Publications

Included Properties

Data Type
  • Publication72
    • Project
    Lab
    Journal
    Experiment Types
    Number of Experiment Sets
  • 1 N
    • Status
    72 Results
    Title
    Year
    Journal
    Exp Sets
    Project
    Bromodomains regulate dynamic targeting of the PBAF chromatin remodeling complex to chromatin hubs.
    Kenworthy CAHaque NLiou SHChandris PWong VDziuba PLavis LDLiu WLSinger RHColeman RA
    2022
    Biophysical journal
    8
    4DN
    Massively parallel genomic perturbations with multi-target CRISPR reveal new insights on Cas9 activity and DNA damage responses at endogenous sites
    Zou RSMarin-Gonzalez ALiu YLiu HBShen LDveirin RLuo JXJKalhor RHa T
    2022
    bioRxiv
    42
    4DN
    CRISPR Cas13-Based Tools to Track and Manipulate Endogenous Telomeric Repeat-Containing RNAs in Live Cells.
    Xu MChigumira TChen ZTones JZhao RDahl KNChenoweth DMZhang H
    2021
    Frontiers in molecular biosciences
    2
    4DN
    Cryomilling Tethered Chromatin Conformation Capture reveal new insights into inter-chromosomal interactions
    Xu JKumar SHua NKou YLei XRout MAitchison JAlber FChen L
    2022
    bioRxiv
    7
    4DN
    Cell-type specialization is encoded by specific chromatin topologies.
    Winick-Ng WKukalev AHarabula IZea-Redondo LSzabo DMeijer MSerebreni LZhang YBianco SChiariello AMIrastorza-Azcarate IThieme CJSparks TMCarvalho SFiorillo LMusella FIrani ETriglia ETKolodziejczyk AAAbentung Aet al.
    2021
    Nature
    4
    4DN
    Capturing cell type-specific chromatin compartment patterns by applying topic modeling to single-cell Hi-C data.
    Kim HJYardimci GGBonora GRamani VLiu JQiu RLee CHesson JWare CBShendure JDuan ZNoble WS
    2020
    PLoS computational biology
    6
    4DN
    Histone H3 lysine 4 monomethylation modulates long-range chromatin interactions at enhancers.
    Yan JChen SALocal ALiu TQiu YDorighi KMPreissl SRivera CMWang CYe ZGe KHu MWysocka JRen B
    2018
    Cell research
    8
    4DN
    Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.
    Kubo NIshii HXiong XBianco SMeitinger FHu RHocker JDConte MGorkin DYu MLi BDixon JRHu MNicodemi MZhao HRen B
    2021
    Nature structural & molecular biology
    4
    4DN
    Kinetic principles underlying pioneer function of GAGA transcription factor in live cells
    Tang XLi TLiu SWisniewski JZheng QLavis LRong YWu C
    2022
    bioRxiv
    30
    4DN
    Single-cell landscape of nuclear configuration and gene expression during stem cell differentiation and X inactivation.
    Bonora GRamani VSingh RFang HJackson DLSrivatsan SQiu RLee CTrapnell CShendure JDuan ZDeng XNoble WSDisteche CM
    2021
    Genome biology
    43
    4DN
    Systematic evaluation of chromosome conformation capture assays.
    Akgol Oksuz BYang LAbraham SVenev SVKrietenstein NParsi KMOzadam HOomen MENand AMao HGenga RMJMaehr RRando OJMirny LAGibcus JHDekker J
    2021
    Nature methods
    69
    4DN
    High-resolution Repli-Seq defines the temporal choreography of initiation, elongation and termination of replication in mammalian cells.
    Zhao PASasaki TGilbert DM
    2020
    Genome biology
    18
    4DN
    Screening thousands of transcribed coding and non-coding regions reveals sequence determinants of RNA polymerase II elongation potential
    Vlaming HMimoso CAMartin BJField ARAdelman K
    2021
    bioRxiv
    1
    4DN
    Three-dimensional organization of chromatin associated RNAs and their role in chromatin architecture in human cells
    Calandrelli RWen XNguyen TCChen C-JQi ZChen WYan ZWu WZaleta-Rivera KHu RYu MWang YMa JRen BZhong S
    2021
    bioRxiv
    11
    4DN
    The conserved sex regulator DMRT1 recruits SOX9 in sexual cell fate reprogramming.
    Lindeman REMurphy MWAgrimson KSGewiss RLBardwell VJGearhart MDZarkower D
    2021
    Nucleic acids research
    2
    External
    CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.
    Huang HZhu QJussila AHan YBintu BKern CConte MZhang YBianco SChiariello AMYu MHu RTastemel MJuric IHu MNicodemi MZhuang XRen B
    2021
    Nature genetics
    31
    4DN
    Multiplexed imaging of nucleome architectures in single cells of mammalian tissue.
    Liu MLu YYang BChen YRadda JSDHu MKatz SGWang S
    2020
    Nature communications
    1
    External
    Disruption of nuclear architecture as a cause of COVID-19 induced anosmia.
    Zazhytska MKodra AHoagland DAFullard JFShayya HOmer AFirestein SGong QCanoll PDGoldman JERoussos PtenOever BROverdevest JBLomvardas S
    2021
    bioRxiv : the preprint server for biology
    43
    4DN
    Liquid chromatin Hi-C characterizes compartment-dependent chromatin interaction dynamics.
    Belaghzal HBorrman TStephens ADLafontaine DLVenev SVWeng ZMarko JFDekker J
    2021
    Nature genetics
    30
    4DN
    Cohesin-mediated loop anchors confine the location of human replication origins
    Emerson DJZhao PAKlein KGe CZhou LSasaki TYang LVenvev SVGibcus JHDekker JGilbert DMPhillips-Cremins JE
    2021
    bioRxiv
    66
    4DN
    Dynamic interplay between enhancer-promoter topology and gene activity.
    Chen HLevo MBarinov LFujioka MJaynes JBGregor T
    2018
    Nature genetics
    3
    4DN
    TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes.
    Zhang LZhang YChen YGholamalamdari OWang YMa JBelmont AS
    2020
    Genome research
    58
    4DN
    DMA-tudor interaction modules control the specificity of in vivo condensates.
    Courchaine EMBarentine AESStraube KLee DRBewersdorf JNeugebauer KM
    2021
    Cell
    13
    4DN
    Multi-contact 3C reveals that the human genome during interphase is largely not entangled.
    Tavares-Cadete FNorouzi DDekker BLiu YDekker J
    2020
    Nature structural & molecular biology
    1
    4DN
    Cell cycle dynamics of lamina-associated DNA.
    van Schaik TVos MPeric-Hupkes DHn Celie Pvan Steensel B
    2020
    EMBO reports
    50
    4DN