Computational 3D genome modeling using Chrom3D

Constrained release of lamina-associated enhancers and genes from the nuclear envelope during T-cell activation facilitates their association in chromosome compartments

(2017) Michael I. Robson et al.   GENOME RESEARCH

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data

(2017) Borbala Mifsud et al.   PLoS One

An integrated 3-Dimensional Genome Modeling Engine for data-driven simulation of spatial genome organization

(2016) Przemysław Szałaj et al.   GENOME RESEARCH

A-type lamins bind both hetero- and euchromatin, the latter being regulated by lamina-associated polypeptide 2 alpha

(2016) Kevin Gesson et al.   GENOME RESEARCH

Tissue-Specific Gene Repositioning by Muscle Nuclear Membrane Proteins Enhances Repression of Critical Developmental Genes during Myogenesis

(2016) Michael I. Robson et al.   MOLECULAR CELL

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

(2016) Harianto Tjong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Laminopathies disrupt epigenomic developmental programs and cell fate

(2016) Jelena Perovanovic et al.   Science Translational Medicine

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

(2016) Chao Dai et al.   Nature Communications

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

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

(2015) François Serra et al.   FEBS LETTERS

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

(2015) Eivind G Lund et al.   Nucleus

Distinct features of lamin A-interacting chromatin domains mapped by ChIP-sequencing from sonicated or micrococcal nuclease-digested chromatin

(2015) Eivind G Lund et al.   Nucleus

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

(2014) Suhas S.P. Rao et al.   CELL

3D genome reconstruction from chromosomal contacts

(2014) Annick Lesne et al.   NATURE METHODS

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations

(2014) Eivind Lund et al.   NUCLEIC ACIDS RESEARCH

Ring Polymers in the Melt State: The Physics of Crumpling

(2014) Angelo Rosa et al.   PHYSICAL REVIEW LETTERS

Closing the (nuclear) envelope on the genome: How nuclear lamins interact with promoters and modulate gene expression

(2013) Philippe Collas et al.   BIOESSAYS

Single-Cell Dynamics of Genome-Nuclear Lamina Interactions

(2013) Jop Kind et al.   CELL

Lamin A/C-promoter interactions specify chromatin state-dependent transcription outcomes

(2013) E. Lund et al.   GENOME RESEARCH

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

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

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

(2012) Davide Baù 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

Expression-Dependent Folding of Interphase Chromatin

(2012) Hansjoerg Jerabek et al.   PLoS One

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

Identifying elemental genomic track types and representing them uniformly

(2011) Sveinung Gundersen et al.   BMC BIOINFORMATICS

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

(2011) Mathieu Rousseau et al.   BMC BIOINFORMATICS

UCSF Chimera, MODELLER, and IMP: An integrated modeling system

(2011) Zheng Yang et al.   JOURNAL OF STRUCTURAL BIOLOGY

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

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

Repulsive Forces Between Looping Chromosomes Induce Entropy-Driven Segregation

(2011) Manfred Bohn et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Structure determination of genomic domains by satisfaction of spatial restraints

(2010) Davide Baù et al.   CHROMOSOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

A three-dimensional model of the yeast genome

(2010) Zhijun Duan et al.   NATURE

Genomics tools for unraveling chromosome architecture

(2010) Bas van Steensel et al.   NATURE BIOTECHNOLOGY

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

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

Entropic organization of interphase chromosomes

(2009) Peter R. Cook et al.   JOURNAL OF CELL BIOLOGY

Non-specific interactions are sufficient to explain the position of heterochromatic chromocenters and nucleoli in interphase nuclei

(2009) S. de Nooijer et al.   NUCLEIC ACIDS RESEARCH

Spatially confined folding of chromatin in the interphase nucleus

(2009) J. Mateos-Langerak et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE