Publications

Included Properties

Data Type
  • Publication106
    • Project
    Lab
    Journal
    Experiment Types
    Number of Experiment Sets
  • 1 N
    • Status
    106 Results
    Title
    Year
    Journal
    Exp Sets
    Project
    Improved cohesin HiChIP protocol and bioinformatic analysis for robust detection of chromatin loops and stripes
    Jodkowska KParteka-Tojek ZAgarwal ADenkiewicz MKorsak SChilinski MBanecki KPlewczynski D
    2024
    bioRxiv
    2
    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
    Super-enhancer interactomes from single cells link clustering and transcription.
    Le DJHafner AGaddam SWang KCBoettiger AN
    2024
    bioRxiv : the preprint server for biology
    2
    4DN
    Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function.
    Gholamalamdari Ovan Schaik TWang YKumar PZhang LZhang YGonzalez GAHVouzas AEZhao PAGilbert DMMa Jvan Steensel BBelmont AS
    2024
    bioRxiv : the preprint server for biology
    18
    4DN
    Conserved and divergent gene regulatory programs of the mammalian neocortex.
    Zemke NRArmand EJWang WLee SZhou JLi YELiu HTian WNery JRCastanon RGBartlett AOsteen JKLi DZhuo XXu VChang LDong KIndralingam HSRink JAXie YMiller MKrienen FMZhang QTaskin NTing JFeng GMcCarroll SAet al.
    2023
    Nature
    36
    4DN
    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 Avan Schaik TPeric-Hupkes DSasaki TGilbert DMvan Steensel BMa JKaufman PDBelmont AS
    2023
    bioRxiv : the preprint server for biology
    32
    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
    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
    Loop stacking organizes genome folding from TADs to chromosomes.
    Hafner APark MBerger SEMurphy SENora EPBoettiger AN
    2023
    Molecular cell
    40
    4DN