Single-cell absolute contact probability detection reveals chromosomes are organized by multiple low-frequency yet specific interactions

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map

(2017) Kyle P. Eagen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nanometer resolved single-molecule colocalization of nuclear factors by two-color super resolution microscopy imaging

(2016) Mariya Georgieva et al.   METHODS

Chromatin Domains: The Unit of Chromosome Organization

(2016) Jesse R. Dixon et al.   MOLECULAR CELL

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

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

(2015) Suhas S.P. Rao et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

Active chromatin and transcription play a key role in chromosome partitioning into topologically associating domains

(2015) Sergey V. Ulianov et al.   GENOME RESEARCH

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

SR-Tesseler: a method to segment and quantify localization-based super-resolution microscopy data

(2015) Florian Levet 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

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

SIMcheck: a Toolbox for Successful Super-resolution Structured Illumination Microscopy

(2015) Graeme Ball et al.   Scientific Reports

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

Coordinate-based co-localization-mediated analysis of arrestin clustering upon stimulation of the C–C chemokine receptor 5 with RANTES/CCL5 analogues

(2014) Laura Tarancón Díez et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Stochastic genome-nuclear lamina interactions

(2014) Jop Kind et al.   Nucleus

Statistical tests for measures of colocalization in biological microscopy

(2013) JOHN H. MCDONALD et al.   JOURNAL OF MICROSCOPY

Topology of mammalian developmental enhancers and their regulatory landscapes

(2013) Wouter de Laat et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

Super-Resolution Imaging of Bacteria in a Microfluidics Device

(2013) Diego I. Cattoni et al.   PLoS One

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

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

Real-Time Dynamics of RNA Polymerase II Clustering in Live Human Cells

(2013) I. I. Cisse et al.   SCIENCE

Recruitment, Assembly, and Molecular Architecture of the SpoIIIE DNA Pump Revealed by Superresolution Microscopy

(2013) Jean-Bernard Fiche et al.   PLOS BIOLOGY

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

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

Progressive Polycomb Assembly on H3K27me3 Compartments Generates Polycomb Bodies with Developmentally Regulated Motion

(2012) Thierry Cheutin et al.   PLoS Genetics

modMine: flexible access to modENCODE data

(2011) S. Contrino et al.   NUCLEIC ACIDS RESEARCH

Polycomb group proteins: repression in 3D

(2011) Frédéric Bantignies et al.   TRENDS IN GENETICS

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Expression in Aneuploid Drosophila S2 Cells

(2010) Yu Zhang et al.   PLOS BIOLOGY

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

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

Subdiffraction-Resolution Fluorescence Imaging with Conventional Fluorescent Probes

(2008) Mike Heilemann et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Three-Dimensional Resolution Doubling in Wide-Field Fluorescence Microscopy by Structured Illumination

(2008) Mats G.L. Gustafsson et al.   BIOPHYSICAL JOURNAL

Dynamic multiple-target tracing to probe spatiotemporal cartography of cell membranes

(2008) Arnauld Sergé et al.   NATURE METHODS

Three-Dimensional Super-Resolution Imaging by Stochastic Optical Reconstruction Microscopy

(2008) B. Huang et al.   SCIENCE

BEAF Regulates Cell-Cycle Genes through the Controlled Deposition of H3K9 Methylation Marks into Its Conserved Dual-Core Binding Sites

(2008) Eldon Emberly et al.   PLOS BIOLOGY