Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation

A resource of targeted mutant mouse lines for 5,061 genes

(2021) Marie-Christine Birling et al.   NATURE GENETICS

BANP opens chromatin and activates CpG-island-regulated genes

(2021) Ralph S. Grand et al.   NATURE

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

The Bivalent Genome: Characterization, Structure, and Regulation

(2019) Enrique Blanco et al.   TRENDS IN GENETICS

Stella safeguards the oocyte methylome by preventing de novo methylation mediated by DNMT1

(2018) Yingfeng Li et al.   NATURE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

Cooperative Action between SALL4A and TET Proteins in Stepwise Oxidation of 5-Methylcytosine

(2016) Jun Xiong et al.   MOLECULAR CELL

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Opposing Roles for the lncRNA Haunt and Its Genomic Locus in Regulating HOXA Gene Activation during Embryonic Stem Cell Differentiation

(2015) Yafei Yin et al.   Cell Stem Cell

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Structural Basis for Hydroxymethylcytosine Recognition by the SRA Domain of UHRF2

(2014) Ting Zhou et al.   MOLECULAR CELL

Gene Silencing Triggers Polycomb Repressive Complex 2 Recruitment to CpG Islands Genome Wide

(2014) Eva Madi Riising et al.   MOLECULAR CELL

Redundant Mechanisms to Form Silent Chromatin at Pericentromeric Regions Rely on BEND3 and DNA Methylation

(2014) Nehmé Saksouk et al.   MOLECULAR CELL

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

CpG island-mediated global gene regulatory modes in mouse embryonic stem cells

(2014) Samuel Beck et al.   Nature Communications

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors

(2013) Q. Dai et al.   GENES & DEVELOPMENT

Global genomic profiling reveals an extensive p53-regulated autophagy program contributing to key p53 responses

(2013) D. Kenzelmann Broz et al.   GENES & DEVELOPMENT

Tagmentation-based whole-genome bisulfite sequencing

(2013) Qi Wang et al.   Nature Protocols

The Mll2 branch of the COMPASS family regulates bivalent promoters in mouse embryonic stem cells

(2013) Deqing Hu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

(2013) Mario Iurlaro et al.   GENOME BIOLOGY

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Transcription factors: from enhancer binding to developmental control

(2012) François Spitz et al.   NATURE REVIEWS GENETICS

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

(2011) Felix Krueger et al.   BIOINFORMATICS

A BEN-domain-containing protein associates with heterochromatin and represses transcription

(2011) K. M. Sathyan et al.   JOURNAL OF CELL SCIENCE

Experimental phasing withSHELXC/D/E: combining chain tracing with density modification

(2010) George M. Sheldrick   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

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

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

MOODS: fast search for position weight matrix matches in DNA sequences

(2009) J. Korhonen 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

On the nature of human housekeeping genes

(2008) Jiang Zhu et al.   TRENDS IN GENETICS

Genomewide Analysis of PRC1 and PRC2 Occupancy Identifies Two Classes of Bivalent Domains

(2008) Manching Ku et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY