Publications

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Data Type
  • Publication11
    • Lab
  • 4DN DCIC, HMS2
  • Andrew Belmont, ILLINOIS2
  • Jay Ashok Shendure, UW2
  • Bing Ren, UCSD1
  • David Baddeley, YALE1
  • Jan Liphardt, STANFORD1
  • Mitchell Guttman, CALTECH1
  • Yarui Diao, DUKE1
    • Journal
    Experiment Types
    Categories
  • technology development11
    • Status
    1 Common Properties
     Project
    4DN
    11 Results
    Title
    Year
    Journal
    Exp Sets
    Project
    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
    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
    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
    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
    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
    Comprehensive single-cell transcriptional profiling of a multicellular organism.
    Cao JPacker JSRamani VCusanovich DAHuynh CDaza RQiu XLee CFurlan SNSteemers FJAdey AWaterston RHTrapnell CShendure J
    2017
    Science(New York, N.Y.)
    -
    4DN
    Multiplex single cell profiling of chromatin accessibility by combinatorial cellular indexing.
    Cusanovich DADaza RAdey APliner HAChristiansen LGunderson KLSteemers FJTrapnell CShendure J
    2015
    Science(New York, N.Y.)
    -
    4DN
    A fluorogenic array for temporally unlimited single-molecule tracking.
    Ghosh RPFranklin JMDraper WEShi QBeltran BSpakowitz AJLiphardt JT
    2019
    Nature chemical biology
    -
    4DN
    MAPS: Model-based analysis of long-range chromatin interactions from PLAC-seq and HiChIP experiments.
    Juric IYu MAbnousi ARaviram RFang RZhao YZhang YQiu YYang YLi YRen BHu M
    2019
    PLoS computational biology
    2
    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
    - fin -