BART3D: inferring transcriptional regulators associated with differential chromatin interactions from Hi-C data

Large DNA Methylation Nadirs Anchor Chromatin Loops Maintaining Hematopoietic Stem Cell Identity

(2020) Xiaotian Zhang et al.   MOLECULAR CELL

CHESS enables quantitative comparison of chromatin contact data and automatic feature extraction

(2020) Silvia Galan et al.   NATURE GENETICS

Antisense lncRNA Transcription Mediates DNA Demethylation to Drive Stochastic Protocadherin α Promoter Choice

(2019) Daniele Canzio et al.   CELL

Selfish: discovery of differential chromatin interactions via a self-similarity measure

(2019) Abbas Roayaei Ardakany et al.   BIOINFORMATICS

The role of 3D genome organization in development and cell differentiation

(2019) Hui Zheng et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

An Integrative Approach for Fine-Mapping Chromatin Interactions

(2019) Artur Jaroszewicz et al.   BIOINFORMATICS

BART: a transcription factor prediction tool with query gene sets or epigenomic profiles

(2018) Zhenjia Wang et al.   BIOINFORMATICS

FIND: difFerential chromatin INteractions Detection using a spatial Poisson process

(2018) Mohamed Nadhir Djekidel et al.   GENOME RESEARCH

Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming

(2018) Ralph Stadhouders et al.   NATURE GENETICS

Srf destabilizes cellular identity by suppressing cell-type-specific gene expression programs

(2018) Takashi Ikeda et al.   Nature Communications

HiCcompare: an R-package for joint normalization and comparison of HI-C datasets

(2018) John C. Stansfield et al.   BMC BIOINFORMATICS

Smchd1 regulates long-range chromatin interactions on the inactive X chromosome and at Hox clusters

(2018) Natasha Jansz et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Smchd1 Targeting to the Inactive X Is Dependent on the Xist-HnrnpK-PRC1 Pathway

(2018) Natasha Jansz et al.   Cell Reports

Mapping of long-range chromatin interactions by proximity ligation-assisted ChIP-seq

(2016) Rongxin Fang et al.   CELL RESEARCH

Modelingcis-regulation with a compendium of genome-wide histone H3K27ac profiles

(2016) Su Wang et al.   GENOME RESEARCH

Transcription factors mediate condensin recruitment and global chromosomal organization in fission yeast

(2016) Kyoung-Dong Kim et al.   NATURE GENETICS

HiChIP: efficient and sensitive analysis of protein-directed genome architecture

(2016) Maxwell R Mumbach et al.   NATURE METHODS

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

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

(2015) Li Li et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

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

Chromatin Loops as Allosteric Modulators of Enhancer-Promoter Interactions

(2014) Boryana Doyle et al.   PLoS Computational Biology

HiCNorm: removing biases in Hi-C data via Poisson regression

(2012) Ming Hu et al.   BIOINFORMATICS

GATA-3 regulates hematopoietic stem cell maintenance and cell-cycle entry

(2012) C.-J. Ku et al.   BLOOD

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

TIF1  regulates the pluripotency of embryonic stem cells in a phosphorylation-dependent manner

(2010) Y. Seki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The cohesin complex and its roles in chromosome biology

(2008) J.-M. Peters et al.   GENES & DEVELOPMENT