ArticleNature2021
Integrated spatial genomics reveals global architecture of single nuclei.
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In one paragraph
Article in Nature, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 260 papers, 1 of them a synthesis that pooled it.
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260citing papers in PubMed, 1 pooled it
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
260 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Multi-omics and high-spatial-resolution omics: deciphering complexity in neurological disorders.GigaScience · 2025Pooled it
- Euchromatin forms condensed domains with short active regions on the surface.Nature genetics · 2026Article
- Spatial chromatin architecture and accessibility co-profiling of mammalian tissues.Nature methods · 2026Article
- Insights Into Spatial Transcriptomics: Exploring Recent Technical Developments and Their Diverse Applications.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2026Review
- Review
- Acidic transcription factors position the genome at nuclear speckles through transcription-dependent and -independent mechanisms.Molecular cell · 2026Article
- SpaMOAL is a deep learning method that enables accurate spatial domain identification from multi-omics data.PLoS biology · 2026Article
- Mega-enhancers compartmentalize transcriptionally active long genes in the brain.Nature cell biology · 2026Article
- Nuclear speckle-associated perispeckle networks partition active chromatin into gene expression niches.Cell reports · 2026Article
- MuSpAn: a toolbox for multiscale spatial analysis.Nature communications · 2026Article
- Sequential-GAM constructs the single-cell geometric 3D genome structure.Nucleic acids research · 2026Article
- Single-cell chromatin state transitions during epigenetic memory formation.Science advances · 2026Article
- Advances in spatial omics for the analysis of prostate cancer.Analytical and bioanalytical chemistry · 2026Review
- Towards the construction of a virtual yeast.Nature · 2026Review
- Multiplexed Detection of Reactive Biomolecules via Chemoresponsive DNA Accumulation on Fluorescence-Encoded Beads.Chemical & biomedical imaging · 2026Article
- Review
- Spatially tunable multiomic sequencing using light-driven combinatorial barcoding of molecules in tissues.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Beyond the Cell Atlas: Functional Communities as the Essential Pathologic Units Driving Kidney Disease.Journal of the American Society of Nephrology : JASN · 2026Review
- Mapping the genetic landscape of hereditary diffuse-type gastric cancer progression.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- A Guide for Spatial Omics Technologies: Innovation, Evaluation, and Application.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Review
200 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
13 authors.
Yodai TakeiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Jina YunDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Shiwei ZhengDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0001-6682-6743
Noah OllikainenDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Nico PiersonDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Jonathan WhiteDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.ORCID http://orcid.org/0000-0002-7009-3332
Sheel ShahDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Julian ThomassieDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Shengbao SuoDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, USA.
Chee-Huat Linus EngDivision of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA.
Mitchell GuttmanDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
Guo-Cheng YuanDepartment of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard T.H.Chan School of Public Health, Boston, MA, USA.ORCID http://orcid.org/0000-0002-2283-4714
Long CaiDivision of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA. lcai@caltech.edu.ORCID http://orcid.org/0000-0002-7154-5361
Funding
MEMOIR: Recording, and in situ readout of cell lineage and transcriptional historyR01MH116508 · NIMH · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, ELOWITZ, MICHAEL B · 2017 to 2021
$6.9MDynamics of chromosome organization and chromatin states in single cellsU01DK127420 · NIDDK · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, ELOWITZ, MICHAEL B · 2020 to 2024
$5.7MHi-resolution dynamic imaging of chromosomes in single cells by combined CRISPR imaging and sequential FISHU01DA047732 · NIDA · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, QI, LEI STANLEY · 2018 to 2019
$1.6MHi-resolution dynamic imaging of chromosomes in single cells by combined CRISPR imaging and sequential FISHU01EB021240 · NIBIB · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, QI, LEI STANLEY · 2015 to 2017
$1.4MIn situ transcriptome profiling in single cellsUG3HL145609 · NHLBI · CALIFORNIA INSTITUTE OF TECHNOLOGY · PI CAI, LONG, YUAN, GUO-CHENG · 2018 to 2019
$750kNHLBI NIH HHS UG3 HL145609NIBIB NIH HHS U01 EB021240NIDA NIH HHS U01 DA047732NIDDK NIH HHS U01 DK127420NIH HHS 4DN DA047732NIMH NIH HHS R01 MH116508
Abstract
Identifying the relationships between chromosome structures, nuclear bodies, chromatin states and gene expression is an overarching goal of nuclear-organization studies
Indexed as
AnimalsCell CompartmentationCell LineCell NucleusChromatinChromosomes, MammalianClone CellsFluorescent Antibody TechniqueGenetic MarkersGenomicsHistonesLysineMaleMiceMouse Embryonic Stem CellsSingle-Cell AnalysisChromatinGenetic MarkersHistonesLysine
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.