The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

NAD+ cleavage activity by animal and plant TIR domains in cell death pathways

(2019) Shane Horsefield et al.   SCIENCE

LSD1 Inhibition Promotes Epithelial Differentiation through Derepression of Fate-Determining Transcription Factors

(2019) Shaun Egolf et al.   Cell Reports

MTF2 recruits Polycomb Repressive Complex 2 by helical-shape-selective DNA binding

(2018) Matteo Perino et al.   NATURE GENETICS

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

(2018) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

An Mll4/COMPASS-Lsd1 epigenetic axis governs enhancer function and pluripotency transition in embryonic stem cells

(2018) Kaixiang Cao et al.   Science Advances

Not All H3K4 Methylations Are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification

(2017) Deqing Hu et al.   MOLECULAR CELL

Polycomb-like proteins link the PRC2 complex to CpG islands

(2017) Haojie Li et al.   NATURE

GEPIA: a web server for cancer and normal gene expression profiling and interactive analyses

(2017) Zefang Tang et al.   NUCLEIC ACIDS RESEARCH

The SET1 Complex Selects Actively Transcribed Target Genes via Multivalent Interaction with CpG Island Chromatin

(2017) David A. Brown et al.   Cell Reports

Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC

(2016) Felice Frey et al.   GENES & DEVELOPMENT

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

(2016) Jun Xiong et al.   MOLECULAR CELL

Chromatin topology is coupled to Polycomb group protein subnuclear organization

(2016) Ajazul H. Wani et al.   Nature Communications

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Disruption of histone methylation in developing sperm impairs offspring health transgenerationally

(2015) K. Siklenka et al.   SCIENCE

Proteins that bind regulatory regions identified by histone modification chromatin immunoprecipitations and mass spectrometry

(2015) Erik Engelen et al.   Nature Communications

Zinc Finger Independent Genome-Wide Binding of Sp2 Potentiates Recruitment of Histone-Fold Protein Nf-y Distinguishing It from Sp1 and Sp3

(2015) Sara Völkel et al.   PLoS Genetics

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Quantitative ChIP-Seq Normalization Reveals Global Modulation of the Epigenome

(2014) David A. Orlando et al.   Cell Reports

ZF-CxxC domain-containing proteins, CpG islands and the chromatin connection

(2013) Hannah K. Long et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

SAM Domain Polymerization Links Subnuclear Clustering of PRC1 to Gene Silencing

(2013) Kyoichi Isono et al.   DEVELOPMENTAL CELL

SFMBT1 functions with LSD1 to regulate expression of canonical histone genes and chromatin-related factors

(2013) J. Zhang et al.   GENES & DEVELOPMENT

A double take on bivalent promoters

(2013) P. Voigt et al.   GENES & DEVELOPMENT

From keys to bulldozers: expanding roles for winged helix domains in nucleic-acid-binding proteins

(2013) Gábor M. Harami et al.   TRENDS IN BIOCHEMICAL SCIENCES

Systematic repression of transcription factors reveals limited patterns of gene expression changes in ES cells

(2013) Akira Nishiyama et al.   Scientific Reports

A DNA-Centric Protein Interaction Map of Ultraconserved Elements Reveals Contribution of Transcription Factor Binding Hubs to Conservation

(2013) Tar Viturawong et al.   Cell Reports

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

The Histone Demethylase KDM1A Sustains the Oncogenic Potential of MLL-AF9 Leukemia Stem Cells

(2012) William J. Harris et al.   CANCER CELL

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

(2012) P. Yu et al.   GENOME RESEARCH

Histone Recognition by Human Malignant Brain Tumor Domains

(2012) Nataliya Nady et al.   JOURNAL OF MOLECULAR BIOLOGY

KDM2B links the Polycomb Repressive Complex 1 (PRC1) to recognition of CpG islands

(2012) Anca M Farcas et al.   eLife

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Cistrome: an integrative platform for transcriptional regulation studies

(2011) Tao Liu et al.   GENOME BIOLOGY

Features and development ofCoot

(2010) P. Emsley et al.   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

Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation

(2010) Till Bartke et al.   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

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Streamlined analysis schema for high-throughput identification of endogenous protein complexes

(2010) A. Malovannaya et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

MBT domain proteins in development and disease

(2009) Roberto Bonasio et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

(2009) Chunlei Wu et al.   GENOME BIOLOGY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY