Evaluating the role of the nuclear microenvironment in gene function by population-based modeling

Integrated intracellular organization and its variations in human iPS cells

(2023) Matheus P. Viana et al.   NATURE

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

(2022) Andrea Esposito et al.   Cell Reports

Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations

(2022) Lorenzo Boninsegna et al.   NATURE METHODS

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics

(2021) Houda Belaghzal et al.   NATURE GENETICS

Multiscale modeling of genome organization with maximum entropy optimization

(2021) Xingcheng Lin et al.   JOURNAL OF CHEMICAL PHYSICS

Single-cell nuclear architecture across cell types in the mouse brain

(2021) Yodai Takei et al.   SCIENCE

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Mechanisms and Functions of Chromosome Compartmentalization

(2020) Erica M. Hildebrand et al.   TRENDS IN BIOCHEMICAL SCIENCES

Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data

(2020) Haitham Ashoor et al.   Nature Communications

GPSeq reveals the radial organization of chromatin in the cell nucleus

(2020) Gabriele Girelli et al.   NATURE BIOTECHNOLOGY

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

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

(2020) Yifeng Qi et al.   BIOPHYSICAL JOURNAL

The Self-Organizing Genome: Principles of Genome Architecture and Function

(2020) Tom Misteli   CELL

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Cell cycle dynamics of lamina‐associated DNA

(2020) Tom van Schaik et al.   EMBO REPORTS

Multiplex chromatin interactions with single-molecule precision

(2019) Meizhen Zheng et al.   NATURE

Constitutive splicing and economies of scale in gene expression

(2019) Fangyuan Ding et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Two major mechanisms of chromosome organization

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

Two contrasting classes of nucleolus-associated domains in mouse fibroblast heterochromatin

(2019) Anastassiia Vertii et al.   GENOME RESEARCH

Single-cell RNA sequencing of a European and an African lymphoblastoid cell line

(2019) Daniel Osorio et al.   Scientific Data

Molecular basis and biological function of variability in spatial genome organization

(2019) Elizabeth H. Finn et al.   SCIENCE

Revealing Hi-C subcompartments by imputing inter-chromosomal chromatin interactions

(2019) Kyle Xiong et al.   Nature Communications

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

(2018) Sofia A. Quinodoz et al.   CELL

Producing genome structure populations with the dynamic and automated PGS software

(2018) Nan Hua et al.   Nature Protocols

High-resolution 3D models of Caulobacter crescentus chromosome reveal genome structural variability and organization

(2018) Asli Yildirim et al.   NUCLEIC ACIDS RESEARCH

The role of 3D genome organization in disease: From compartments to single nucleotides

(2018) Abhijit Chakraborty et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler

(2018) Yu Chen et al.   JOURNAL OF CELL BIOLOGY

Three-dimensional genome structures of single diploid human cells

(2018) Longzhi Tan et al.   SCIENCE

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

(2018) Bogdan Bintu et al.   SCIENCE

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

(2017) Tao Yang et al.   GENOME RESEARCH

Complex multi-enhancer contacts captured by genome architecture mapping

(2017) Robert A. Beagrie et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Massively multiplex single-cell Hi-C

(2017) Vijay Ramani et al.   NATURE METHODS

Long-read ChIA-PET for base-pair-resolution mapping of haplotype-specific chromatin interactions

(2017) Xingwang Li et al.   Nature Protocols

Automatic analysis and 3D-modelling of Hi-C data using TADbit reveals structural features of the fly chromatin colors

(2017) François Serra et al.   PLoS Computational Biology

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

(2016) Rongxin Fang et al.   CELL RESEARCH

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

(2016) Maxwell R Mumbach et al.   NATURE METHODS

Transferable model for chromosome architecture

(2016) Michele Di Pierro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Polymer physics of chromosome large-scale 3D organisation

(2016) Andrea M. Chiariello et al.   Scientific Reports

Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization

(2016) Marco Di Stefano et al.   Scientific Reports

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

(2015) Jop Kind et al.   CELL

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

(2015) Tsung-Han S. Hsieh et al.   CELL

TopDom: an efficient and deterministic method for identifying topological domains in genomes

(2015) Hanjun Shin et al.   NUCLEIC ACIDS RESEARCH

Topology, structures, and energy landscapes of human chromosomes

(2015) Bin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2014) Suhas S.P. Rao et al.   CELL

HSP70 Transgene Directed Motion to Nuclear Speckles Facilitates Heat Shock Activation

(2014) Nimish Khanna et al.   CURRENT BIOLOGY

Topologically associating domains are stable units of replication-timing regulation

(2014) Benjamin D. Pope et al.   NATURE

Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers

(2014) Leighton J Core et al.   NATURE GENETICS

The Spatial Organization of the Human Genome

(2013) Wendy A. Bickmore   Annual Review of Genomics and Human Genetics

Genome Architecture: Domain Organization of Interphase Chromosomes

(2013) Wendy A. Bickmore et al.   CELL

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

(2013) Takashi Nagano et al.   NATURE

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

A Predictive Computational Model of the Dynamic 3D Interphase Yeast Nucleus

(2012) Hua Wong et al.   CURRENT BIOLOGY

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

(2012) H. Tjong et al.   GENOME RESEARCH

Complexity of chromatin folding is captured by the strings and binders switch model

(2012) M. Barbieri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Three-Dimensional Architecture of a Bacterial Genome and Its Alteration by Genetic Perturbation

(2011) Mark A. Umbarger et al.   MOLECULAR CELL

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

(2011) Reza Kalhor et al.   NATURE BIOTECHNOLOGY

The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

(2010) Davide Baù et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Initial Genomics of the Human Nucleolus

(2010) Attila Németh et al.   PLoS Genetics

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

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

The Meaning of Gene Positioning

(2008) Takumi Takizawa et al.   CELL

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

(2008) Lars Guelen et al.   NATURE