Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization

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

(2015) Bryan R. Lajoie et al.   METHODS

Comparative analysis of metazoan chromatin organization

(2014) Joshua W. K. Ho 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

Co-binding by YY1 identifies the transcriptionally active, highly conserved set of CTCF-bound regions in primate genomes

(2014) Petra C Schwalie et al.   GENOME BIOLOGY

Function of YY1 in Long-Distance DNA Interactions

(2014) Michael L. Atchison   Frontiers in Immunology

Interactome Maps of Mouse Gene Regulatory Domains Reveal Basic Principles of Transcriptional Regulation

(2013) Kyong-Rim Kieffer-Kwon et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

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

Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments

(2013) V. C. Seitan et al.   GENOME RESEARCH

A hypofunctional PAX1 mutation causes autosomal recessively inherited otofaciocervical syndrome

(2013) Esther Pohl et al.   HUMAN GENETICS

H4K20 methylation regulates quiescence and chromatin compaction

(2013) Adam G. Evertts et al.   MOLECULAR BIOLOGY OF THE CELL

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

(2013) Takashi Nagano et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells

(2013) Robert Nechanitzky et al.   NATURE IMMUNOLOGY

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

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

Divergence of Mammalian Higher Order Chromatin Structure Is Associated with Developmental Loci

(2013) Emily V. Chambers et al.   PLoS Computational Biology

Regulation of the Boundaries of Accessible Chromatin

(2013) Xiaoran Chai et al.   PLoS Genetics

Consistency Test of the Cell Cycle: Roles for p53 and EGR1

(2012) Y. Zwang et al.   CANCER RESEARCH

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

(2012) Tom Sexton et al.   CELL

c-Myc Is a Universal Amplifier of Expressed Genes in Lymphocytes and Embryonic Stem Cells

(2012) Zuqin Nie et al.   CELL

Embryonic stem cell and induced pluripotent stem cell: an epigenetic perspective

(2012) Gaoyang Liang et al.   CELL RESEARCH

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence

(2012) W. Meuleman et al.   GENOME RESEARCH

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

Positive intergenic feedback circuitry, involving EBF1 and FOXO1, orchestrates B-cell fate

(2012) R. Mansson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions

(2012) Manching Ku et al.   GENOME BIOLOGY

Combinatorial Patterning of Chromatin Regulators Uncovered by Genome-wide Location Analysis in Human Cells

(2011) Oren Ram et al.   CELL

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

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Profiling of histone H3 lysine 9 trimethylation levels predicts transcription factor activity and survival in acute myeloid leukemia

(2010) C. Muller-Tidow et al.   BLOOD

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis

(2009) I. Hiratani et al.   GENOME RESEARCH

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

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

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY