Defining genome architecture at base-pair resolution

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

A sensitive assay for dNTPs based on long synthetic oligonucleotides, EvaGreen dye and inhibitor-resistant high-fidelity DNA polymerase

(2020) Janne Purhonen et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9 genome editing in human hematopoietic stem cells

(2018) Rasmus O Bak et al.   Nature Protocols

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains

(2018) A. Marieke Oudelaar et al.   NATURE GENETICS

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

How best to identify chromosomal interactions: a comparison of approaches

(2017) James O J Davies 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

Editing an α-globin enhancer in primary human hematopoietic stem cells as a treatment for β-thalassemia

(2017) Sachith Mettananda et al.   Nature Communications

An immortalized adult human erythroid line facilitates sustainable and scalable generation of functional red cells

(2017) Kongtana Trakarnsanga et al.   Nature Communications

Accurate Promoter and Enhancer Identification in 127 ENCODE and Roadmap Epigenomics Cell Types and Tissues by GenoSTAN

(2017) Benedikt Zacher et al.   PLoS One

Genetic dissection of the α-globin super-enhancer in vivo

(2016) Deborah Hay et al.   NATURE GENETICS

Micro-C XL: assaying chromosome conformation from the nucleosome to the entire genome

(2016) Tsung-Han S Hsieh et al.   NATURE METHODS

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

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

ChIP-nexus enables improved detection of in vivo transcription factor binding footprints

(2015) Qiye He et al.   NATURE BIOTECHNOLOGY

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

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

(2013) Warren A. Whyte et al.   CELL

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Causes and Consequences of Chromatin Variation between Inbred Mice

(2013) Mona Hosseini et al.   PLoS Genetics

Intragenic Enhancers Act as Alternative Promoters

(2012) Monika S. Kowalczyk et al.   MOLECULAR CELL

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Robust 4C-seq data analysis to screen for regulatory DNA interactions

(2012) Harmen J G van de Werken et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

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

(2011) Michael B. Stadler et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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