StripeDiff: Model-based algorithm for differential analysis of chromatin stripe

Stripenn detects architectural stripes from chromatin conformation data using computer vision

(2022) Sora Yoon et al.   Nature Communications

Human Condensin I and II Drive Extensive ATP-Dependent Compaction of Nucleosome-Bound DNA

(2020) Muwen Kong et al.   MOLECULAR CELL

Chromosome organization by one-sided and two-sided loop extrusion

(2020) Edward J Banigan et al.   eLife

Cohesin and condensin extrude DNA loops in a cell-cycle dependent manner

(2020) Stefan Golfier et al.   eLife

How the Genome Folds: The Biophysics of Four-Dimensional Chromatin Organization

(2019) Jyotsana J. Parmar et al.   Annual Review of Biophysics

Enhancer accessibility and CTCF occupancy underlie asymmetric TAD architecture and cell type specific genome topology

(2019) Christopher Barrington et al.   Nature Communications

Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory

(2019) Alessandro Bertero et al.   Nature Communications

DNA loop extrusion by human cohesin

(2019) Iain F. Davidson et al.   SCIENCE

Human cohesin compacts DNA by loop extrusion

(2019) Yoori Kim et al.   SCIENCE

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Three-dimensional organization and dynamics of the genome

(2018) Przemyslaw Szalaj et al.   CELL BIOLOGY AND TOXICOLOGY

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

(2018) Mohamed Nadhir Djekidel et al.   GENOME RESEARCH

Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells

(2018) Gangqing Hu et al.   IMMUNITY

Chromatin organization by an interplay of loop extrusion and compartmental segregation

(2018) Johannes Nuebler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Organizational principles of 3D genome architecture

(2018) M. Jordan Rowley et al.   NATURE REVIEWS GENETICS

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Erratum: Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

A Compendium of Chromatin Contact Maps Reveals Spatially Active Regions in the Human Genome

(2016) Anthony D. Schmitt et al.   Cell Reports

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

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

diffHic: a Bioconductor package to detect differential genomic interactions in Hi-C data

(2015) Aaron T.L. Lun et al.   BMC BIOINFORMATICS

Disruptions of Topological Chromatin Domains Cause Pathogenic Rewiring of Gene-Enhancer Interactions

(2015) Darío G. Lupiáñez et al.   CELL

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

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

(2013) Takashi Nagano et al.   NATURE

Normalization of a chromosomal contact map

(2012) Axel Cournac et al.   BMC GENOMICS

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

(2012) K. Chen et al.   GENOME RESEARCH

A fast algorithm for matrix balancing

(2012) P. A. Knight et al.   IMA JOURNAL OF NUMERICAL ANALYSIS

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

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

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

ChIP-based methods for the identification of long-range chromatin interactions

(2009) Melissa J. Fullwood et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

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

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY