Mammalian SWI/SNF continuously restores local accessibility to chromatin

Acute BAF perturbation causes immediate changes in chromatin accessibility

(2021) Sandra Schick et al.   NATURE GENETICS

Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1

(2020) Julia Minderjahn et al.   Nature Communications

Chromatin replication and epigenetic cell memory

(2020) Kathleen R. Stewart-Morgan et al.   NATURE CELL BIOLOGY

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

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

(2019) Darko Barisic et al.   NATURE

Opposing chromatin remodelers control transcription initiation frequency and start site selection

(2019) Slawomir Kubik et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

Modular Organization and Assembly of SWI/SNF Family Chromatin Remodeling Complexes

(2018) Nazar Mashtalir et al.   CELL

Discovery of Orally Active Inhibitors of Brahma Homolog (BRM)/SMARCA2 ATPase Activity for the Treatment of Brahma Related Gene 1 (BRG1)/SMARCA4-Mutant Cancers

(2018) Julien P. N. Papillon et al.   JOURNAL OF MEDICINAL CHEMISTRY

Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci

(2017) Ziying Liu et al.   MOLECULAR CELL

hnRNPK Recruits PCGF3/5-PRC1 to the Xist RNA B-Repeat to Establish Polycomb-Mediated Chromosomal Silencing

(2017) Greta Pintacuda et al.   MOLECULAR CELL

Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes

(2017) Cedric R. Clapier et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin

(2017) Erik L Miller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

TOP2 synergizes with BAF chromatin remodeling for both resolution and formation of facultative heterochromatin

(2017) Erik L Miller et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Widespread Mitotic Bookmarking by Histone Marks and Transcription Factors in Pluripotent Stem Cells

(2017) Yiyuan Liu et al.   Cell Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

ATP-dependent chromatin remodeling during mammalian development

(2016) Swetansu K. Hota et al.   DEVELOPMENT

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

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

Regulating the Chromatin Landscape: Structural and Mechanistic Perspectives

(2014) Blaine Bartholomew   Annual Review of Biochemistry

QuasR: quantification and annotation of short reads in R

(2014) Dimos Gaidatzis et al.   BIOINFORMATICS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Mechanisms and Functions of ATP-Dependent Chromatin-Remodeling Enzymes

(2013) Geeta J. Narlikar et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Proteomic and bioinformatic analysis of mammalian SWI/SNF complexes identifies extensive roles in human malignancy

(2013) Cigall Kadoch et al.   NATURE GENETICS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

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

Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels

(2012) Sylvia C Tippmann et al.   Molecular Systems Biology

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

ATP-dependent chromatin remodeling: genetics, genomics and mechanisms

(2011) Diana C Hargreaves et al.   CELL RESEARCH

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

(2011) G. Hu et al.   GENOME RESEARCH

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

(2011) Michael B. Stadler et al.   NATURE

esBAF facilitates pluripotency by conditioning the genome for LIF/STAT3 signalling and by regulating polycomb function

(2011) Lena Ho et al.   NATURE CELL BIOLOGY

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

Distinct Factors Control Histone Variant H3.3 Localization at Specific Genomic Regions

(2010) Aaron D. Goldberg 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

Mitotic bookmarking of genes: a novel dimension to epigenetic control

(2010) Sayyed K. Zaidi et al.   NATURE REVIEWS GENETICS

rtracklayer: an R package for interfacing with genome browsers

(2009) M. Lawrence et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL