标题
The era of 3D and spatial genomics
作者
关键词
-
出版物
TRENDS IN GENETICS
Volume -, Issue -, Pages -
出版商
Elsevier BV
发表日期
2022-06-07
DOI
10.1016/j.tig.2022.05.010
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- RNA gradients: Shapers of 3D genome architecture
- (2022) Britta A.M. Bouwman et al. CURRENT OPINION IN CELL BIOLOGY
- Spatially resolved single-cell genomics and transcriptomics by imaging
- (2021) Xiaowei Zhuang NATURE METHODS
- Spatially resolved transcriptomics adds a new dimension to genomics
- (2021) Ludvig Larsson et al. NATURE METHODS
- Genome oligopaint via local denaturation fluorescence in situ hybridization
- (2021) Yanbo Wang et al. MOLECULAR CELL
- Integrated spatial genomics reveals global architecture of single nuclei
- (2021) Yodai Takei et al. NATURE
- Chromatin tracing and multiplexed imaging of nucleome architectures (MINA) and RNAs in single mammalian cells and tissue
- (2021) Miao Liu et al. Nature Protocols
- Understanding 3D genome organization by multidisciplinary methods
- (2021) Ivana Jerkovic´ et al. NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Chorus2: design of genome‐scale oligonucleotide‐based probes for fluorescence in situ hybridization
- (2021) Tao Zhang et al. PLANT BIOTECHNOLOGY JOURNAL
- Single‐cell imaging of genome organization and dynamics
- (2021) Liangqi Xie et al. Molecular Systems Biology
- Single-cell measurement of higher-order 3D genome organization with scSPRITE
- (2021) Mary V. Arrastia et al. NATURE BIOTECHNOLOGY
- Systematic evaluation of chromosome conformation capture assays
- (2021) Betul Akgol Oksuz et al. NATURE METHODS
- PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments
- (2021) Elliot A. Hershberg et al. NATURE METHODS
- Distinct nuclear compartment-associated genome architecture in the developing mammalian brain
- (2021) Sajad Hamid Ahanger et al. NATURE NEUROSCIENCE
- RNA promotes the formation of spatial compartments in the nucleus
- (2021) Sofia A. Quinodoz et al. CELL
- The CRISPR-Cas toolbox and gene editing technologies
- (2021) Guanwen Liu et al. MOLECULAR CELL
- Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
- (2021) Tongtong Zhao et al. NATURE
- Single-cell nuclear architecture across cell types in the mouse brain
- (2021) Yodai Takei et al. SCIENCE
- The two waves in single-cell 3D genomics
- (2021) Sergey V. Ulianov et al. SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY
- A Shift in Paradigms: Spatial Genomics Approaches to Reveal Single-Cell Principles of Genome Organization
- (2021) Andres M. Cardozo Gizzi Frontiers in Genetics
- FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains
- (2021) Antonina Maslova et al. Frontiers in Cell and Developmental Biology
- Biased visibility in Hi-C datasets marks dynamically regulated condensed and decondensed chromatin states genome-wide
- (2020) Keerthivasan Raanin Chandradoss et al. BMC GENOMICS
- Lamina-Dependent Stretching and Unconventional Chromosome Compartments in Early C. elegans Embryos
- (2020) Ahilya N. Sawh et al. MOLECULAR CELL
- Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function
- (2020) Rachel Patton McCord et al. MOLECULAR CELL
- Visualizing the genome in high resolution challenges our textbook understanding
- (2020) Melike Lakadamyali et al. NATURE METHODS
- Multi-contact 4C: long-molecule sequencing of complex proximity ligation products to uncover local cooperative and competitive chromatin topologies
- (2020) Carlo Vermeulen et al. Nature Protocols
- Monitoring the spatio-temporal organization and dynamics of the genome
- (2020) Haitham A Shaban et al. NUCLEIC ACIDS RESEARCH
- Advances in Chromatin Imaging at Kilobase-Scale Resolution
- (2020) Alistair Boettiger et al. TRENDS IN GENETICS
- Radial Organization in the Mammalian Nucleus
- (2020) Nicola Crosetto et al. Frontiers in Genetics
- GPSeq reveals the radial organization of chromatin in the cell nucleus
- (2020) Gabriele Girelli et al. NATURE BIOTECHNOLOGY
- Simultaneous quantification of protein–DNA interactions and transcriptomes in single cells with scDam&T-seq
- (2020) Corina M. Markodimitraki et al. Nature Protocols
- Evolving methodologies and concepts in 4D nucleome research
- (2020) Thomas M. Sparks et al. CURRENT OPINION IN CELL BIOLOGY
- 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing
- (2020) Huy Q. Nguyen et al. NATURE METHODS
- Multiplexed imaging of nucleome architectures in single cells of mammalian tissue
- (2020) Miao Liu et al. Nature Communications
- Coupling chromatin structure and dynamics by live super-resolution imaging
- (2020) R. Barth et al. Science Advances
- Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
- (2020) Jun-Han Su et al. CELL
- High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection
- (2020) Pranitha Vangala et al. MOLECULAR CELL
- Direct DNA crosslinking with CAP-C uncovers transcription-dependent chromatin organization at high resolution
- (2020) Qiancheng You et al. NATURE BIOTECHNOLOGY
- TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
- (2020) Liguo Zhang et al. GENOME RESEARCH
- Chromatin Tracing: Imaging 3D Genome and Nucleome
- (2020) Mengwei Hu et al. TRENDS IN CELL BIOLOGY
- ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization
- (2020) Mengwei Hu et al. Scientific Reports
- Novel orthogonal methods to uncover the complexity and diversity of nuclear architecture
- (2020) Sjoerd JD Tjalsma et al. CURRENT OPINION IN GENETICS & DEVELOPMENT
- Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
- (2019) Samuel G. Rodriques et al. SCIENCE
- Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
- (2019) Chee-Huat Linus Eng et al. NATURE
- Visualizing DNA folding and RNA in embryos at single-cell resolution
- (2019) Leslie J. Mateo et al. NATURE
- Multiplex chromatin interactions with single-molecule precision
- (2019) Meizhen Zheng et al. NATURE
- Microscopy-Based Chromosome Conformation Capture Enables Simultaneous Visualization of Genome Organization and Transcription in Intact Organisms
- (2019) Andrés M. Cardozo Gizzi et al. MOLECULAR CELL
- DamC reveals principles of chromatin folding in vivo without crosslinking and ligation
- (2019) Josef Redolfi et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans
- (2019) Brandon D Fields et al. eLife
- Simultaneous quantification of protein–DNA contacts and transcriptomes in single cells
- (2019) Koos Rooijers et al. NATURE BIOTECHNOLOGY
- iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture
- (2019) Eleni Gelali et al. Nature Communications
- CRISPR-mediated live imaging of genome editing and transcription
- (2019) Haifeng Wang et al. SCIENCE
- Methods for mapping 3D chromosome architecture
- (2019) Rieke Kempfer et al. NATURE REVIEWS GENETICS
- Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus
- (2018) Sofia A. Quinodoz et al. CELL
- OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
- (2018) Brian J. Beliveau et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Transcription-coupled changes in nuclear mobility of mammalian cis-regulatory elements
- (2018) Bo Gu et al. SCIENCE
- Mapping 3D genome organization relative to nuclear compartments using TSA-Seq as a cytological ruler
- (2018) Yu Chen et al. JOURNAL OF CELL BIOLOGY
- Three-dimensional genome structures of single diploid human cells
- (2018) Longzhi Tan et al. SCIENCE
- A tissue-specific self-interacting chromatin domain forms independently of enhancer-promoter interactions
- (2018) Jill M. Brown et al. Nature Communications
- Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells
- (2018) Bogdan Bintu et al. SCIENCE
- Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag
- (2018) Baohui Chen et al. Nature Communications
- Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling
- (2018) Guy Nir et al. PLoS Genetics
- Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation
- (2017) Houda Belaghzal et al. METHODS
- Complex multi-enhancer contacts captured by genome architecture mapping
- (2017) Robert A. Beagrie et al. NATURE
- Massively multiplex single-cell Hi-C
- (2017) Vijay Ramani et al. NATURE METHODS
- (Po)STAC (Polycistronic SunTAg modified CRISPR) enables live-cell and fixed-cell super-resolution imaging of multiple genes
- (2017) Maria V Neguembor et al. NUCLEIC ACIDS RESEARCH
- An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites
- (2017) Peter J Skene et al. eLife
- Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow
- (2016) Hanhui Ma et al. NATURE BIOTECHNOLOGY
- Mapping the 3D genome: Aiming for consilience
- (2016) Job Dekker NATURE REVIEWS MOLECULAR CELL BIOLOGY
- Spatial organization of chromatin domains and compartments in single chromosomes
- (2016) Siyuan Wang et al. SCIENCE
- CRISPR-dCas9 and sgRNA scaffolds enable dual-colour live imaging of satellite sequences and repeat-enriched individual loci
- (2016) Yi Fu et al. Nature Communications
- An RNA-aptamer-based two-color CRISPR labeling system
- (2016) Siyuan Wang et al. Scientific Reports
- Genome-wide Maps of Nuclear Lamina Interactions in Single Human Cells
- (2015) Jop Kind et al. CELL
- Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
- (2015) Tsung-Han S. Hsieh et al. CELL
- CASFISH: CRISPR/Cas9-mediated in situ labeling of genomic loci in fixed cells
- (2015) Wulan Deng et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Spatially resolved, highly multiplexed RNA profiling in single cells
- (2015) K. H. Chen et al. SCIENCE
- Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
- (2015) Brian J. Beliveau et al. Nature Communications
- A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
- (2014) Suhas S.P. Rao et al. CELL
- Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization
- (2014) Iain Williamson et al. GENES & DEVELOPMENT
- Single-cell in situ RNA profiling by sequential hybridization
- (2014) Eric Lubeck et al. NATURE METHODS
- Implementing personalized cancer care
- (2014) Richard L. Schilsky Nature Reviews Clinical Oncology
- Spatially resolved transcriptomics and beyond
- (2014) Nicola Crosetto et al. NATURE REVIEWS GENETICS
- Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System
- (2013) Baohui Chen et al. CELL
- Single-cell Hi-C reveals cell-to-cell variability in chromosome structure
- (2013) Takashi Nagano et al. NATURE
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position
- (2013) Jason D Buenrostro et al. NATURE METHODS
- Disclosure of a structural milieu for the proximity ligation reveals the elusive nature of an active chromatin hub
- (2013) Alexey A. Gavrilov et al. NUCLEIC ACIDS RESEARCH
- Topological domains in mammalian genomes identified by analysis of chromatin interactions
- (2012) Jesse R. Dixon et al. NATURE
- A versatile genome-scale PCR-based pipeline for high-definition DNA FISH
- (2012) Magda Bienko et al. NATURE METHODS
- Intratumor Heterogeneity and Branched Evolution Revealed by Multiregion Sequencing
- (2012) Marco Gerlinger et al. NEW ENGLAND JOURNAL OF MEDICINE
- Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes
- (2012) B. J. Beliveau et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis
- (2011) Shelagh Boyle et al. CHROMOSOME RESEARCH
- Visualization of Fine-Scale Genomic Structure by Oligonucleotide-Based High-Resolution FISH
- (2011) N.A. Yamada et al. CYTOGENETIC AND GENOME RESEARCH
- Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture
- (2011) Eitan Yaffe et al. NATURE GENETICS
- Counting absolute numbers of molecules using unique molecular identifiers
- (2011) Teemu Kivioja et al. NATURE METHODS
- Genome organization in and around the nucleolus
- (2011) Attila Németh et al. TRENDS IN GENETICS
- Nuclear Speckles
- (2010) D. L. Spector et al. Cold Spring Harbor Perspectives in Biology
- Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
- (2009) E. Lieberman-Aiden et al. SCIENCE
- Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions
- (2008) Lars Guelen et al. NATURE
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