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

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

(2012) Tom Sexton et al.   CELL

Higher-order chromatin structure: bridging physics and biology

(2012) Geoffrey Fudenberg et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

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

(2012) H. Tjong et al.   GENOME RESEARCH

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Evidence for Transcript Networks Composed of Chimeric RNAs in Human Cells

(2012) Sarah Djebali et al.   PLoS One

Probing the Entanglement and Locating Knots in Ring Polymers: A Comparative Study of Different Arc Closure Schemes

(2012) Luca Tubiana et al.   PROGRESS OF THEORETICAL PHYSICS SUPPLEMENT

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

(2011) Leonid A. Mirny   CHROMOSOME RESEARCH

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

(2011) Eitan Yaffe et al.   NATURE GENETICS

Transcriptional gene network inference from a massive dataset elucidates transcriptome organization and gene function

(2011) Vincenzo Belcastro et al.   NUCLEIC ACIDS RESEARCH

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

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

Looping Probabilities in Model Interphase Chromosomes

(2010) Angelo Rosa et al.   BIOPHYSICAL JOURNAL

Structure determination of genomic domains by satisfaction of spatial restraints

(2010) Davide Baù et al.   CHROMOSOME RESEARCH

Biopolymer organization upon confinement

(2010) D Marenduzzo et al.   JOURNAL OF PHYSICS-CONDENSED MATTER

Chromosome arm length and nuclear constraints determine the dynamic relationship of yeast subtelomeres

(2010) P. Therizols et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial and Topological Organization of DNA Chains Induced by Gene Co-localization

(2010) Ivan Junier et al.   PLoS Computational Biology

Activation of Estrogen-Responsive Genes Does Not Require Their Nuclear Co-Localization

(2010) Silvia Kocanova et al.   PLoS Genetics

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

A Model for all Genomes: The Role of Transcription Factories

(2009) Peter R. Cook   JOURNAL OF MOLECULAR BIOLOGY

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

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

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

Virus Infection Induces NF-κB-Dependent Interchromosomal Associations Mediating Monoallelic IFN-β Gene Expression

(2008) Effie Apostolou et al.   CELL

Mean clustering coefficients: the role of isolated nodes and leafs on clustering measures for small-world networks

(2008) Marcus Kaiser   NEW JOURNAL OF PHYSICS

Structure and Dynamics of Interphase Chromosomes

(2008) Angelo Rosa et al.   PLoS Computational Biology