Chromatin Loop Extrusion and Chromatin Unknotting

Knoto-ID: a tool to study the entanglement of open protein chains using the concept of knotoids

(2018) Julien Dorier et al.   BIOINFORMATICS

DNA Supercoiling, Topoisomerases, and Cohesin: Partners in Regulating Chromatin Architecture?

(2018) Camilla Björkegren et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Two convergent pathways of DNA knotting in replicating DNA molecules as revealed by θ-curve analysis

(2018) Danielle O’Donnol et al.   NUCLEIC ACIDS RESEARCH

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

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

(2017) Tim J. Stevens et al.   NATURE

Transcription-induced supercoiling as the driving force of chromatin loop extrusion during formation of TADs in interphase chromosomes

(2017) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

DNA knots occur in intracellular chromatin

(2017) Antonio Valdés et al.   NUCLEIC ACIDS RESEARCH

Are There Knots in Chromosomes?

(2017) Jonathan Siebert et al.   Polymers

CTCF and cohesin regulate chromatin loop stability with distinct dynamics

(2017) Anders S Hansen et al.   eLife

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Compaction and segregation of sister chromatids via active loop extrusion

(2016) Anton Goloborodko et al.   eLife

Strong scaling of general-purpose molecular dynamics simulations on GPUs

(2015) Jens Glaser et al.   COMPUTER PHYSICS COMMUNICATIONS

Generation of supercoils in nicked and gapped DNA drives DNA unknotting and postreplicative decatenation

(2015) Dusan Racko et al.   NUCLEIC ACIDS RESEARCH

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

(2015) Adrian L. Sanborn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Suhas S.P. Rao et al.   CELL

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

Self-organization of domain structures by DNA-loop-extruding enzymes

(2012) E. Alipour et al.   NUCLEIC ACIDS RESEARCH

GPU Based Molecular Dynamics Simulations of Polymer Rings in Concentrated Solution: Structure and Scaling

(2012) Daniel Reith 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

Topological origins of chromosomal territories

(2009) Julien Dorier 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

General purpose molecular dynamics simulations fully implemented on graphics processing units

(2008) Joshua A. Anderson et al.   JOURNAL OF COMPUTATIONAL PHYSICS