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

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

(2021) Longzhi Tan et al.   CELL

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei et al.   NATURE

Joint profiling of histone modifications and transcriptome in single cells from mouse brain

(2021) Chenxu Zhu et al.   NATURE METHODS

Comprehensive analysis of single cell ATAC-seq data with SnapATAC

(2021) Rongxin Fang et al.   Nature Communications

Single-cell measurement of higher-order 3D genome organization with scSPRITE

(2021) Mary V. Arrastia et al.   NATURE BIOTECHNOLOGY

Multiplexed single-cell profiling of chromatin states at genomic loci by expansion microscopy

(2021) Marcus A Woodworth et al.   NUCLEIC ACIDS RESEARCH

Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos

(2020) Ahilya N. Sawh et al.   MOLECULAR CELL

Single-cell multimodal omics: the power of many

(2020) Chenxu Zhu et al.   NATURE METHODS

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

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

(2020) Miao Liu et al.   Nature Communications

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

A connectome and analysis of the adult Drosophila central brain

(2020) Louis K Scheffer et al.   eLife

TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes

(2020) Liguo Zhang et al.   GENOME RESEARCH

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms

(2019) Andrés M. Cardozo Gizzi et al.   MOLECULAR CELL

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

(2019) Jocelyn Y. Kishi et al.   NATURE METHODS

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

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

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

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

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

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

X-Chromosome Inactivation: A Crossroads Between Chromosome Architecture and Gene Regulation

(2018) Rafael Galupa et al.   Annual Review of Genetics

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing

(2018) William Renthal et al.   NATURE NEUROSCIENCE

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

(2018) Bogdan Bintu et al.   SCIENCE

Density imaging of heterochromatin in live cells using orientation-independent-DIC microscopy

(2017) Ryosuke Imai et al.   MOLECULAR BIOLOGY OF THE CELL

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging

(2017) Sarit S. Agasti et al.   Chemical Science

Structural organization of the inactive X chromosome in the mouse

(2016) Luca Giorgetti et al.   NATURE

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

(2016) Alistair N. Boettiger et al.   NATURE

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

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

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

A High-Resolution Imaging Approach to Investigate Chromatin Architecture in Complex Tissues

(2015) Michael W. Linhoff et al.   CELL

Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

(2015) Sigal Shachar et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation

(2015) A. Minajigi et al.   SCIENCE

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

DNA methylation reader MECP2: cell type- and differentiation stage-specific protein distribution

(2014) Congdi Song et al.   Epigenetics & Chromatin

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions

(2013) A. R. Prickett et al.   GENOME RESEARCH

Fast and High-Accuracy Localization for Three-Dimensional Single-Particle Tracking

(2013) Shu-Lin Liu et al.   Scientific Reports

Three-Dimensional Folding and Functional Organization Principles of the Drosophila Genome

(2012) Tom Sexton et al.   CELL

Automatic segmentation and supervised learning-based selection of nuclei in cancer tissue images

(2012) Kaustav Nandy et al.   CYTOMETRY PART A

A fast algorithm for matrix balancing

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

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

Spatial partitioning of the regulatory landscape of the X-inactivation centre

(2012) Elphège P. Nora et al.   NATURE

Rapid, accurate particle tracking by calculation of radial symmetry centers

(2012) Raghuveer Parthasarathy   NATURE METHODS

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A top-down analysis of Xa- and Xi-territories reveals differences of higher order structure at ≥ 20 Mb genomic length scales

(2011) Kathrin Teller et al.   Nucleus

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution

(2009) Irina Solovei et al.   CELL

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

The Epigenetics of rRNA Genes: From Molecular to Chromosome Biology

(2008) Brian McStay et al.   Annual Review of Cell and Developmental Biology