiodic response of aphids

(2013) GAEL LE TRIONNAIRE et al.   PHYSIOLOGICAL ENTOMOLOGY

Sex-Biased Gene Expression during Head Development in a Sexually Dimorphic Stalk-Eyed Fly

(2013) Gerald S. Wilkinson et al.   PLoS One

The Xist lncRNA Exploits Three-Dimensional Genome Architecture to Spread Across the X Chromosome

(2013) J. M. Engreitz et al.   SCIENCE

Masculinization of the X Chromosome in the Pea Aphid

(2013) Julie Jaquiéry et al.   PLoS Genetics

Condensin controls recruitment of RNA polymerase II to achieve nematode X-chromosome dosage compensation

(2013) William S Kruesi et al.   eLife

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Transcriptomic profiling of the reproductive mode switch in the pea aphid in response to natural autumnal photoperiod

(2012) Gaël Le Trionnaire et al.   JOURNAL OF INSECT PHYSIOLOGY

Caenorhabditis elegans Dosage Compensation Regulates Histone H4 Chromatin State on X Chromosomes

(2012) M. B. Wells et al.   MOLECULAR AND CELLULAR BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA

(2012) Jeremy M Simon et al.   Nature Protocols

Dosage compensation in Drosophila melanogaster: epigenetic fine-tuning of chromosome-wide transcription

(2012) Thomas Conrad et al.   NATURE REVIEWS GENETICS

Expression reduction in mammalian X chromosome evolution refutes Ohno's hypothesis of dosage compensation

(2012) F. Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mammalian X chromosome inactivation evolved as a dosage-compensation mechanism for dosage-sensitive genes on the X chromosome

(2012) E. Pessia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mechanisms and Evolutionary Patterns of Mammalian and Avian Dosage Compensation

(2012) Philippe Julien et al.   PLOS BIOLOGY

Measuring reproducibility of high-throughput experiments

(2011) Qunhua Li et al.   Annals of Applied Statistics

Exploratory analysis of genomic segmentations with Segtools

(2011) Orion J Buske et al.   BMC BIOINFORMATICS

SOME INCONVENIENT TRUTHS ABOUT SEX CHROMOSOME DOSAGE COMPENSATION AND THE POTENTIAL ROLE OF SEXUAL CONFLICT

(2011) Judith E. Mank et al.   EVOLUTION

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

(2011) L. Song et al.   GENOME RESEARCH

Accelerated Evolution of Sex Chromosomes in Aphids, an X0 System

(2011) J. Jaquiery et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster

(2011) Xinxian Deng et al.   NATURE GENETICS

Sex-chromosome evolution: recent progress and the influence of male and female heterogamety

(2011) Hans Ellegren   NATURE REVIEWS GENETICS

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development

(2011) Sean Thomas et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Hyperexpression of the X Chromosome in Both Sexes Results in Extensive Female Bias of X-Linked Genes in the Flour Beetle

(2010) Eldon G. Prince et al.   Genome Biology and Evolution

The Activation Potential of MOF Is Constrained for Dosage Compensation

(2010) Matthias Prestel et al.   MOLECULAR CELL

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Accessibility of the Drosophila genome discriminates PcG repression, H4K16 acetylation and replication timing

(2010) Oliver Bell et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Drosophila dosage compensation: a complex voyage to the X chromosome

(2009) M. E. Gelbart et al.   DEVELOPMENT

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

X Chromosome Dosage Compensation: How Mammals Keep the Balance

(2008) Bernhard Payer et al.   Annual Review of Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY