Spatial organization of chromatin domains and compartments in single chromosomes

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

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

(2016) Alistair N. Boettiger et al.   NATURE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Stable Chromosome Condensation Revealed by Chromosome Conformation Capture

(2015) Kyle P. Eagen et al.   CELL

X-chromosome inactivation: new insights into cis and trans regulation

(2015) Rafael Galupa et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Nanoscale spatial organization of theHoxDgene cluster in distinct transcriptional states

(2015) Pierre J. Fabre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Effects of topological constraints on globular polymers

(2015) Maxim V. Imakaev et al.   Soft Matter

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

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

Looping Back to Leap Forward: Transcription Enters a New Era

(2014) Michael Levine et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

(2014) Iain Williamson et al.   GENES & DEVELOPMENT

Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging

(2014) S. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From a melt of rings to chromosome territories: the role of topological constraints in genome folding

(2014) Jonathan D Halverson et al.   REPORTS ON PROGRESS IN PHYSICS

X Chromosome Inactivation and Epigenetic Responses to Cellular Reprogramming

(2013) Derek Lessing et al.   Annual Review of Genomics and Human Genetics

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

Single-chromosome transcriptional profiling reveals chromosomal gene expression regulation

(2013) Marshall J Levesque et al.   NATURE METHODS

The potential of 3D-FISH and super-resolution structured illumination microscopy for studies of 3D nuclear architecture

(2012) Yolanda Markaki et al.   BIOESSAYS

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

(2012) Tom Sexton et al.   CELL

The macrosatellite DXZ4 mediates CTCF-dependent long-range intrachromosomal interactions on the human inactive X chromosome

(2012) Andrea H. Horakova et al.   HUMAN MOLECULAR GENETICS

Independence of Repressive Histone Marks and Chromatin Compaction during Senescent Heterochromatic Layer Formation

(2012) Tamir Chandra et al.   MOLECULAR 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

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

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

Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis

(2011) Shelagh Boyle et al.   CHROMOSOME RESEARCH

The fractal globule as a model of chromatin architecture in the cell

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH

(2011) N.A. Yamada et al.   CYTOGENETIC AND GENOME RESEARCH

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Fast, three-dimensional super-resolution imaging of live cells

(2011) Sara A Jones et al.   NATURE METHODS

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Analysis of Active and Inactive X Chromosome Architecture Reveals the Independent Organization of 30 nm and Large-Scale Chromatin Structures

(2010) Catherine Naughton et al.   MOLECULAR CELL

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Chromosome Territories

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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