MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions

A computational strategy to adjust for copy number in tumor Hi-C data

(2016) Hua-Jun Wu et al.   BIOINFORMATICS

The three-dimensional genome: principles and roles of long-distance interactions

(2016) M Jordan Rowley et al.   CURRENT OPINION IN CELL BIOLOGY

TAD disruption as oncogenic driver

(2016) Anne-Laure Valton et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Breaking TADs: How Alterations of Chromatin Domains Result in Disease

(2016) Darío G. Lupiáñez et al.   TRENDS IN GENETICS

Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities

(2016) Chao Dai et al.   Nature Communications

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

(2016) Raphaël Mourad et al.   PLoS Computational Biology

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

Structural and functional diversity of Topologically Associating Domains

(2015) Job Dekker et al.   FEBS LETTERS

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

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

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Cell-of-origin chromatin organization shapes the mutational landscape of cancer

(2015) Paz Polak et al.   NATURE

Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C

(2015) Borbala Mifsud et al.   NATURE GENETICS

Unraveling the 3D genome: genomics tools for multiscale exploration

(2015) Viviana I. Risca et al.   TRENDS IN GENETICS

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

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Comparative analysis of regulatory information and circuits across distant species

(2014) Alan P. Boyle et al.   NATURE

CTCF: an architectural protein bridging genome topology and function

(2014) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Architectural proteins: regulators of 3D genome organization in cell fate

(2014) Elena Gómez-Díaz et al.   TRENDS IN CELL BIOLOGY

OrthoClust: an orthology-based network framework for clustering data across multiple species

(2014) Koon-Kiu Yan et al.   GENOME BIOLOGY

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

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

A complex network framework for unbiased statistical analyses of DNA–DNA contact maps

(2012) Kai Kruse et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Networking the nucleus

(2010) Indika Rajapakse et al.   Molecular Systems Biology

CHD7 Targets Active Gene Enhancer Elements to Modulate ES Cell-Specific Gene Expression

(2010) Michael P. Schnetz et al.   PLoS Genetics

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

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

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT