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References from Spatially resolved genome architecture in mouse embryonic development. Local targets link to admitted publications; unresolved targets remain external evidence.
Cell-cycle dynamics of chromosomal organization at single-cell resolution
10.1038/nature23001 · 2017 · External reference
Organizational principles of 3D genome architecture
10.1038/s41576-018-0060-8 · 2018 · External reference
Chromatin as dynamic 10-nm fibers
10.1007/s00412-014-0460-2 · 2014 · External reference
ChromEMT: Visualizing 3D chromatin structure and compaction in interphase and mitotic cells
10.1126/science.aag0025 · 2017 · External reference
Liquid-like chromatin in the cell: What can we learn from imaging and computational modeling?
10.1016/j.sbi.2021.06.004 · 2021 · External reference
Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
10.1016/j.cell.2020.07.032 · 2020 · External reference
Single-nucleus Hi-C reveals unique chromatin reorganization at oocyte-to-zygote transition
10.1038/nature21711 · 2017 · External reference
Methods for mapping 3D chromosome architecture
10.1038/s41576-019-0195-2 · 2020 · External reference
Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
10.1038/nature12593 · 2013 · External reference
Super-resolution imaging reveals the evolution of higher-order chromatin folding in early carcinogenesis
2020 · External reference
Lifelong restructuring of 3D genome architecture in cerebellar granule cells
10.1126/science.adh3253 · 2023 · External reference
The dawn of spatial omics
10.1126/science.abq4964 · 2023 · External reference
Spatially resolved transcriptomics: a comprehensive review of their technological advances, applications, and challenges
10.1016/j.jgg.2023.03.011 · 2023 · External reference
High-Spatial-Resolution Multi-omics Sequencing via Deterministic Barcoding in Tissue
10.1016/j.cell.2020.10.026 · 2020 · External reference
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
10.1126/science.aaw1219 · 2019 · External reference
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
10.1126/science.aaf2403 · 2016 · External reference
Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level
10.1126/science.abg7216 · 2022 · External reference
Spatial profiling of chromatin accessibility in mouse and human tissues
10.1038/s41586-022-05094-1 · 2022 · External reference
Spatial epigenome–transcriptome co-profiling of mammalian tissues
10.1038/s41586-023-05795-1 · 2023 · External reference
Spatial joint profiling of DNA methylome and transcriptome in tissues
10.1038/s41586-025-09478-x · 2025 · External reference
Complex multi-enhancer contacts captured by genome architecture mapping
10.1038/nature21411 · 2017 · External reference
Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
10.1016/j.cell.2018.05.024 · 2018 · External reference
Single-cell measurement of higher-order 3D genome organization with scSPRITE
10.1038/s41587-021-00998-1 · 2022 · External reference
Dynamic changes in P300 enhancers and enhancer-promoter contacts control mouse cardiomyocyte maturation
10.1016/j.devcel.2023.03.020 · 2023 · External reference
Ultrafast and interpretable single-cell 3D genome analysis with Fast-Higashi
10.1016/j.cels.2022.09.004 · 2022 · External reference
Multiscale and integrative single-cell Hi-C analysis with Higashi
10.1038/s41587-021-01034-y · 2022 · External reference
An atlas of dynamic chromatin landscapes in mouse fetal development
10.1038/s41586-020-2093-3 · 2020 · External reference
Evolutionarily Conserved Principles Predict 3D Chromatin Organization
10.1016/j.molcel.2017.07.022 · 2017 · External reference
Data navigation on the ENCODE portal
10.1038/s41467-025-64343-9 · 2025 · External reference
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
10.1016/j.cell.2022.04.003 · 2022 · External reference
Comprehensive mapping of long-range interactions reveals folding principles of the human genome
10.1126/science.1181369 · 2009 · External reference
Three-dimensional genome structures of single diploid human cells
10.1126/science.aat5641 · 2018 · External reference
Decoder-seq enhances mRNA capture efficiency in spatial RNA sequencing
10.1038/s41587-023-02086-y · 2024 · External reference
Gene regulatory landscape dissected by single-cell four-omics sequencing
10.1038/s41586-026-10322-z · 2026 · External reference
Polyploidy in liver development, homeostasis and disease
10.1038/s41575-020-0284-x · 2020 · External reference
Liver cell polyploidization: a pivotal role for binuclear hepatocytes
10.1074/jbc.m300982200 · 2003 · External reference
Histology atlas of the developing mouse hepatobiliary system with emphasis on embryonic days 9.5–18.5
10.1177/0192623310374329 · 2010 · External reference
High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq
10.1038/s41587-023-01676-0 · 2023 · External reference
Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues
10.1016/j.cell.2024.09.001 · 2024 · External reference
Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development
10.1038/s41592-023-01884-1 · 2023 · External reference
Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
2020 · External reference
High-definition spatial transcriptomics for in situ tissue profiling
10.1038/s41592-019-0548-y · 2019 · External reference
Microscopic examination of spatial transcriptome using Seq-Scope
10.1016/j.cell.2021.05.010 · 2021 · External reference
Global reorganization of genome architecture at the transition to gametogenesis
10.1038/s41594-026-01747-1 · 2026 · External reference
Impact of genome architecture on the functional activation and repression of Hox regulatory landscapes
10.1186/s12915-019-0677-x · 2019 · External reference
fastp: an ultra-fast all-in-one FASTQ preprocessor
10.1093/bioinformatics/bty560 · 2018 · External reference
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
10.1371/journal.pone.0163962 · 2016 · External reference
STAR: ultrafast universal RNA-seq aligner
10.1093/bioinformatics/bts635 · 2013 · External reference
The Sequence Alignment/Map format and SAMtools
10.1093/bioinformatics/btp352 · 2009 · External reference
SCANPY: large-scale single-cell gene expression data analysis
10.1186/s13059-017-1382-0 · 2018 · External reference
Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization
10.1093/nar/gky504 · 2018 · External reference
Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization
10.1093/nar/gkaa220 · 2020 · External reference
Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp
10.1002/imt2.107 · 2023 · External reference
Predicting the molecular complexity of sequencing libraries
10.1038/nmeth.2375 · 2013 · External reference
EpiScanpy: integrated single-cell epigenomic analysis
10.1038/s41467-021-25131-3 · 2021 · External reference
Dissecting cell identity via network inference and in silico gene perturbation
10.1038/s41586-022-05688-9 · 2023 · External reference
dcHiC detects differential compartments across multiple Hi-C datasets
10.1038/s41467-022-34626-6 · 2022 · External reference
Cooler: scalable storage for Hi-C data and other genomically labeled arrays
10.1093/bioinformatics/btz540 · 2020 · External reference
Cooltools: Enabling high-resolution Hi-C analysis in Python
2024 · External reference
Linking genome structures to functions by simultaneous single-cell Hi-C and RNA-seq
10.1126/science.adg3797 · 2023 · External reference
Cellpose-SAM: superhuman generalization for cellular segmentation
2025 · External reference
GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
10.1093/bioinformatics/btac757 · 2023 · External reference
Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq
10.1126/science.aad0501 · 2016 · External reference
