BANP opens chromatin and activates CpG-island-regulated genes

Acute BAF perturbation causes immediate changes in chromatin accessibility

(2021) Sandra Schick et al.   NATURE GENETICS

Mammalian SWI/SNF continuously restores local accessibility to chromatin

(2021) Mario Iurlaro et al.   NATURE GENETICS

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

(2021) Bastian Stielow et al.   Science Advances

A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity

(2020) Paul Adrian Ginno et al.   Nature Communications

Global reference mapping of human transcription factor footprints

(2020) Jeff Vierstra et al.   NATURE

Genome-wide analysis in the mouse embryo reveals the importance of DNA methylation for transcription integrity

(2020) Thomas Dahlet et al.   Nature Communications

Molecular Co-occupancy Identifies Transcription Factor Binding Cooperativity In Vivo

(2020) Can Sönmezer et al.   MOLECULAR CELL

CG dinucleotides enhance promoter activity independent of DNA methylation

(2019) Dominik Hartl et al.   GENOME RESEARCH

Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors

(2019) Darko Barisic et al.   NATURE

Quantification of experimentally induced nucleotide conversions in high-throughput sequencing datasets

(2019) Tobias Neumann et al.   BMC BIOINFORMATICS

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

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Sensitivity of transcription factors to DNA methylation

(2019) Éléa Héberlé et al.   Essays in Biochemistry

PAQMAN: Protein-nucleic acid affinity quantification by MAss spectrometry in nuclear extracts

(2019) Cathrin Gräwe et al.   METHODS

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

The dTAG system for immediate and target-specific protein degradation

(2018) Behnam Nabet et al.   Nature Chemical Biology

SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis

(2018) Matthias Muhar et al.   SCIENCE

Global profiling of protein–DNA and protein–nucleosome binding affinities using quantitative mass spectrometry

(2018) Matthew M. Makowski et al.   Nature Communications

Activity-dependent neuroprotective protein recruits HP1 and CHD4 to control lineage-specifying genes

(2018) Veronika Ostapcuk et al.   NATURE

A methyl-sensitive element induces bidirectional transcription in TATA-less CpG island-associated promoters

(2018) Amin Mahpour et al.   PLoS One

MethMotif: an integrative cell specific database of transcription factor binding motifs coupled with DNA methylation profiles

(2018) Quy Xiao Xuan Lin et al.   NUCLEIC ACIDS RESEARCH

The PRIDE database and related tools and resources in 2019: improving support for quantification data

(2018) Yasset Perez-Riverol et al.   NUCLEIC ACIDS RESEARCH

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

(2017) M Ryan Corces et al.   NATURE METHODS

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

Genome-scale high-resolution mapping of activating and repressive nucleotides in regulatory regions

(2016) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The Perseus computational platform for comprehensive analysis of (prote)omics data

(2016) Stefka Tyanova et al.   NATURE METHODS

Epigenetic Determinants of Cancer

(2016) Stephen B. Baylin et al.   Cold Spring Harbor Perspectives in Biology

Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family

(2015) Qi Dai et al.   GENES & DEVELOPMENT

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation

(2015) Dimos Gaidatzis et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

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

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

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

Accurate Proteome-wide Label-free Quantification by Delayed Normalization and Maximal Peptide Ratio Extraction, Termed MaxLFQ

(2014) Jürgen Cox et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2014) Nehmé Saksouk et al.   MOLECULAR CELL

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes

(2014) Dimos Gaidatzis et al.   PLoS Genetics

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

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

Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells

(2013) Yingsha Zhang et al.   NEURON

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

(2012) P. Arnold et al.   GENOME RESEARCH

CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters

(2012) R. Fenouil et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Ectopic Expression of Neurogenin 2 Alone is Sufficient to Induce Differentiation of Embryonic Stem Cells into Mature Neurons

(2012) Eva C. Thoma et al.   PLoS One

Molecular basis for recognition of methylated and specific DNA sequences by the zinc finger protein Kaiso

(2012) B. A. Buck-Koehntop et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

CpG islands and the regulation of transcription

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

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

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

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

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Reversed-phase chromatography with multiple fraction concatenation strategy for proteome profiling of human MCF10A cells

(2011) Yuexi Wang et al.   PROTEOMICS

Accurate inference of transcription factor binding from DNA sequence and chromatin accessibility data

(2010) R. Pique-Regi et al.   GENOME RESEARCH

Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

(2010) Nina C. Hubner et al.   JOURNAL OF CELL BIOLOGY

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

Nuclear Matrix protein SMAR1 represses HIV-1 LTR mediated transcription through chromatin remodeling

(2010) Kadreppa Sreenath et al.   VIROLOGY

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

Genetics and epigenetics: stability and plasticity during cellular differentiation

(2009) Fabio Mohn et al.   TRENDS IN GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A set of baculovirus transfer vectors for screening of affinity tags and parallel expression strategies

(2008) Wassim Abdulrahman et al.   ANALYTICAL BIOCHEMISTRY

Lineage-Specific Polycomb Targets and De Novo DNA Methylation Define Restriction and Potential of Neuronal Progenitors

(2008) Fabio Mohn et al.   MOLECULAR CELL

The Insulator Binding Protein CTCF Positions 20 Nucleosomes around Its Binding Sites across the Human Genome

(2008) Yutao Fu et al.   PLoS Genetics

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY