Restraint-based three-dimensional modeling of genomes and genomic domains

The pluripotent regulatory circuitry connecting promoters to their long-range interacting elements

(2015) Stefan Schoenfelder et al.   GENOME RESEARCH

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

(2015) Bryan R. Lajoie et al.   METHODS

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Aquaria: simplifying discovery and insight from protein structures

(2015) Seán I O'Donoghue et al.   NATURE METHODS

Assessing the limits of restraint-based 3D modeling of genomes and genomic domains

(2015) Marie Trussart et al.   NUCLEIC ACIDS RESEARCH

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

(2014) N. Varoquaux et al.   BIOINFORMATICS

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

Distinct structural transitions of chromatin topological domains correlate with coordinated hormone-induced gene regulation

(2014) François Le Dily et al.   GENES & DEVELOPMENT

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

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

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

(2014) Daniel Jost et al.   NUCLEIC ACIDS RESEARCH

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Targeted Chromatin Capture (T2C): a novel high resolution high throughput method to detect genomic interactions and regulatory elements

(2014) Petros Kolovos et al.   Epigenetics & Chromatin

New insights into the helical structure of 30-nm chromatin fibers

(2014) Ping Chen et al.   Protein & Cell

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

A model of the large-scale organization of chromatin

(2013) Mariano Barbieri et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

Segmental folding of chromosomes: A basis for structural and regulatory chromosomal neighborhoods?

(2013) Elphège P. Nora et al.   BIOESSAYS

3D Chromosome Modeling with Semi-Definite Programming and Hi-C Data

(2013) ZhiZhuo Zhang et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

(2013) Takashi Nagano et al.   NATURE

Chromosomes captured one by one

(2013) Job Dekker et al.   NATURE

Exploring long-range genome interactions using the WashU Epigenome Browser

(2013) Xin Zhou et al.   NATURE METHODS

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

The sequencing bias relaxed characteristics of Hi-C derived data and implications for chromatin 3D modeling

(2013) Cheng Peng et al.   NUCLEIC ACIDS RESEARCH

Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub

(2013) Alexey A. Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Organization of the Mitotic Chromosome

(2013) N. Naumova et al.   SCIENCE

Bayesian Inference of Spatial Organizations of Chromosomes

(2013) Ming Hu et al.   PLoS Computational Biology

Colocalization of Coregulated Genes: A Steered Molecular Dynamics Study of Human Chromosome 19

(2013) Marco Di Stefano et al.   PLoS Computational Biology

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

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

Clustering of Tissue-Specific Sub-TADs Accompanies the Regulation of HoxA Genes in Developing Limbs

(2013) Soizik Berlivet et al.   PLoS Genetics

The genome in space and time: Does form always follow function?

(2012) Zhijun Duan et al.   BIOESSAYS

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

(2012) H. Tjong et al.   GENOME RESEARCH

Genome structure determination via 3C-based data integration by the Integrative Modeling Platform

(2012) Davide Baù et al.   METHODS

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

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

Recovering ensembles of chromatin conformations from contact probabilities

(2012) Dario Meluzzi et al.   NUCLEIC ACIDS RESEARCH

On the assessment of statistical significance of three-dimensional colocalization of sets of genomic elements

(2012) Daniela M. Witten et al.   NUCLEIC ACIDS RESEARCH

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

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Chromatin globules: a common motif of higher order chromosome structure?

(2011) Amartya Sanyal et al.   CURRENT OPINION IN CELL BIOLOGY

Super-resolution fluorescence microscopy as a tool to study the nanoscale organization of chromosomes

(2011) Cristina Flors et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

A view of the chromatin landscape

(2011) Lindsy M. Rapkin et al.   MICRON

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

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

Evidence for short-range helical order in the 30-nm chromatin fibers of erythrocyte nuclei

(2011) M. P. Scheffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bridging the Resolution Gap in Structural Modeling of 3D Genome Organization

(2011) Marc A. Marti-Renom et al.   PLoS Computational Biology

Genome3D: a viewer-model framework for integrating and visualizing multi-scale epigenomic information within a three-dimensional genome

(2010) Thomas M Asbury et al.   BMC BIOINFORMATICS

Breaking the Diffraction Barrier: Super-Resolution Imaging of Cells

(2010) Bo Huang et al.   CELL

Structure determination of genomic domains by satisfaction of spatial restraints

(2010) Davide Baù et al.   CHROMOSOME RESEARCH

MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data

(2010) M Meyer et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

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

The folding and unfolding of eukaryotic chromatin

(2009) Andrew Bassett et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

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

Chromatin conformation signatures of cellular differentiation

(2009) James Fraser et al.   GENOME BIOLOGY

Micromechanical studies of mitotic chromosomes

(2008) John F. Marko   CHROMOSOME RESEARCH

Hydrodynamic Studies on Defined Heterochromatin Fragments Support a 30-nm Fiber Having Six Nucleosomes per Turn

(2008) Rodolfo Ghirlando et al.   JOURNAL OF MOLECULAR BIOLOGY