Systematic evaluation of chromosome conformation capture assays

The structural basis for cohesin–CTCF-anchored loops

(2020) Yan Li et al.   NATURE

The nf-core framework for community-curated bioinformatics pipelines

(2020) Philip A. Ewels et al.   NATURE BIOTECHNOLOGY

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

Expanded encyclopaedias of DNA elements in the human and mouse genomes

(2020) Jill E. Moore et al.   NATURE

An integrative ENCODE resource for cancer genomics

(2020) Jing Zhang et al.   Nature Communications

Multi-contact 3C reveals that the human genome during interphase is largely not entangled

(2020) Filipe Tavares-Cadete et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

(2019) Ryan M.J. Genga et al.   Cell Reports

Cooler: scalable storage for Hi-C data and other genomically labeled arrays

(2019) Nezar Abdennur et al.   BIOINFORMATICS

CUT&Tag for efficient epigenomic profiling of small samples and single cells

(2019) Hatice S. Kaya-Okur et al.   Nature Communications

Automated in situ chromatin profiling efficiently resolves cell types and gene regulatory programs

(2018) Derek H. Janssens et al.   Epigenetics & Chromatin

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

(2017) Houda Belaghzal et al.   METHODS

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

The second decade of 3C technologies: detailed insights into nuclear organization

(2016) Annette Denker et al.   GENES & DEVELOPMENT

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

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

Genome-wide mapping and analysis of chromosome architecture

(2016) Anthony D. Schmitt et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

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

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Gene Density, Transcription, and Insulators Contribute to the Partition of the Drosophila Genome into Physical Domains

(2012) Chunhui Hou et al.   MOLECULAR CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mediator and cohesin connect gene expression and chromatin architecture

(2010) Michael H. Kagey et al.   NATURE

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

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