Publications

Included Properties

Data Type
  • Publication97
    • Project
    Lab
    Journal
    Experiment Types
    Number of Experiment Sets
  • 1 N
    • Status
    97 Results
    Title
    Year
    Journal
    Exp Sets
    2
    Project
    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
    Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells.
    Bintu BMateo LJSu JHSinnott-Armstrong NAParker MKinrot SYamaya KBoettiger ANZhuang X
    2018
    Science(New York, N.Y.)
    10
    External
    Detailed Regulatory Interaction Map of the Human Heart Facilitates Gene Discovery for Cardiovascular Disease
    Bianchi VGeeven GTucker NHilvering CREHall AWRoselli CHill MCMartin JFMargulies KBEllinor PTdeLaat W
    2019
    bioRxiv
    8
    External
    Integrated spatial genomics reveals global architecture of single nuclei.
    Takei YYun JZheng SOllikainen NPierson NWhite JShah SThomassie JSuo SEng CLGuttman MYuan GCCai L
    2021
    Nature
    1
    4DN
    Single-cell nuclear architecture across cell types in the mouse brain.
    Takei YZheng SYun JShah SPierson NWhite JSchindler STischbirek CHYuan GCCai L
    2021
    Science(New York, N.Y.)
    1
    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
    Cohesin-mediated loop anchors confine the locations of human replication origins.
    Emerson DJZhao PACook ALBarnett RJKlein KNSaulebekova DGe CZhou LSimandi ZMinsk MKTitus KRWang WGong WZhang DYang LVenev SVGibcus JHYang HSasaki TKanemaki MTYue FDekker JChen CLGilbert DMPhillips-Cremins JE
    2022
    Nature
    66
    4DN
    Beyond A and B Compartments: how major nuclear locales define nuclear genome organization and function
    Gholamalamdari OvanSchaik TWang YKumar PZhang LZhang YGonzalez GAHVouzas AEZhao PAGilbert DMMa JvanSteensel BBelmont AS
    2024
    bioRxiv
    12
    4DN
    Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler.
    Chen YZhang YWang YZhang LBrinkman EKAdam SAGoldman Rvan Steensel BMa JBelmont AS
    2018
    The Journal of cell biology
    28
    4DN
    Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus.
    Quinodoz SAOllikainen NTabak BPalla ASchmidt JMDetmar ELai MMShishkin AABhat PTakei YTrinh VAznauryan ERussell PCheng CJovanovic MChow ACai LMcDonel PGarber MGuttman M
    2018
    Cell
    22
    4DN
    Extensive Heterogeneity and Intrinsic Variation in Spatial Genome Organization.
    Finn EHPegoraro GBrandao HBValton ALOomen MEDekker JMirny LMisteli T
    2019
    Cell
    246
    4DN
    A pathway for mitotic chromosome formation.
    Gibcus JHSamejima KGoloborodko ASamejima INaumova NNuebler JKanemaki MTXie LPaulson JREarnshaw WCMirny LADekker J
    2018
    Science(New York, N.Y.)
    42
    External
    Orientation-dependent Dxz4 contacts shape the 3D structure of the inactive X chromosome.
    Bonora GDeng XFang HRamani VQiu RBerletch JBFilippova GNDuan ZShendure JNoble WSDisteche CM
    2018
    Nature communications
    28
    4DN
    Ultrastructural Details of Mammalian Chromosome Architecture.
    Krietenstein NAbraham SVenev SVAbdennur NGibcus JHsieh TSParsi KMYang LMaehr RMirny LADekker JRando OJ
    2020
    Molecular cell
    4
    4DN
    Heterochromatin drives compartmentalization of inverted and conventional nuclei.
    Falk MFeodorova YNaumova NImakaev MLajoie BRLeonhardt HJoffe BDekker JFudenberg GSolovei IMirny LA
    2019
    Nature
    4
    External
    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
    Dynamics of genome reorganization during human cardiogenesis reveal an RBM20-dependent splicing factory.
    Bertero AFields PARamani VBonora GYardimci GGReinecke HPabon LNoble WSShendure JMurry CE
    2019
    Nature communications
    18
    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
    Non-cell-autonomous disruption of nuclear architecture as a potential cause of COVID-19-induced anosmia.
    Zazhytska MKodra AHoagland DAFrere JFullard JFShayya HMcArthur NGMoeller RUhl SOmer ADGottesman MEFirestein SGong QCanoll PDGoldman JERoussos PtenOever BRJonathan B OverdevestLomvardas S
    2022
    Cell
    43
    4DN
    A chromosome folding intermediate at the condensin-to-cohesin transition during telophase.
    Abramo KValton ALVenev SVOzadam HFox ANDekker J
    2019
    Nature cell biology
    194
    4DN
    The Energetics and Physiological Impact of Cohesin Extrusion.
    Vian LPekowska ARao SSPKieffer-Kwon KRJung SBaranello LHuang SCEl Khattabi LDose MPruett NSanborn ALCanela AMaman YOksanen AResch WLi XLee BKovalchuk ALTang ZNelson SDi Pierro MCheng RRMachol ISt Hilaire BGet al.
    2018
    Cell
    77
    External
    Transcriptional Burst Initiation and Polymerase Pause Release Are Key Control Points of Transcriptional Regulation.
    Bartman CRHamagami NKeller CAGiardine BHardison RCBlobel GARaj A
    2018
    Molecular cell
    74
    4DN
    Robust model-based analysis of single-particle tracking experiments with Spot-On.
    Hansen ASWoringer MGrimm JBLavis LDTjian RDarzacq X
    2018
    eLife
    60
    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
    A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping.
    Rao SSHuntley MHDurand NCStamenova EKBochkov IDRobinson JTSanborn ALMachol IOmer ADLander ESAiden EL
    2014
    Cell
    55
    External