Alteration of genome folding via contact domain boundary insertion

Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding

(2020) Tsung-Han S. Hsieh et al.   MOLECULAR CELL

Ultrastructural Details of Mammalian Chromosome Architecture

(2020) Nils Krietenstein et al.   MOLECULAR CELL

Chromatin features constrain structural variation across evolutionary timescales

(2019) Geoff Fudenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Evaluation of Statistical Methods for Identifying Looping Interactions in 5C Data

(2019) Thomas G. Gilgenast et al.   Cell Systems

DamC reveals principles of chromatin folding in vivo without crosslinking and ligation

(2019) Josef Redolfi et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Functional dissection of the Sox9–Kcnj2 locus identifies nonessential and instructive roles of TAD architecture

(2019) Alexandra Despang et al.   NATURE GENETICS

Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

(2019) Yanxiao Zhang et al.   NATURE GENETICS

Chromatin structure dynamics during the mitosis-to-G1 phase transition

(2019) Haoyue Zhang et al.   NATURE

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix

(2018) Giovanna Ambrosini et al.   BIOINFORMATICS

The Energetics and Physiological Impact of Cohesin Extrusion

(2018) Laura Vian et al.   CELL

Necroptosis in development and diseases

(2018) Bing Shan et al.   GENES & DEVELOPMENT

Repeat associated mechanisms of genome evolution and function revealed by theMus caroliandMus paharigenomes

(2018) David Thybert et al.   GENOME RESEARCH

Detecting hierarchical genome folding with network modularity

(2018) Heidi K Norton et al.   NATURE METHODS

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

A TAD boundary is preserved upon deletion of the CTCF-rich Firre locus

(2018) A. Rasim Barutcu et al.   Nature Communications

Transcription Elongation Can Affect Genome 3D Structure

(2018) Sven Heinz et al.   CELL

Organizational principles of 3D genome architecture

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

Necroptosis and RIPK1-mediated neuroinflammation in CNS diseases

(2018) Junying Yuan et al.   NATURE REVIEWS NEUROSCIENCE

Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element

(2017) Peng Huang et al.   GENES & DEVELOPMENT

Reciprocal insulation analysis of Hi-C data shows that TADs represent a functionally but not structurally privileged scale in the hierarchical folding of chromosomes

(2017) Yinxiu Zhan et al.   GENOME RESEARCH

Chromatin Domain Organization of the TCRb Locus and Its Perturbation by Ectopic CTCF Binding

(2017) Pratishtha Rawat et al.   MOLECULAR AND CELLULAR BIOLOGY

Evolutionarily Conserved Principles Predict 3D Chromatin Organization

(2017) M. Jordan Rowley et al.   MOLECULAR CELL

Two independent modes of chromatin organization revealed by cohesin removal

(2017) Wibke Schwarzer et al.   NATURE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Cohesin is positioned in mammalian genomes by transcription, CTCF and Wapl

(2017) Georg A. Busslinger et al.   NATURE

Comparison of computational methods for Hi-C data analysis

(2017) Mattia Forcato et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Genome-wide mapping of infection-induced SINE RNAs reveals a role in selective mRNA export

(2017) John Karijolich et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

(2017) Aziz Khan et al.   NUCLEIC ACIDS RESEARCH

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

(2016) William J. Astle et al.   CELL

Cell-of-Origin-Specific 3D Genome Structure Acquired during Somatic Cell Reprogramming

(2016) Peter Hugo Lodewijk Krijger et al.   Cell Stem Cell

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances

(2016) Orsolya Symmons et al.   DEVELOPMENTAL CELL

A hyperactive transcriptional state marks genome reactivation at the mitosis–G1 transition

(2016) Chris C.-S. Hsiung et al.   GENES & DEVELOPMENT

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Activation of proto-oncogenes by disruption of chromosome neighborhoods

(2016) D. Hnisz et al.   SCIENCE

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg 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

Native Elongating Transcript Sequencing Reveals Human Transcriptional Activity at Nucleotide Resolution

(2015) Andreas Mayer et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

(2015) James O J Davies et al.   NATURE METHODS

ENCODE data at the ENCODE portal

(2015) Cricket A. Sloan 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

CTCF establishes discrete functional chromatin domains at theHoxclusters during differentiation

(2015) Varun Narendra et al.   SCIENCE

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

(2015) Matteo Vietri Rudan et al.   Cell Reports

Identification of alternative topological domains in chromatin

(2014) Darya Filippova et al.   Algorithms for Molecular Biology

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

(2014) Suhas S.P. Rao et al.   CELL

Widespread contribution of transposable elements to the innovation of gene regulatory networks

(2014) Vasavi Sundaram et al.   GENOME RESEARCH

Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins

(2014) S. Kim et al.   GENOME RESEARCH

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

(2014) Jim R Hughes et al.   NATURE GENETICS

Insulator function and topological domain border strength scale with architectural protein occupancy

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

Architectural Protein Subclasses Shape 3D Organization of Genomes during Lineage Commitment

(2013) Jennifer E. Phillips-Cremins et al.   CELL

Chromatin connectivity maps reveal dynamic promoter–enhancer long-range associations

(2013) Yubo Zhang et al.   NATURE

A high-resolution map of the three-dimensional chromatin interactome in human cells

(2013) Fulai Jin et al.   NATURE

Meta-analysis identifies four new loci associated with testicular germ cell tumor

(2013) Charles C Chung et al.   NATURE GENETICS

Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells

(2013) Ryo Kurita et al.   PLoS One

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Mixed Lineage Kinase Domain-like Protein Mediates Necrosis Signaling Downstream of RIP3 Kinase

(2012) Liming Sun et al.   CELL

Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages

(2012) Dominic Schmidt et al.   CELL

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Mixed lineage kinase domain-like is a key receptor interacting protein 3 downstream component of TNF-induced necrosis

(2012) J. Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Ebola virus entry requires the cholesterol transporter Niemann–Pick C1

(2011) Jan E. Carette et al.   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates

(2009) Lajos Mátés et al.   NATURE GENETICS

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

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

Evolution of the mammalian transcription factor binding repertoire via transposable elements

(2008) G. Bourque et al.   GENOME RESEARCH

CTCF-dependent enhancer-blocking by alternative chromatin loop formation

(2008) C. Hou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA