Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

Inferential modeling of 3D chromatin structure

(2015) Siyu Wang et al.   NUCLEIC ACIDS RESEARCH

Topology, structures, and energy landscapes of human chromosomes

(2015) Bin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A statistical approach for inferring the 3D structure of the genome

(2014) N. Varoquaux et al.   BIOINFORMATICS

Quantitatively Imaging Chromosomes by Correlated Cryo-Fluorescence and Soft X-Ray Tomographies

(2014) Elizabeth A. Smith et al.   BIOPHYSICAL JOURNAL

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti 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

Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression

(2014) F. Ay et al.   GENOME RESEARCH

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

(2014) Wenxiu Ma et al.   NATURE METHODS

Integrative Analysis of Many Weighted Co-Expression Networks Using Tensor Computation

(2014) Wenyuan Li et al.   PLoS Computational Biology

The Cell Biology of Genomes: Bringing the Double Helix to Life

(2013) Tom Misteli   CELL

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

The Hierarchy of the 3D Genome

(2013) Johan H. Gibcus et al.   MOLECULAR CELL

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

(2013) Takashi Nagano et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

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

(2012) Tom Sexton et al.   CELL

Nuclear Aggregation of Olfactory Receptor Genes Governs Their Monogenic Expression

(2012) E. Josephine Clowney et al.   CELL

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

(2012) Hua Wong et al.   CURRENT BIOLOGY

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

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

Parallel genome universes

(2012) Tom Misteli   NATURE BIOTECHNOLOGY

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

(2012) Maxim Imakaev et al.   NATURE METHODS

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

CTCF-mediated transcriptional regulation through cell type-specific chromosome organization in the β-globin locus

(2012) Ivan Junier et al.   NUCLEIC ACIDS RESEARCH

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Putting the Pieces Together: Integrative Modeling Platform Software for Structure Determination of Macromolecular Assemblies

(2012) Daniel Russel et al.   PLOS BIOLOGY

Three-dimensional modeling of chromatin structure from interaction frequency data using Markov chain Monte Carlo sampling

(2011) Mathieu Rousseau et al.   BMC BIOINFORMATICS

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

Structure determination of genomic domains by satisfaction of spatial restraints

(2010) Davide Baù et al.   CHROMOSOME RESEARCH

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Mapping of long-range associations throughout the fission yeast genome reveals global genome organization linked to transcriptional regulation

(2010) Hideki Tanizawa et al.   NUCLEIC ACIDS RESEARCH

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

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

The Meaning of Gene Positioning

(2008) Takumi Takizawa et al.   CELL

High-resolution statistical mapping reveals gene territories in live yeast

(2008) Axel B Berger et al.   NATURE METHODS