Micro- and nanoscale devices for the investigation of epigenetics and chromatin dynamics

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Fast Translocation of Proteins through Solid State Nanopores

(2013) Calin Plesa et al.   NANO LETTERS

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

(2013) Yun Liu et al.   NATURE BIOTECHNOLOGY

Detection of histone modifications at specific gene loci in single cells in histological sections

(2013) Delphine Gomez et al.   NATURE METHODS

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Determinants of nucleosome positioning

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

Integrated view of genome structure and sequence of a single DNA molecule in a nanofluidic device

(2013) R. Marie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells

(2013) P. J. Murphy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ordered Arrays of Native Chromatin Molecules for High-Resolution Imaging and Analysis

(2012) Aline Cerf et al.   ACS Nano

Resolution limit for DNA barcodes in the Odijk regime

(2012) Yanwei Wang et al.   Biomicrofluidics

Regulated Noise in the Epigenetic Landscape of Development and Disease

(2012) Elisabet Pujadas et al.   CELL

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Nucleosomal Elements that Control the Topography of the Barrier to Transcription

(2012) Lacramioara Bintu et al.   CELL

Sequential ChIP-bisulfite sequencing enables direct genome-scale investigation of chromatin and DNA methylation cross-talk

(2012) Arie B. Brinkman et al.   GENOME RESEARCH

Enhanced discrimination of DNA molecules in nanofluidic channels through multiple measurements

(2012) Yi-Heng Sen et al.   LAB ON A CHIP

Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells

(2012) Jaime J. Benítez et al.   LAB ON A CHIP

High throughput automated chromatin immunoprecipitation as a platform for drug screening and antibody validation

(2012) Angela R. Wu et al.   LAB ON A CHIP

Fragmentation of DNA in a sub-microliter microfluidic sonication device

(2012) Qingzong Tseng et al.   LAB ON A CHIP

Nanopore Detection of Single Molecule RNAP–DNA Transcription Complex

(2012) C. Raillon et al.   NANO LETTERS

Nanoscale Squeezing in Elastomeric Nanochannels for Single Chromatin Linearization

(2012) Toshiki Matsuoka et al.   NANO LETTERS

Detection of Nucleosomal Substructures using Solid-State Nanopores

(2012) Gautam V. Soni et al.   NANO LETTERS

Fast and automatic processing of multi-level events in nanopore translocation experiments

(2012) C. Raillon et al.   Nanoscale

An integrated encyclopedia of DNA elements in the human genome

(2012)   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

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

(2012) Elizabeth A Manrao et al.   NATURE BIOTECHNOLOGY

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Studying genomic processes at the single-molecule level: introducing the tools and applications

(2012) David Dulin et al.   NATURE REVIEWS GENETICS

NAP1-Assisted Nucleosome Assembly on DNA Measured in Real Time by Single-Molecule Magnetic Tweezers

(2012) Rifka Vlijm et al.   PLoS One

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel

(2012) B. R. Cipriany et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Physical manipulation of the Escherichia coli chromosome reveals its soft nature

(2012) J. Pelletier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stacked Graphene-Al2O3 Nanopore Sensors for Sensitive Detection of DNA and DNA–Protein Complexes

(2011) Bala Murali Venkatesan et al.   ACS Nano

Single DNA Molecule Patterning for High-Throughput Epigenetic Mapping

(2011) Aline Cerf et al.   ANALYTICAL CHEMISTRY

DNA methylation profiling in nanochannels

(2011) Shuang Fang Lim et al.   Biomicrofluidics

Regulation of chromatin by histone modifications

(2011) Andrew J Bannister et al.   CELL RESEARCH

Recent advances in single molecule studies of nucleosomes

(2011) Jessica L Killian et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Synthetic Reversal of Epigenetic Silencing

(2011) Karmella A. Haynes et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A device for extraction, manipulation and stretching of DNA from single human chromosomes

(2011) Kristian H. Rasmussen et al.   LAB ON A CHIP

Histone modification analysis by chromatin immunoprecipitation from a low number of cells on a microfluidic platform

(2011) Tao Geng et al.   LAB ON A CHIP

Transfer-Printing of Single DNA Molecule Arrays on Graphene for High-Resolution Electron Imaging and Analysis

(2011) Aline Cerf et al.   NANO LETTERS

Microfluidic DNA fragmentation for on-chip genomic analysis

(2011) Lingling Shui et al.   NANOTECHNOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

High order chromatin architecture shapes the landscape of chromosomal alterations in cancer

(2011) Geoff Fudenberg et al.   NATURE BIOTECHNOLOGY

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

(2011) Chun-Xiao Song et al.   NATURE METHODS

Nanopore sensors for nucleic acid analysis

(2011) Bala Murali Venkatesan et al.   Nature Nanotechnology

Optical tweezers study life under tension

(2011) Furqan M Fazal et al.   Nature Photonics

Histone fold modifications control nucleosome unwrapping and disassembly

(2011) M. Simon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Breast Cancer Methylomes Establish an Epigenomic Foundation for Metastasis

(2011) F. Fang et al.   Science Translational Medicine

Single Molecule Epigenetic Analysis in a Nanofluidic Channel

(2010) Benjamin R. Cipriany et al.   ANALYTICAL CHEMISTRY

Identification of epigenetic DNA modifications with a protein nanopore

(2010) Emma V. B. Wallace et al.   CHEMICAL COMMUNICATIONS

Continuous separation of cells and particles in microfluidic systems

(2010) Andreas Lenshof et al.   CHEMICAL SOCIETY REVIEWS

Epigenome Mapping in Normal and Disease States

(2010) Alika K. Maunakea et al.   CIRCULATION RESEARCH

Discrimination of Methylcytosine from Hydroxymethylcytosine in DNA Molecules

(2010) Meni Wanunu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nanofluidic single-molecule sorting of DNA: a new concept in separation and analysis of biomolecules towards ultimate level performance

(2010) Takatoki Yamamoto et al.   NANOTECHNOLOGY

Graphene as a subnanometre trans-electrode membrane

(2010) S. Garaj et al.   NATURE

Relationship between nucleosome positioning and DNA methylation

(2010) Ramakrishna K. Chodavarapu et al.   NATURE

Linking cell signaling and the epigenetic machinery

(2010) Helai P Mohammad et al.   NATURE BIOTECHNOLOGY

Whole-genome molecular haplotyping of single cells

(2010) H Christina Fan et al.   NATURE BIOTECHNOLOGY

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

Soft lithography for micro- and nanoscale patterning

(2010) Dong Qin et al.   Nature Protocols

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier

(2010) Jing Jin et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Pathology tissue-chromatin immunoprecipitation, coupled with high-throughput sequencing, allows the epigenetic profiling of patient samples

(2010) M. Fanelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation and Characterization of Circulating Tumor Cells from Patients with Localized and Metastatic Prostate Cancer

(2010) S. L. Stott et al.   Science Translational Medicine

The histone shuffle: histone chaperones in an energetic dance

(2010) Chandrima Das et al.   TRENDS IN BIOCHEMICAL SCIENCES

Data Analysis of Translocation Events in Nanopore Experiments

(2009) Daniel Pedone et al.   ANALYTICAL CHEMISTRY

Nanoelectromechanics of Methylated DNA in a Synthetic Nanopore

(2009) U. Mirsaidov et al.   BIOPHYSICAL JOURNAL

Automated microfluidic chromatin immunoprecipitation from 2,000 cells

(2009) Angela R. Wu et al.   LAB ON A CHIP

Stretching chromatin through confinement

(2009) Diana E. Streng et al.   LAB ON A CHIP

Detection of Local Protein Structures along DNA Using Solid-State Nanopores

(2009) Stefan W. Kowalczyk et al.   NANO LETTERS

Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA

(2009) Alon Goren et al.   NATURE METHODS

Linking DNA methylation and histone modification: patterns and paradigms

(2009) Howard Cedar et al.   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber

(2009) Maarten Kruithof et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

(2009) Michael A Hall et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition

(2009) Mari-Liis Visnapuu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

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

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

Histone Modifications and Chromatin Remodeling during Bacterial Infections

(2008) Mélanie Anne Hamon et al.   Cell Host & Microbe

DNA Curtains and Nanoscale Curtain Rods: High-Throughput Tools for Single Molecule Imaging

(2008) Teresa Fazio et al.   LANGMUIR

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy

(2008) Keir C Neuman et al.   NATURE METHODS

Genome-wide approaches to studying chromatin modifications

(2008) Dustin E. Schones et al.   NATURE REVIEWS GENETICS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE