Setdb1-mediated H3K9 methylation is enriched on the inactive X and plays a role in its epigenetic silencing

SETDB1 modulates PRC2 activity at developmental genes independently of H3K9 trimethylation in mouse ES cells

(2015) Qi Fei et al.   GENOME RESEARCH

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

The Mbd1-Atf7ip-Setdb1 pathway contributes to the maintenance of X chromosome inactivation

(2014) Alissa Minkovsky et al.   Epigenetics & Chromatin

Cdyl, a New Partner of the Inactive X Chromosome and Potential Reader of H3K27me3 and H3K9me2

(2013) M. Escamilla-Del-Arenal et al.   MOLECULAR AND CELLULAR BIOLOGY

The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote

(2013) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

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

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

UHRF1 targets DNMT1 for DNA methylation through cooperative binding of hemi-methylated DNA and methylated H3K9

(2013) Xiaoli Liu et al.   Nature Communications

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

An ENU mutagenesis screen identifies novel and known genes involved in epigenetic processes in the mouse

(2013) Lucia Daxinger et al.   GENOME BIOLOGY

Smchd1-Dependent and -Independent Pathways Determine Developmental Dynamics of CpG Island Methylation on the Inactive X Chromosome

(2012) Anne-Valerie Gendrel et al.   DEVELOPMENTAL CELL

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

(2012) Patrick Boyle et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

LINE-1 Activity in Facultative Heterochromatin Formation during X Chromosome Inactivation

(2010) Jennifer C. Chow et al.   CELL

The Matrix Protein hnRNP U Is Required for Chromosomal Localization of Xist RNA

(2010) Yuko Hasegawa et al.   DEVELOPMENTAL CELL

A Subset of the Histone H3 Lysine 9 Methyltransferases Suv39h1, G9a, GLP, and SETDB1 Participate in a Multimeric Complex

(2010) Lauriane Fritsch 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

Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET

(2010) Toshiyuki Matsui et al.   NATURE

The A-repeat links ASF/SF2-dependent Xist RNA processing with random choice during X inactivation

(2010) Morgan E Royce-Tolland et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic modifications on X chromosomes in marsupial and monotreme mammals and implications for evolution of dosage compensation

(2010) Willem Rens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficiency of Xist-mediated silencing on autosomes is linked to chromosomal domain organisation

(2010) Y Amy Tang et al.   Epigenetics & Chromatin

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

Eset partners with Oct4 to restrict extraembryonic trophoblast lineage potential in embryonic stem cells

(2009) P. Yuan et al.   GENES & DEVELOPMENT

High-resolution analysis of epigenetic changes associated with X inactivation

(2009) H. Marks et al.   GENOME RESEARCH

Mosaic heterochromatin of the inactive X chromosome in vole Microtus rossiaemeridionalis

(2009) Alexander I. Shevchenko et al.   MAMMALIAN GENOME

ERG-associated protein with SET domain (ESET)-Oct4 interaction regulates pluripotency and represses the trophectoderm lineage

(2009) Leng-Siew Yeap et al.   Epigenetics & Chromatin

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

The ground state of embryonic stem cell self-renewal

(2008) Qi-Long Ying et al.   NATURE

SmcHD1, containing a structural-maintenance-of-chromosomes hinge domain, has a critical role in X inactivation

(2008) Marnie E Blewitt et al.   NATURE GENETICS

Spatial Distribution of Histone Isoforms on the Bovine Active and Inactive X Chromosomes

(2008) G. Coppola et al.   Sexual Development

Polycomb Repressive Complex 2 (PRC2) Restricts Hematopoietic Stem Cell Activity

(2008) Ian J Majewski et al.   PLOS BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY