IC-Finder: inferring robustly the hierarchical organization of chromatin folding

The 3D Genome as Moderator of Chromosomal Communication

(2016) Job Dekker et al.   CELL

Simulated binding of transcription factors to active and inactive regions folds human chromosomes into loops, rosettes and topological domains

(2016) Chris A. Brackley et al.   NUCLEIC ACIDS RESEARCH

Constructing 3D interaction maps from 1D epigenomes

(2016) Yun Zhu et al.   Nature Communications

Computational Identification of Genomic Features That Influence 3D Chromatin Domain Formation

(2016) Raphaël Mourad et al.   PLoS Computational Biology

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

Modeling chromosomes: Beyond pretty pictures

(2015) Maxim V. Imakaev et al.   FEBS LETTERS

On the demultiplexing of chromosome capture conformation data

(2015) Ivan Junier 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

Hierarchical folding and reorganization of chromosomes are linked to transcriptional changes in cellular differentiation

(2015) J. Fraser et al.   Molecular Systems Biology

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

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

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

Two-dimensional segmentation for analyzing Hi-C data

(2014) C. Levy-Leduc et al.   BIOINFORMATICS

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

(2014) Suhas S.P. Rao et al.   CELL

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho et al.   NATURE

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

HiCNorm: removing biases in Hi-C data via Poisson regression

(2012) Ming Hu et al.   BIOINFORMATICS

Normalization of a chromosomal contact map

(2012) Axel Cournac et al.   BMC GENOMICS

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

(2012) Tom Sexton et al.   CELL

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2012) Maxim Imakaev et al.   NATURE METHODS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

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

(2011) Eitan Yaffe et al.   NATURE GENETICS