3DGenBench: a web-server to benchmark computational models for 3D Genomics

Polymer physics reveals a combinatorial code linking 3D chromatin architecture to 1D chromatin states

(2022) Andrea Esposito et al.   Cell Reports

Predicting Genome Architecture: Challenges and Solutions

(2021) Polina Belokopytova et al.   Frontiers in Genetics

3D-GNOME 2.0: a three-dimensional genome modeling engine for predicting structural variation-driven alterations of chromatin spatial structure in the human genome

(2020) Michal Wlasnowolski et al.   NUCLEIC ACIDS RESEARCH

Computational approaches from polymer physics to investigate chromatin folding

(2020) Simona Bianco et al.   CURRENT OPINION IN CELL BIOLOGY

Polymer physics indicates chromatin folding variability across single-cells results from state degeneracy in phase separation

(2020) Mattia Conte et al.   Nature Communications

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization

(2020) Yifeng Qi et al.   BIOPHYSICAL JOURNAL

Computational methods for the prediction of chromatin interaction and organization using sequence and epigenomic profiles

(2020) Huan Tao et al.   BRIEFINGS IN BIOINFORMATICS

4D nucleome modeling

(2020) Marco Di Stefano et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Serial genomic inversions induce tissue-specific architectural stripes, gene misexpression and congenital malformations

(2019) Katerina Kraft et al.   NATURE CELL BIOLOGY

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

(2019) Oluwatosin Oluwadare et al.   BIOLOGICAL PROCEDURES ONLINE

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

C-TALE, a new cost-effective method for targeted enrichment of Hi-C/3C-seq libraries

(2019) Arkadiy K. Golov et al.   METHODS

Heterochromatin drives compartmentalization of inverted and conventional nuclei

(2019) Martin Falk et al.   NATURE

Preformed chromatin topology assists transcriptional robustness of Shh during limb development

(2019) Christina Paliou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Predicting three-dimensional genome organization with chromatin states

(2019) Yifeng Qi et al.   PLoS Computational Biology

Quantitative prediction of enhancer–promoter interactions

(2019) Polina S. Belokopytova et al.   GENOME RESEARCH

Polymer physics predicts the effects of structural variants on chromatin architecture

(2018) Simona Bianco et al.   NATURE GENETICS

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

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

TADs are 3D structural units of higher-order chromosome organization in Drosophila

(2018) Quentin Szabo et al.   Science Advances

Dynamic 3D chromatin architecture contributes to enhancer specificity and limb morphogenesis

(2018) Bjørt K. Kragesteen et al.   NATURE GENETICS

Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells

(2018) Bogdan Bintu et al.   SCIENCE

TheHoxDcluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes

(2017) Eddie Rodríguez-Carballo et al.   GENES & DEVELOPMENT

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Tissue-specific CTCF–cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo

(2017) Lars L. P. Hanssen et al.   NATURE CELL BIOLOGY

Formation of new chromatin domains determines pathogenicity of genomic duplications

(2016) Martin Franke et al.   NATURE

Different enhancer classes in Drosophila bind distinct architectural proteins and mediate unique chromatin interactions and 3D architecture

(2016) Caelin Cubeñas-Potts et al.   NUCLEIC ACIDS RESEARCH

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

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

CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription

(2015) Zhonghui Tang et al.   CELL

Predictive Polymer Modeling Reveals Coupled Fluctuations in Chromosome Conformation and Transcription

(2014) Luca Giorgetti et al.   CELL

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

(2014) Suhas S.P. Rao et al.   CELL