Integrative characterization of G-Quadruplexes in the three-dimensional chromatin structure

Allele-specific control of replication timing and genome organization during development

(2018) Juan Carlos Rivera-Mulia et al.   GENOME RESEARCH

Oligomer formation and G-quadruplex binding by purified murine Rif1 protein, a key organizer of higher-order chromatin architecture

(2018) Kenji Moriyama et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture

(2018) Da Lin et al.   NATURE GENETICS

Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing

(2018) Robert Hänsel-Hertsch et al.   Nature Protocols

Real-time imaging of DNA loop extrusion by condensin

(2018) Mahipal Ganji et al.   SCIENCE

Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks

(2018) Mun-Kit Choy et al.   Nature Communications

Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries

(2018) Yixiao Gong et al.   Nature Communications

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes

(2018) Niek van Wietmarschen et al.   Nature Communications

Chromatin Architectural Changes during Cellular Senescence and Aging

(2018) Luyang Sun et al.   Genes

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

(2018) James T. Robinson et al.   Cell Systems

Structural basis of G-quadruplex unfolding by the DEAH/RHA helicase DHX36

(2018) Michael C. Chen et al.   NATURE

DNA G-quadruplex structures mold the DNA methylome

(2018) Shi-Qing Mao et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Decoding topologically associating domains with ultra-low resolution Hi-C data by graph structural entropy

(2018) Angsheng Li et al.   Nature Communications

Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma

(2018) Molly Went et al.   Nature Communications

DNA G-quadruplexes in the human genome: detection, functions and therapeutic potential

(2017) Robert Hänsel-Hertsch et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Computational characterization of chromatin domain boundary-associated genomic elements

(2017) Seungpyo Hong et al.   NUCLEIC ACIDS RESEARCH

ReMap 2018: an updated atlas of regulatory regions from an integrative analysis of DNA-binding ChIP-seq experiments

(2017) Jeanne Chèneby et al.   NUCLEIC ACIDS RESEARCH

Bacillus subtilis SMC complexes juxtapose chromosome arms as they travel from origin to terminus

(2017) Xindan Wang et al.   SCIENCE

G-Quadruplexes: Prediction, Characterization, and Biological Application

(2017) Chun Kit Kwok et al.   TRENDS IN BIOTECHNOLOGY

Motif oriented high-resolution analysis of ChIP-seq data reveals the topological order of CTCF and cohesin proteins on DNA

(2016) Gergely Nagy et al.   BMC GENOMICS

G-quadruplex structures mark human regulatory chromatin

(2016) Robert Hänsel-Hertsch et al.   NATURE GENETICS

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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

A CTCF Code for 3D Genome Architecture

(2015) Michael H. Nichols et al.   CELL

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

(2015) Darío G. Lupiáñez et al.   CELL

The Role of Chromosome Domains in Shaping the Functional Genome

(2015) Tom Sexton et al.   CELL

NeuroD1 reprograms chromatin and transcription factor landscapes to induce the neuronal program

(2015) A. Pataskar et al.   EMBO JOURNAL

Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins

(2015) Michael S. Foulk et al.   GENOME RESEARCH

Widespread Rearrangement of 3D Chromatin Organization Underlies Polycomb-Mediated Stress-Induced Silencing

(2015) Li Li et al.   MOLECULAR CELL

Condensin-driven remodelling of X chromosome topology during dosage compensation

(2015) Emily Crane et al.   NATURE

High-throughput sequencing of DNA G-quadruplex structures in the human genome

(2015) Vicki S Chambers et al.   NATURE BIOTECHNOLOGY

Guanine quadruplex structures localize to heterochromatin

(2015) Roland F. Hoffmann et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2016 update

(2015) Matthew L. Speir et al.   NUCLEIC ACIDS RESEARCH

G-quadruplexes and their regulatory roles in biology

(2015) Daniela Rhodes et al.   NUCLEIC ACIDS RESEARCH

New roles for DNA cytosine modification, eRNA, anchors, and superanchors in developing B cell progenitors

(2015) Christopher Benner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Enhancer-promoter interaction facilitated by transiently forming G-quadruplexes

(2015) Hedi Hegyi   Scientific Reports

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

(2014) Suhas S.P. Rao et al.   CELL

The 3D Genome in Transcriptional Regulation and Pluripotency

(2014) David U. Gorkin et al.   Cell Stem Cell

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

(2014) F. Ay et al.   GENOME RESEARCH

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Kevin Van Bortle et al.   GENOME BIOLOGY

The transcription start site landscape of C. elegans

(2013) T. L. Saito et al.   GENOME RESEARCH

The G4 Genome

(2013) Nancy Maizels et al.   PLoS Genetics

A fast algorithm for matrix balancing

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

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

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

(2012) Cole Trapnell et al.   Nature Protocols

DNA secondary structures: stability and function of G-quadruplex structures

(2012) Matthew L. Bochman et al.   NATURE REVIEWS GENETICS

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors

(2012) Kevin Y Yip et al.   GENOME BIOLOGY

Wide-ranging functions of E2F4 in transcriptional activation and repression revealed by genome-wide analysis

(2011) Bum-Kyu Lee et al.   NUCLEIC ACIDS RESEARCH

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

Histone H4K20/H3K9 demethylase PHF8 regulates zebrafish brain and craniofacial development

(2010) Hank H. Qi et al.   NATURE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Genome-wide analysis predicts DNA structural motifs as nucleosome exclusion signals

(2009) Kangkan Halder et al.   Molecular BioSystems

Genome-wide colonization of gene regulatory elements by G4 DNA motifs

(2009) Zhuo Du 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

Design and analysis of ChIP-seq experiments for DNA-binding proteins

(2008) Peter V Kharchenko et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY