ArticleNature2021
DNA methylation atlas of the mouse brain at single-cell resolution.
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Article in Nature, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 198 papers.
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198citing papers in PubMed
19.0field-weighted citation impact, top 1% of its field
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Who cites it
198 citing papers in PubMed, 299 citations in OpenAlex.
- Article
- Integration of polygenic risk with single cell methylation data using met-scDRS.Bioinformatics (Oxford, England) · 2026Article
- Peripheral blood DNA methylation partially reports on immune cell type composition in the frontal brain.Brain, behavior, & immunity - health · 2026Article
- A cross-species single-cell kidney epigenome atlas reveals epithelial-dominant aging-like states in disease.Nature aging · 2026Article
- SMORE: joint dimension reduction and cell population discovery on single-cell methylome data.bioRxiv : the preprint server for biology · 2026Article
- Maternal immune activation disrupts epigenomic and functional maturation of cortical excitatory neurons.Molecular psychiatry · 2026Article
- MethyAnno: An Interpretable Automated Annotation Method Leveraging Multi-Scale Information and Metric Learning Framework for scDNAm Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrative analysis of single-cell multi-omics reveals heterogeneity in piriform cortex principal neurons and their selective vulnerability in Alzheimer's disease.Clinical and translational medicine · 2026Article
- Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- DNA methylation defines lineage identity yet converges among functionally related cells and is cell‑specifically remodeled during in vitro passaging.BMC genomics · 2026Article
- Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina.Science advances · 2026Article
- Dose-dependent sensitivity of human three-dimensional chromatin to a heart disease-linked transcription factor.Science (New York, N.Y.) · 2026Article
- Neuroepigenetic programming by the maternal environment: part A-epigenome-wide DNA methylation profile in the offspring's olfactory bulb following preconceptional weight loss in mice.Clinical epigenetics · 2026Article
- Human body single-cell atlas of three-dimensional genome organization and DNA methylation.Science (New York, N.Y.) · 2026Article
- Single-cell profiling of DNA methylation in autism spectrum disorder prefrontal cortex reveals distinct regulatory and aging signatures.Cell genomics · 2026Article
- A systematic benchmarking framework and dual-view optimization strategy for single-cell DNA methylation imputation.Briefings in bioinformatics · 2026Article
- Brain Spatial Genomics Atlases.Genes · 2026Review
- Early postnatal DNA methylation dynamics define neuronal subtypes and are disrupted by MECP2 loss.bioRxiv : the preprint server for biology · 2026Article
- MINTsC learns multi-way chromatin interactions from single cell high throughput chromatin conformation data.Nature communications · 2026Article
138 more citing papers are in PubMed but not listed here.
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Authors and funding
29 authors at 3 institutions in 1 country.
Hanqing Liu *Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Jingtian Zhou *Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-2060-1922
Wei TianGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Chongyuan LuoGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Anna BartlettGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Andrew AldridgeGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-1962-8802
Jacinta LuceroComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Julia K OsteenComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Joseph R NeryGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0153-5659
Huaming ChenGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Angeline RivkinGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Rosa G CastanonGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Ben ClockPeptide Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Yang Eric LiLudwig Institute for Cancer Research, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-6997-6018
Xiaomeng HouCenter for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
Olivier B PoirionCenter for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
Sebastian PreisslCenter for Epigenomics, University of California, San Diego School of Medicine, La Jolla, CA, USA.
Antonio Pinto-DuarteComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-2215-7653
Carolyn O'ConnorFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Lara BoggemanFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Conor FitzpatrickFlow Cytometry Core Facility, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Michael NunnGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Eran A MukamelDepartment of Cognitive Science, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-3203-9535
Zhuzhu ZhangGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.
Edward M CallawaySystems Neurobiology Laboratories, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-6366-5267
Bing RenLudwig Institute for Cancer Research, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-5435-1127
Jesse R DixonPeptide Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-6273-2181
M Margarita BehrensComputational Neurobiology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA.ORCID http://orcid.org/0000-0002-7168-8186
Joseph R EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, USA. ecker@salk.edu.ORCID http://orcid.org/0000-0001-5799-5895
Salk Institute for Biological Studies · USUniversity of California San Diego · USLudwig Cancer Research · US
Funding
Viral Vector Core (VVC)P30CA014195 · NCI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI Reuben Shaw · 1985 to 2026
$82.8MGeneration of novel cell type specific mouse genetic toolsU19MH114830 · NIMH · ALLEN INSTITUTE · PI TOLIAS, ANDREAS · 2017 to 2021
$64.7MMolecular SignaturesU19MH114831 · NIMH · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI ECKER, JOSEPH R · 2017 to 2021
$24.6MDevelopment of methods for multi-omic analysis of DNA methylation and chromatin architecture in single cellsR01HG010634 · NHGRI · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI DIXON, JESSE R, ECKER, JOSEPH R · 2019 to 2022
$4.3MBD FACSAria Fusion for Flow Cytometry Core FacilityS10OD023689 · OD · SALK INSTITUTE FOR BIOLOGICAL STUDIES · PI ZHENG, YE · 2018 to 2018
$530kREGULATION OF CORTICAL PHENOTYPE BY BASAL FOREBRAINF30MH011483 · NIMH · UNIVERSITY OF CALIFORNIA IRVINE · PI HA, DUN H · 1997 to 1999
–Howard Hughes Medical InstituteNCI NIH HHS P30 CA014195NHGRI NIH HHS R01 HG010634NIH HHS S10 OD023689NIMH NIH HHS F30 MH011483NIMH NIH HHS U19 MH114830NIMH NIH HHS U19 MH114831
Abstract
Mammalian brain cells show remarkable diversity in gene expression, anatomy and function, yet the regulatory DNA landscape underlying this extensive heterogeneity is poorly understood. Here we carry out a comprehensive assessment of the epigenomes of mouse brain cell types by applying single-nucleus DNA methylation sequencing
Indexed as
DNA MethylationEpigenomeEpigenomicsSingle-Cell AnalysisAnimalsAtlases as TopicBrainChromatinCytosineDatasets as TopicDentate GyrusEnhancer Elements, GeneticGene Expression ProfilingHippocampusMaleMiceChromatinCytosine
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