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Liu Lab

Publications

Selected publications

  1. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

    Liu H*, Zeng Q*, Zhou J, …, Ecker JR

    Nature 2023 · DOI · PMID 38092913 · Code

  2. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

    Luo C*, Liu H*, Xie F*, …, Ecker JR

    Cell Genomics 2022 · DOI · PMID 35419551 · Code

  3. DNA methylation atlas of the mouse brain at single-cell resolution

    Liu H*, Zhou J*, Tian W, …, Ecker JR

    Nature 2021 · DOI · PMID 34616061 · Code · ALLCools

  4. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

    Yao Z*, Liu H*, Xie F*, …, Mukamel EA

    Nature 2021 · DOI · PMID 34616066

All publications

2026

  1. Maternal immune activation disrupts epigenomic and functional maturation of cortical excitatory neurons

    Lai CY*, Arzavala J*, Pinto-Duarte A, …, Liu H, …, Behrens MM

    Molecular Psychiatry · DOI · PMID 42686997

  2. Human body single-cell atlas of three-dimensional genome organization and DNA methylation

    Zhou J*, Wu Y*, Liu H, …, Ecker JR

    Science · DOI · PMID 42490476 · Code

  3. Cell-type-specific transposon demethylation and TAD remodeling in aging mouse brain

    Zeng Q, Wang W, Tian W, …, Liu H, …, Ecker JR

    Cell · DOI · PMID 41819104 · Code

  4. An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

    Wang Z*, Zu S*, Armand EJ, …, Liu H, …, Ren B

    bioRxiv · DOI · PMID 41676689 · Code

  5. Genetics and environment distinctively shape the human immune cell epigenome

    Wang W*, Hariharan M*, Ding W*, …, Liu H, …, Ecker JR

    Nature Genetics · DOI · PMID 41593234 · Code

2025

  1. High-throughput in silico screen uncovers key regulators of 3D genome architecture

    Bai J*, Lyu Q*, Tan J, …, Liu H, …, Xia B

    bioRxiv · DOI · PMID 41415375 · Code

  2. Cell-type-specific enrichment of somatic aneuploidy in the mammalian brain

    Mukamel EA, Liu H, Behrens MM, Ecker JR

    Neuron · DOI · PMID 40907475 · Code

  3. Novel environment exposure drives temporally defined and region-specific chromatin accessibility and gene expression changes in the hippocampus

    Traunmüller L*, Duffy EE*, Liu H, …, Greenberg ME

    Nature Communications · DOI · PMID 40841540 · Code

  4. Deep learning imputes DNA methylation states in single cells and enhances the detection of epigenetic alterations in schizophrenia

    Zhou J, Luo C, Liu H, …, Han S

    Cell Genomics · DOI · PMID 39986279 · Code

2024

  1. Mutation of CRYAB encoding a conserved mitochondrial chaperone and antiapoptotic protein causes hereditary optic atrophy

    Wang C*, Zhang L*, Nie Z*, …, Liu H, …, Guan MX

    JCI Insight · DOI · PMID 39561005

  2. Cell-type-specific effects of age and sex on human cortical neurons

    Chien JF, Liu H, Wang BA, …, Mukamel EA

    Neuron · DOI · PMID 38838671

2023

  1. Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain

    Liu H*, Zeng Q*, Zhou J, …, Ecker JR

    Nature · DOI · PMID 38092913 · Code

  2. Brain-wide correspondence of neuronal epigenomics and distant projections

    Zhou J*, Zhang Z*, Wu M, …, Liu H, …, Callaway EM

    Nature · DOI · PMID 38092919 · Code

  3. Single-cell analysis of chromatin accessibility in the adult mouse brain

    Zu S*, Li YE*, Wang K*, …, Liu H, …, Ren B

    Nature · DOI · PMID 38092917 · Code

  4. Conserved and divergent gene regulatory programs of the mammalian neocortex

    Zemke NR*, Armand EJ*, Wang W, …, Liu H, …, Ren B

    Nature · DOI · PMID 38092918 · Code

  5. Single-cell DNA methylation and 3D genome architecture in the human brain

    Tian W*, Zhou J*, Bartlett A, …, Liu H, …, Ecker JR

    Science · DOI · PMID 37824674 · Code

  6. A guide to the BRAIN Initiative Cell Census Network data ecosystem

    Hawrylycz M, Martone ME, Ascoli GA, …, Liu H, …, Zingg B

    PLOS Biology · DOI · PMID 37390046

  7. Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes

    Xie F*, Armand EJ*, Yao Z, …, Liu H, …, Mukamel EA

    Cell Genomics · DOI · PMID 37492103 · Code

2022

  1. Single nucleus multi-omics identifies human cortical cell regulatory genome diversity

    Luo C*, Liu H*, Xie F*, …, Ecker JR

    Cell Genomics · DOI · PMID 35419551 · Code

2021

  1. DNA methylation atlas of the mouse brain at single-cell resolution

    Liu H*, Zhou J*, Tian W, …, Ecker JR

    Nature · DOI · PMID 34616061 · Code · ALLCools

  2. A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

    Yao Z*, Liu H*, Xie F*, …, Mukamel EA

    Nature · DOI · PMID 34616066

  3. A multimodal cell census and atlas of the mammalian primary motor cortex

    BRAIN Initiative Cell Census Network (BICCN)

    Nature · DOI · PMID 34616075 · Code

  4. Comparative cellular analysis of motor cortex in human, marmoset and mouse

    Bakken TE, Jorstad NL, Hu Q, …, Liu H, …, Lein ES

    Nature · DOI · PMID 34616062 · Code

  5. An atlas of gene regulatory elements in adult mouse cerebrum

    Li YE*, Preissl S*, Hou X, …, Liu H, …, Ren B

    Nature · DOI · PMID 34616068 · Code

  6. Epigenomic diversity of cortical projection neurons in the mouse brain

    Zhang Z*, Zhou J*, Tan P, …, Liu H, …, Callaway EM

    Nature · DOI · PMID 34616065 · Code

  7. Improved pathogenicity prediction for rare human missense variants

    Wu Y, Liu H, Li R, Sun S, Weile J, Roth FP

    The American Journal of Human Genetics · DOI · PMID 34551312

  8. Activity-dependent modulation of synapse-regulating genes in astrocytes

    Farhy-Tselnicker I, Boisvert MM, Liu H, …, Allen NJ

    eLife · DOI · PMID 34494546

  9. Single nucleus multi-omics regulatory landscape of the murine pituitary

    Ruf-Zamojski F, Zhang Z, Zamojski M, …, Liu H, …, Sealfon SC

    Nature Communications · DOI · PMID 33976139

* Equal contribution. The full list is on Google Scholar.