Publications

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Data Type
  • Publication176
    • Project
    Lab
    Journal
    Experiment Types
    Status
    176 Results
    Title
    Year
    Journal
    Exp Sets
    Project
    Cohesin regulation of genome organization in mature granule neurons in the mouse cerebellum.
    Payan Parra OAZhao ZYamada TYang Y
    2025
    Epigenetics & chromatin
    -
    4DN
    Acidic transcription factors position the genome at nuclear speckles through transcription dependent and independent mechanisms
    Chaturvedi PGhosh PZhang LZhang MZhao HBelmont AS
    2025
    bioRxiv
    24
    4DN
    Highly active chromosome regions preferentially associate with two perispeckle networks that partition the interchromatin space
    Venkata NCKim JFaber GMisra SBektash AChaturvedi PHernanadez GDopie JKanemaki MHan KYShav-Tal YBelmont AS
    2025
    bioRxiv
    22
    4DN
    Long-range regulation of transcription scales with genomic distance in a gene-specific manner.
    Jensen CLChen LFSwigut TCrocker OJYao DBassik MCFerrell JE JrBoettiger ANWysocka J
    2025
    Molecular cell
    3
    4DN
    Cell type-specific 3D-genome organization and transcription regulation in the brain.
    Liu SWang CYZheng PJia BBZemke NRRen PPark HLRen BZhuang X
    2025
    Science advances
    3
    4DN
    Single-Allele Chromatin Tracing Reveals Genomic Clustering of Paralogous Transcription Factors as a Mechanism for Developmental Robustness in T Cells.
    Jay AZhou YYoon SAbeje BNChandra AWald JRaj AFaryabi RBVahedi G
    2025
    bioRxiv : the preprint server for biology
    1
    4DN
    Sceptic: pseudotime analysis for time-series single-cell sequencing and imaging data.
    Li GKim HJPendyala SZhang RVert JPDisteche CMDeng XFowler DMNoble WS
    2025
    Genome biology
    5
    4DN
    A leukemia-protective germline variant mediates chromatin module formation via transcription factor nucleation.
    Llimos GGardeux VKoch UKribelbauer JFHafner AAlpern DPezoldt JLitovchenko MRusseil JDainese RMoia RMahmoud AMRossi DGaidano GPlass CLutsik PGerhauser CWaszak SMBoettiger ARadtke FDeplancke B
    2022
    Nature communications
    2
    External
    Context-Dependent and Gene-Specific Role of Chromatin Architecture Mediated by Histone Modifiers and Loop-extrusion Machinery.
    Tastemel MJussila ASaravanan BHuang HXie YZhu QJiang YArmand ERen B
    2025
    bioRxiv : the preprint server for biology
    11
    4DN
    Multiplex DNA fluorescence in situ hybridization to analyze maternal vs. paternal C. elegans chromosomes.
    Gutnik SYou JESawh ANAndriollo AMango SE
    2024
    Genome biology
    6
    External
    Tracing the evolution of single-cell cancer 3D genomes: an atlas for cancer gene discovery.
    Liu MJin SAgabiti SSJensen TBYang TRadda JSDRuiz CFBaldissera GRajaei MTownsend JPMuzumdar MDWang S
    2024
    bioRxiv : the preprint server for biology
    23
    4DN
    Reorganization of the heterochromatin-associated gene-dense subcompartment in early neuronal development.
    Scrutton Alvarado NJZhao ZYamada TYang Y
    2025
    Biology open
    8
    4DN
    Human DNA methylomes at base resolution show widespread epigenomic differences.
    Lister RPelizzola MDowen RHHawkins RDHon GTonti-Filippini JNery JRLee LYe ZNgo QMEdsall LAntosiewicz-Bourget JStewart RRuotti VMillar AHThomson JARen BEcker JR
    2009
    Nature
    -
    4DN
    The establishment of nuclear organization in mouse embryos is orchestrated by multiple epigenetic pathways.
    Pal MSchauer TBurton ANakatani TPecori FHernandez-Gimenez ANadelson IMarti-Renom MATorres-Padilla ME
    2025
    Cell
    51
    4DN
    Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos.
    Sawh ANShafer MERSu JHZhuang XWang SMango SE
    2020
    Molecular cell
    7
    External
    Nucleolus and centromere Tyramide Signal Amplification-Seq reveals variable localization of heterochromatin in different cell types.
    Kumar PGholamalamdari OZhang YZhang LVertii Avan Schaik TPeric-Hupkes DSasaki TGilbert DMvan Steensel BMa JKaufman PDBelmont AS
    2024
    Communications biology
    32
    4DN
    Perturb-tracing enables high-content screening of multiscale 3D genome regulators.
    Cheng YHu MYang BJensen TBYang TYu RMa ZRadda JSDJin SZang CWang S
    2023
    bioRxiv : the preprint server for biology
    15
    4DN
    Dose-dependent sensitivity of human 3D chromatin to a heart disease-linked transcription factor.
    Grant ZLKuang SZhang SHorrillo AJRao KSKameswaran VJoubran CLau PKDong KYang BBartosik WMZemke NRRen BKathiriya ISPollard KSBruneau BG
    2025
    bioRxiv : the preprint server for biology
    53
    4DN
    Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes.
    Buka KParteka-Tojek ZAgarwal ADenkiewicz MKorsak SChilinski MBanecki KHPlewczynski D
    2025
    Communications biology
    2
    4DN
    Single-cell chromatin state transitions during epigenetic memory formation.
    Fujimori TRios-Martinez CThurm ARHinks MMDoughty BRSinha JLe DHafner AGreenleaf WJBoettiger ANBintu L
    2023
    bioRxiv : the preprint server for biology
    22
    4DN
    Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues.
    Yu MZemke NRChen ZJuric IHu RRaviram RAbnousi AFang RZhang YGorkin DULi YEZhao YLee LMishra SSchmitt ADQiu YDickel DEVisel APennacchio LAHu MRen B
    2024
    Nature structural & molecular biology
    35
    4DN
    Epigenetic and 3D genome reprogramming during the aging of human hippocampus.
    Zemke NRLee SMamde SYang BBerchtold NMaximiliano Garduno BIndralingam HSBartosik WMLau PKDong KYang ATani YChen CZeng QAjith VTong LSeng CLi DWang TXu XRen B
    2024
    bioRxiv : the preprint server for biology
    120
    4DN
    Heterogeneity in chromatin structure drives core regulatory pathways in B-cell Acute Lymphoblastic Leukemia
    Sen AXu ZTyndale SYasis JCho CYBump RChandran SLuo LFu YPetersen LKShokhirev MKuo DJMcVicker GPDixon JR
    2024
    bioRxiv
    -
    4DN
    Genome-wide in vivo dynamics of cohesin-mediated loop extrusion and its role in transcription activation
    Popay TMPant AMunting FBlack MEHaghani NDixon J
    2024
    bioRxiv
    74
    4DN
    Determining mRNA Stability by Metabolic RNA Labeling and Chemical Nucleoside Conversion.
    Herzog VAFasching NAmeres SL
    2020
    Methods in molecular biology(Clifton, N.J.)
    -
    4DN