Publications

Browser Suggestion

Google Chrome  or Mozilla Firefox are the recommended browser(s) for using the 4DN Data Portal.

Microsoft Edge, Safari, Opera etc. should work for a majority of portal functions but are not explicitly supported and may present some glitches, e.g. during submission.

Included Properties

Data Type
  • Publication112
    • Project
  • 4DN89
  • External23
    • Lab
  • Bing Ren, UCSD11
  • Alistair Boettiger, STANFORD8
  • Job Dekker, UMMS6
  • 4DN DCIC, HMS5
  • Siyuan Wang, YALE5
  • Ana Pombo, MDC4
  • Christine Disteche, UW3
  • Chuck Murry, UW3
  • David Gilbert, SDBRI3
  • Erez Lieberman Aiden, BCM3
    • View 49 More61
    Journal
    Experiment Types
    Number of Experiment Sets
  • 1 N
    • Status
    112 Results
    Title
    Year
    Journal
    Exp Sets
    Project
    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
    80
    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
    Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin.
    Su JHZheng PKinrot SSBintu BZhuang X
    2020
    Cell
    3
    4DN
    Long range regulation of transcription scales with genomic distance in a gene specific manner.
    Jensen CLChen LFSwigut TCrocker OJYao DBassik MCFerrell JEBoettiger ANWysocka J
    2024
    bioRxiv : the preprint server for biology
    3
    4DN
    3D chromatin interactions involving Drosophila insulators are infrequent but preferential and arise before TADs and transcription.
    Messina ORaynal FGurgo JFiche JBPancaldi VNollmann M
    2023
    Nature communications
    2
    External
    Multifaceted roles of cohesin in regulating transcriptional loops.
    Kim MWang PClow PAChien IEWang XPeng JChai HLiu XLee BNgan CYYue FMilenkovic OChuang JHWei CLCasellas RCheng AWRuan Y
    2024
    bioRxiv : the preprint server for biology
    42
    4DN
    A single dose of cocaine rewires the 3D genome structure of midbrain dopamine neurons.
    Szabo DFranke VBianco SBatiuk MYPaul EJKukalev APfisterer UGIrastorza-Azcarate IChiariello AMDemharter SZea-Redondo LLopez-Atalaya JPNicodemi MAkalin AKhodosevich KUngless MAWinick-Ng WPombo A
    2024
    bioRxiv : the preprint server for biology
    3
    4DN
    Extensive folding variability between homologous chromosomes in mammalian cells.
    Irastorza-Azcarate IKukalev AKempfer RThieme CJMastrobuoni GMarkowski JLoof GSparks TMBrookes ENatarajan KNSauer SFisher AGNicodemi MRen BSchwarz RFKempa SPombo A
    2024
    bioRxiv : the preprint server for biology
    1
    4DN