Publications

Included Properties

Data Type
  • Publication98
    • Project
  • 4DN98
    • Lab
    Journal
    Experiment Types
    Status
    98 Results
    Title
    Year
    Journal
    Exp Sets
    Project
    Cell-type-specific 3D-genome organization and transcription regulation in the brain.
    Liu SZheng PWang CYJia BBZemke NRRen BZhuang X
    2023
    bioRxiv : the preprint server for biology
    2
    4DN
    TERRA-LSD1 phase separation promotes R-loop formation for telomere maintenance in ALT cancer cells.
    Xu MSenanayaka DZhao RChigumira TTripathi ATones JLackner RMWondisford ARMoneysmith LNHirschi ACraig SAlishiri SO'Sullivan RJChenoweth DMReiter NJZhang H
    2024
    Nature communications
    2
    4DN
    Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition.
    Murphy SEBoettiger AN
    2024
    Nature genetics
    5
    4DN
    Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum.
    Zhao ZParra OPMusella FScrutton-Alvarado NFujita SIAlber FYang YYamada T
    2023
    bioRxiv : the preprint server for biology
    12
    4DN
    Foxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity.
    Liu ZLee DSLiang YZheng YDixon JR
    2023
    Nature communications
    38
    4DN
    Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development.
    Hung TCKingsley DMBoettiger AN
    2024
    Nature genetics
    1
    4DN
    Pseudotime analysis for time-series single-cell sequencing and imaging data
    Li GKim H-JPendyala SZhang RDisteche CMVert J-PDeng XFowler DMNoble WS
    2024
    bioRxiv
    5
    4DN
    Systematic mapping and modeling of 3D enhancer-promoter interactions in early mouse embryonic lineages reveal regulatory principles that determine the levels and cell-type specificity of gene expression.
    Murphy DSalataj EDi Giammartino DCRodriguez-Hernaez JKloetgen AGarg VChar EUyehara CMEe LSLee UStadtfeld MHadjantonakis AKTsirigos APolyzos AApostolou E
    2023
    bioRxiv : the preprint server for biology
    34
    4DN
    Nucleolus and centromere TSA-Seq reveals variable localization of heterochromatin in different cell types
    Kumar PGholamalamdari OZhang YZhang LVertii AvanSchaik TPeric-Hupkes DSasaki TGilbert DMvanSteensel BMa JKaufman PDBelmont AS
    2023
    bioRxiv
    30
    4DN
    4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis.
    Krijger PHLGeeven GBianchi VHilvering CREde Laat W
    2020
    Methods(San Diego, Calif.)
    -
    4DN
    Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells.
    Calandrelli RWen XCharles Richard JLLuo ZNguyen TCChen CJQi ZXue SChen WYan ZWu WZaleta-Rivera KHu RYu MWang YLi WMa JRen BZhong S
    2023
    Nature communications
    11
    4DN
    Spatial organization of chromatin domains and compartments in single chromosomes.
    Wang SSu JHBeliveau BJBintu BMoffitt JRWu CTZhuang X
    2016
    Science(New York, N.Y.)
    5
    4DN
    Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells.
    Pulecio JTayyebi ZLiu DWong WLuo RDamodaran JRKaplan SCho HYan JMurphy DRickert RWShukla AZhong AGonzalez FYang DLi WZhou TApostolou ELeslie CSHuangfu D
    2023
    bioRxiv : the preprint server for biology
    -
    4DN
    Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.
    Luo RYan JOh JWXi WShigaki DWong WCho HSMurphy DCutler RRosen BPPulecio JYang DGlenn RAChen TLi QVVierbuchen TSidoli SApostolou EHuangfu DBeer MA
    2023
    Nature genetics
    6
    4DN
    Female naive human pluripotent stem cells carry X chromosomes with Xa-like and Xi-like folding conformations.
    Patterson BYang BTanaka YKim KYCakir BXiang YKim JWang SPark IH
    2023
    Science advances
    21
    4DN
    Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C.
    Beagrie RAThieme CJAnnunziatella CBaugher CZhang YSchueler MKukalev AKempfer RChiariello AMBianco SLi YDavis TScialdone AWelch LRNicodemi MPombo A
    2023
    Nature methods
    1
    4DN
    HiCAR is a robust and sensitive method to analyze open-chromatin-associated genome organization.
    Wei XXiang YPeters DTMarius CSun TShan ROu JLin XYue FLi WSoutherland KWDiao Y
    2022
    Molecular cell
    -
    4DN
    Loop stacking organizes genome folding from TADs to chromosomes.
    Hafner APark MBerger SEMurphy SENora EPBoettiger AN
    2023
    Molecular cell
    40
    4DN
    Structural elements promote architectural stripe formation and facilitate ultra-long-range gene regulation at a human disease locus.
    Chen LFLong HKPark MSwigut TBoettiger ANWysocka J
    2023
    Molecular cell
    5
    4DN
    An integrated platform for high-throughput nanoscopy.
    Barentine AESLin YCourvan EMKidd PLiu MBalduf LPhan TRivera-Molina FGrace MRMarin ZLessard MRios Chen JWang SNeugebauer KMBewersdorf JBaddeley D
    2023
    Nature biotechnology
    5
    4DN
    A spatial genome aligner for resolving chromatin architectures from multiplexed DNA FISH.
    Jia BBJussila AKern CZhu QRen B
    2023
    Nature biotechnology
    -
    4DN
    Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation.
    Alavattam KGMitzelfelt KABonora GFields PAYang XChiu HSPabon LBertero APalpant NJNoble WSMurry CE
    2022
    Stem cell reports
    8
    4DN
    TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.
    Wang WChandra AGoldman NYoon SFerrari EKNguyen SCJoyce EFVahedi G
    2022
    Nature immunology
    24
    4DN
    Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.
    Zou RSMarin-Gonzalez ALiu YLiu HBShen LDveirin RKLuo JXJKalhor RHa T
    2022
    Nature cell biology
    42
    4DN
    Kinetic principles underlying pioneer function of GAGA transcription factor in live cells.
    Tang XLi TLiu SWisniewski JZheng QRong YLavis LDWu C
    2022
    Nature structural & molecular biology
    30
    4DN