Single-cell Hi-C data analysis: safety in numbers

Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development

(2021) Longzhi Tan et al.   CELL

Order and stochasticity in the folding of individual Drosophila genomes

(2021) Sergey V. Ulianov et al.   Nature Communications

Scool: a new data storage format for single-cell Hi-C data

(2021) Joachim Wolff et al.   BIOINFORMATICS

CTCF looping is established during gastrulation in medaka embryos

(2021) Ryohei Nakamura et al.   GENOME RESEARCH

scHiCTools: A computational toolbox for analyzing single-cell Hi-C data

(2021) Xinjun Li et al.   PLoS Computational Biology

GiniQC: a measure for quantifying noise in single-cell Hi-C data

(2020) Connor A Horton et al.   BIOINFORMATICS

Coolpup.py: versatile pile-up analysis of Hi-C data

(2020) Ilya M Flyamer et al.   BIOINFORMATICS

Advances in Chromatin Imaging at Kilobase-Scale Resolution

(2020) Alistair Boettiger et al.   TRENDS IN GENETICS

Parental-to-embryo switch of chromosome organization in early embryogenesis

(2020) Samuel Collombet et al.   NATURE

Studying RNA–DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics

(2020) Alexey A Gavrilov et al.   NUCLEIC ACIDS RESEARCH

Bayesian inference of chromatin structure ensembles from population-averaged contact data

(2020) Simeon Carstens et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cumulative contact frequency of a chromatin region is an intrinsic property linked to its function

(2020) Margarita D. Samborskaia et al.   PeerJ

DeepC: predicting 3D genome folding using megabase-scale transfer learning

(2020) Ron Schwessinger et al.   NATURE METHODS

Predicting 3D genome folding from DNA sequence with Akita

(2020) Geoff Fudenberg et al.   NATURE METHODS

Multi-contact 3C reveals that the human genome during interphase is largely not entangled

(2020) Filipe Tavares-Cadete et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data

(2020) Hyeon-Jin Kim et al.   PLoS Computational Biology

A Comparative Study of Supervised Machine Learning Algorithms for the Prediction of Long-Range Chromatin Interactions

(2020) Thomas Vanhaeren et al.   Genes

A machine learning framework for the prediction of chromatin folding in Drosophila using epigenetic features

(2020) Michal B. Rozenwald et al.   PeerJ Computer Science

Tracking and interpreting long-range chromatin interactions with super-resolution live-cell imaging

(2020) Hugo B. Brandão et al.   CURRENT OPINION IN CELL BIOLOGY

SCL: A lattice-based approach to infer three-dimensional chromosome structures from single-cell Hi-C data

(2019) Hao Zhu et al.   BIOINFORMATICS

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems

(2019) Longzhi Tan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Chromatin three-dimensional interactions mediate genetic effects on gene expression

(2019) O. Delaneau et al.   SCIENCE

Principles of genome folding into topologically associating domains

(2019) Quentin Szabo et al.   Science Advances

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

(2019) Arkadiy K. Golov et al.   METHODS

Robust single-cell Hi-C clustering by convolution- and random-walk–based imputation

(2019) Jingtian Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatiotemporal structure of cell fate decisions in murine neural crest

(2019) Ruslan Soldatov et al.   SCIENCE

Comparison of computational methods for 3D genome analysis at single-cell Hi-C level

(2019) Xiao Li et al.   METHODS

Simultaneous profiling of 3D genome structure and DNA methylation in single human cells

(2019) Dong-Sung Lee et al.   NATURE METHODS

Joint profiling of DNA methylation and chromatin architecture in single cells

(2019) Guoqiang Li et al.   NATURE METHODS

TADs as the Caller Calls Them

(2019) Elzo de Wit   JOURNAL OF MOLECULAR BIOLOGY

Chromosome organization in bacteria: mechanistic insights into genome structure and function

(2019) Remus T. Dame et al.   NATURE REVIEWS GENETICS

Quantitative prediction of enhancer–promoter interactions

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

Key role for CTCF in establishing chromatin structure in human embryos

(2019) Xuepeng Chen et al.   NATURE

Unsupervised embedding of single-cell Hi-C data

(2018) Jie Liu et al.   BIOINFORMATICS

Combining fluorescence imaging with Hi-C to study 3D genome architecture of the same single cell

(2018) David Lando et al.   Nature Protocols

KSHV episomes reveal dynamic chromatin loop formation with domain-specific gene regulation

(2018) Mel Campbell et al.   Nature Communications

Systemic Loss and Gain of Chromatin Architecture throughout Zebrafish Development

(2018) Lucas J.T. Kaaij et al.   Cell Reports

Chromatin-associated RNA sequencing (ChAR-seq) maps genome-wide RNA-to-DNA contacts

(2018) Jason C Bell et al.   eLife

Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols

(2018) David Lando et al.   Nucleus

Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols

(2018) David Lando et al.   Nucleus

A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

(2018) Darren A. Cusanovich et al.   CELL

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

Allelic reprogramming of 3D chromatin architecture during early mammalian development

(2017) Zhenhai Du et al.   NATURE

Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition

(2017) Ilya M. Flyamer et al.   NATURE

3D structures of individual mammalian genomes studied by single-cell Hi-C

(2017) Tim J. Stevens et al.   NATURE

Cell-cycle dynamics of chromosomal organization at single-cell resolution

(2017) Takashi Nagano et al.   NATURE

GRID-seq reveals the global RNA–chromatin interactome

(2017) Xiao Li et al.   NATURE BIOTECHNOLOGY

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Enhancer–promoter interactions are encoded by complex genomic signatures on looping chromatin

(2016) Sean Whalen et al.   NATURE GENETICS

Organization and function of the 3D genome

(2016) Boyan Bonev et al.   NATURE REVIEWS GENETICS

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

(2016) Harianto Tjong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Three-dimensional reconstruction of single-cell chromosome structure using recurrence plots

(2016) Yoshito Hirata et al.   Scientific Reports

Formation of Chromosomal Domains by Loop Extrusion

(2016) Geoffrey Fudenberg et al.   Cell Reports

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data

(2016) Simeon Carstens et al.   PLoS Computational Biology

Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells

(2015) Jop Kind et al.   CELL

Modeling chromosomes: Beyond pretty pictures

(2015) Maxim V. Imakaev et al.   FEBS LETTERS

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

Multiplexed analysis of chromosome conformation at vastly improved sensitivity

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

Machine learning applications in genetics and genomics

(2015) Maxwell W. Libbrecht et al.   NATURE REVIEWS GENETICS

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

(2013) Takashi Nagano et al.   NATURE

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

(2013) Job Dekker et al.   NATURE REVIEWS GENETICS

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

Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

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

(2011) Eitan Yaffe et al.   NATURE GENETICS

Modernizing Reference Genome Assemblies

(2011) Deanna M. Church et al.   PLOS BIOLOGY

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

(2010) Peter V. Kharchenko et al.   NATURE

Chromosome Territories

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

Redefining the Progression of Lineage Segregations during Mammalian Embryogenesis by Clonal Analysis

(2009) Elena Tzouanacou et al.   DEVELOPMENTAL CELL

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

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