Single-molecule regulatory architectures captured by chromatin fiber sequencing

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

(2020) Zohar Shipony et al.   NATURE METHODS

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials

(2019) Alexa B. R. McIntyre et al.   Nature Communications

Single-molecule long-read sequencing reveals the chromatin basis of gene expression

(2019) Yunhao Wang et al.   GENOME RESEARCH

Genome-wide Rules of Nucleosome Phasing in Drosophila

(2018) Sandro Baldi et al.   MOLECULAR CELL

Genome-wide Single-Molecule Footprinting Reveals High RNA Polymerase II Turnover at Paused Promoters

(2017) Arnaud R. Krebs et al.   MOLECULAR CELL

DNA N6-methyladenine in metazoans: functional epigenetic mark or bystander?

(2017) Guan-Zheng Luo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The non-specific adenine DNA methyltransferase M.EcoGII

(2017) Iain A Murray et al.   NUCLEIC ACIDS RESEARCH

DNA N6-methyladenine in metazoans: functional epigenetic mark or bystander?

(2017) Guan-Zheng Luo et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture

(2017) Athma A Pai et al.   eLife

Comparative Methylome Analysis of the Occasional Ruminant Respiratory Pathogen Bibersteinia trehalosi

(2016) Brian P. Anton et al.   PLoS One

MNase titration reveals differences between nucleosome occupancy and chromatin accessibility

(2016) Jakub Mieczkowski et al.   Nature Communications

Genome-wide profiling of nucleosome sensitivity and chromatin accessibility inDrosophila melanogaster

(2015) Răzvan V. Chereji et al.   NUCLEIC ACIDS RESEARCH

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

(2014) J. Vierstra et al.   SCIENCE

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes

(2013) Andrew B. Stergachis et al.   CELL

Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma

(2013) N. H. Nabilsi et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Determinants of nucleosome positioning

(2013) Kevin Struhl et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

BEDOPS: high-performance genomic feature operations

(2012) Shane Neph et al.   BIOINFORMATICS

Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules

(2012) T. K. Kelly et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

(2012) Matthew T. Maurano et al.   PLoS Genetics

Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism

(2011) Ty C. Voss et al.   CELL

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Novel non-specific DNA adenine methyltransferases

(2011) Marek Drozdz et al.   NUCLEIC ACIDS RESEARCH

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Nucleosome positioning and gene regulation: advances through genomics

(2009) Cizhong Jiang et al.   NATURE REVIEWS GENETICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Dynamic Regulation of Nucleosome Positioning in the Human Genome

(2008) Dustin E. Schones et al.   CELL

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE