标题
Spatial omics and multiplexed imaging to explore cancer biology
作者
关键词
-
出版物
NATURE METHODS
Volume 18, Issue 9, Pages 997-1012
出版商
Springer Science and Business Media LLC
发表日期
2021-08-03
DOI
10.1038/s41592-021-01203-6
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Spatially resolved transcriptomics adds a new dimension to genomics
- (2021) Ludvig Larsson et al. NATURE METHODS
- Integrated spatial genomics reveals global architecture of single nuclei
- (2021) Yodai Takei et al. NATURE
- Robust decomposition of cell type mixtures in spatial transcriptomics
- (2021) Dylan M. Cable et al. NATURE BIOTECHNOLOGY
- SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes
- (2021) Marc Elosua-Bayes et al. NUCLEIC ACIDS RESEARCH
- Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems
- (2021) Shahar Alon et al. SCIENCE
- Inter- and intra-tumor heterogeneity of metastatic prostate cancer determined by digital spatial gene expression profiling
- (2021) Lauren Brady et al. Nature Communications
- Imaging cell lineage with a synthetic digital recording system
- (2021) Ke-Huan K. Chow et al. SCIENCE
- Spatial transcriptomics at subspot resolution with BayesSpace
- (2021) Edward Zhao et al. NATURE BIOTECHNOLOGY
- Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
- (2020) Reuben Moncada et al. NATURE BIOTECHNOLOGY
- Computational methods for single-cell omics across modalities
- (2020) Mirjana Efremova et al. NATURE METHODS
- Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies
- (2020) Shiquan Sun et al. NATURE METHODS
- SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation
- (2020) Joseph Bergenstråhle et al. BMC BIOINFORMATICS
- Intratumor Heterogeneity: The Rosetta Stone of Therapy Resistance
- (2020) Andriy Marusyk et al. CANCER CELL
- Plasticity of Lgr5-Negative Cancer Cells Drives Metastasis in Colorectal Cancer
- (2020) Arianna Fumagalli et al. Cell Stem Cell
- CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues
- (2020) Caleb R. Stoltzfus et al. Cell Reports
- nucleAIzer: A Parameter-free Deep Learning Framework for Nucleus Segmentation Using Image Style Transfer
- (2020) Reka Hollandi et al. Cell Systems
- Seamless integration of image and molecular analysis for spatial transcriptomics workflows
- (2020) Joseph Bergenstråhle et al. BMC GENOMICS
- Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
- (2020) Andrew L. Ji et al. CELL
- Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front
- (2020) Christian M. Schürch et al. CELL
- Generalizing RNA velocity to transient cell states through dynamical modeling
- (2020) Volker Bergen et al. NATURE BIOTECHNOLOGY
- Highly specific multiplexed RNA imaging in tissues with split-FISH
- (2020) Jolene Jie Lin Goh et al. NATURE METHODS
- 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing
- (2020) Huy Q. Nguyen et al. NATURE METHODS
- ZipSeq: barcoding for real-time mapping of single cell transcriptomes
- (2020) Kenneth H. Hu et al. NATURE METHODS
- A deep learning model to predict RNA-Seq expression of tumours from whole slide images
- (2020) Benoît Schmauch et al. Nature Communications
- Immune surveillance in clinical regression of pre-invasive squamous cell lung cancer
- (2020) Adam Pennycuick et al. Cancer Discovery
- A Rainbow Reporter Tracks Single Cells and Reveals Heterogeneous Cellular Dynamics among Pluripotent Stem Cells and Their Differentiated Derivatives
- (2020) Danny El-Nachef et al. Stem Cell Reports
- Integrating spatial gene expression and breast tumour morphology via deep learning
- (2020) Bryan He et al. Nature Biomedical Engineering
- Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin
- (2020) Jun-Han Su et al. CELL
- Single-cell sequencing techniques from individual to multiomics analyses
- (2020) Yukie Kashima et al. EXPERIMENTAL AND MOLECULAR MEDICINE
- Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
- (2020) Daniel Gyllborg et al. NUCLEIC ACIDS RESEARCH
- Multi-color clonal tracking reveals intra-stage proliferative heterogeneity during mammary tumor progression
- (2020) Stefanie Tiede et al. ONCOGENE
- STARCH: Copy number and clone inference from spatial transcriptomics data
- (2020) Rebecca Elyanow et al. PHYSICAL BIOLOGY
- High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
- (2020) Yang Liu et al. CELL
- Deep learning model for the prediction of microsatellite instability in colorectal cancer: a diagnostic study
- (2020) Rikiya Yamashita et al. LANCET ONCOLOGY
- Cellpose: a generalist algorithm for cellular segmentation
- (2020) Carsen Stringer et al. NATURE METHODS
- Deep learning-enabled breast cancer hormonal receptor status determination from base-level H&E stains
- (2020) Nikhil Naik et al. Nature Communications
- Barcoding reveals complex clonal behavior in patient-derived xenografts of metastatic triple negative breast cancer
- (2019) D. Merino et al. Nature Communications
- Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
- (2019) Samuel G. Rodriques et al. SCIENCE
- Integrative single-cell analysis
- (2019) Tim Stuart et al. NATURE REVIEWS GENETICS
- Resolving genetic heterogeneity in cancer
- (2019) Samra Turajlic et al. NATURE REVIEWS GENETICS
- FPbase: a community-editable fluorescent protein database
- (2019) Talley J. Lambert NATURE METHODS
- Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
- (2019) Chee-Huat Linus Eng et al. NATURE
- The single-cell transcriptional landscape of mammalian organogenesis
- (2019) Junyue Cao et al. NATURE
- Intraclonal Plasticity in Mammary Tumors Revealed through Large-Scale Single-Cell Resolution 3D Imaging
- (2019) Anne C. Rios et al. CANCER CELL
- Comprehensive Integration of Single-Cell Data
- (2019) Tim Stuart et al. CELL
- Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity
- (2019) Joshua D. Welch et al. CELL
- Rapid Generation of Somatic Mouse Mosaics with Locus-Specific, Stably Integrated Transgenic Elements
- (2019) Gi Bum Kim et al. CELL
- Starfish enterprise: finding RNA patterns in single cells
- (2019) Jeffrey M. Perkel NATURE
- Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues
- (2019) Sinem K. Saka et al. NATURE BIOTECHNOLOGY
- High-definition spatial transcriptomics for in situ tissue profiling
- (2019) Sanja Vickovic et al. NATURE METHODS
- ilastik: interactive machine learning for (bio)image analysis
- (2019) Stuart Berg et al. NATURE METHODS
- Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
- (2019) Chenglong Xia et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- ascend: R package for analysis of single-cell RNA-seq data
- (2019) Anne Senabouth et al. GigaScience
- In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription
- (2019) Amjad Askary et al. NATURE BIOTECHNOLOGY
- Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl
- (2019) Juan C. Caicedo et al. NATURE METHODS
- Mass Cytometry Imaging for the Study of Human Diseases—Applications and Data Analysis Strategies
- (2019) Heeva Baharlou et al. Frontiers in Immunology
- MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure
- (2019) Leeat Keren et al. Science Advances
- SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells
- (2019) Xiao Tan et al. BIOINFORMATICS
- NicheNet: modeling intercellular communication by linking ligands to target genes
- (2019) Robin Browaeys et al. NATURE METHODS
- A cancer rainbow mouse for visualizing the functional genomics of oncogenic clonal expansion
- (2019) Peter G. Boone et al. Nature Communications
- Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics
- (2018) Kelly Street et al. BMC GENOMICS
- Multiclonal Invasion in Breast Tumors Identified by Topographic Single Cell Sequencing
- (2018) Anna K. Casasent et al. CELL
- Placing RNA in context and space - methods for spatially resolved transcriptomics
- (2018) Carina Strell et al. FEBS Journal
- Multicolour lineage tracing reveals clonal dynamics of squamous carcinoma evolution from initiation to metastasis
- (2018) Melissa Q. Reeves et al. NATURE CELL BIOLOGY
- Identification of spatial expression trends in single-cell gene expression data
- (2018) Daniel Edsgärd et al. NATURE METHODS
- The emerging clinical relevance of genomics in cancer medicine
- (2018) Michael F. Berger et al. Nature Reviews Clinical Oncology
- Three-dimensional intact-tissue sequencing of single-cell transcriptional states
- (2018) Xiao Wang et al. SCIENCE
- Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
- (2018) Emelie Berglund et al. Nature Communications
- Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry
- (2018) Daniel Schulz et al. Cell Systems
- Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging
- (2018) Yury Goltsev et al. CELL
- A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging
- (2018) Leeat Keren et al. CELL
- RNA velocity of single cells
- (2018) Gioele La Manno et al. NATURE
- Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data
- (2018) Qian Zhu et al. NATURE BIOTECHNOLOGY
- Spatial organization of the somatosensory cortex revealed by osmFISH
- (2018) Simone Codeluppi et al. NATURE METHODS
- High-resolution clonal mapping of multi-organ metastasis in triple negative breast cancer
- (2018) Gloria V. Echeverria et al. Nature Communications
- Cellular Barcoding Identifies Clonal Substitution as a Hallmark of Local Recurrence in a Surgical Model of Head and Neck Squamous Cell Carcinoma
- (2018) Vincent Roh et al. Cell Reports
- Optical Barcoding for Single-Clone Tracking to Study Tumor Heterogeneity
- (2017) Malte Mohme et al. MOLECULAR THERAPY
- Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance
- (2017) Sydney M. Shaffer et al. NATURE
- Synthetic recording and in situ readout of lineage information in single cells
- (2017) Kirsten L. Frieda et al. NATURE
- Fate mapping of human glioblastoma reveals an invariant stem cell hierarchy
- (2017) Xiaoyang Lan et al. NATURE
- histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data
- (2017) Denis Schapiro et al. NATURE METHODS
- Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq
- (2017) Jun Chen et al. Nature Protocols
- Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq
- (2017) Chiara Medaglia et al. SCIENCE
- Multicolor lineage tracing reveals clonal architecture and dynamics in colon cancer
- (2017) Sebastian Lamprecht et al. Nature Communications
- Quantitative Multiplex Immunohistochemistry Reveals Myeloid-Inflamed Tumor-Immune Complexity Associated with Poor Prognosis
- (2017) Takahiro Tsujikawa et al. Cell Reports
- Genome evolution in ductal carcinomain situ: invasion of the clones
- (2016) Anna K Casasent et al. JOURNAL OF PATHOLOGY
- In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus
- (2016) Sheel Shah et al. NEURON
- Visualization and analysis of gene expression in tissue sections by spatial transcriptomics
- (2016) P. L. Stahl et al. SCIENCE
- Quantitative approaches for investigating the spatial context of gene expression
- (2016) Je H. Lee Wiley Interdisciplinary Reviews-Systems Biology and Medicine
- Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling
- (2016) Susanne Nichterwitz et al. Nature Communications
- Deep Learning Automates the Quantitative Analysis of Individual Cells in Live-Cell Imaging Experiments
- (2016) David A. Van Valen et al. PLoS Computational Biology
- Who discovered messenger RNA?
- (2015) Matthew Cobb CURRENT BIOLOGY
- Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis
- (2015) Tamily A. Weissman et al. GENETICS
- A Big Bang model of human colorectal tumor growth
- (2015) Andrea Sottoriva et al. NATURE GENETICS
- Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues
- (2015) Je Hyuk Lee et al. Nature Protocols
- Spatially resolved, highly multiplexed RNA profiling in single cells
- (2015) K. H. Chen et al. SCIENCE
- Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method
- (2015) Jia-Ren Lin et al. Nature Communications
- Brainbow: New Resources and Emerging Biological Applications for Multicolor Genetic Labeling and Analysis
- (2015) Tamily A. Weissman et al. GENETICS
- Multiplexed immunohistochemistry, imaging, and quantitation: A review, with an assessment of Tyramide signal amplification, multispectral imaging and multiplex analysis
- (2014) Edward C. Stack et al. METHODS
- Multiplexed ion beam imaging of human breast tumors
- (2014) Michael Angelo et al. NATURE MEDICINE
- Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue
- (2014) Ditte Lovatt et al. NATURE METHODS
- Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry
- (2014) Charlotte Giesen et al. NATURE METHODS
- Single-cell in situ RNA profiling by sequential hybridization
- (2014) Eric Lubeck et al. NATURE METHODS
- Highly Multiplexed Subcellular RNA Sequencing in Situ
- (2014) J. H. Lee et al. SCIENCE
- DNA barcoding reveals diverse growth kinetics of human breast tumour subclones in serially passaged xenografts
- (2014) Long V. Nguyen et al. Nature Communications
- In situ sequencing for RNA analysis in preserved tissue and cells
- (2013) Rongqin Ke et al. NATURE METHODS
- Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue
- (2013) M. J. Gerdes et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Error-correcting properties of the SOLiD Exact Call Chemistry
- (2012) Tim Massingham et al. BMC BIOINFORMATICS
- Single-cell systems biology by super-resolution imaging and combinatorial labeling
- (2012) Eric Lubeck et al. NATURE METHODS
- RGB marking with lentiviral vectors for multicolor clonal cell tracking
- (2012) Kristoffer Weber et al. Nature Protocols
- Lineage Tracing Reveals Lgr5+ Stem Cell Activity in Mouse Intestinal Adenomas
- (2012) A. G. Schepers et al. SCIENCE
- Brief Report: Intravital Imaging of Cancer Stem Cell Plasticity in Mammary Tumors
- (2012) Anoek Zomer et al. STEM CELLS
- A note from history: Landmarks in history of cancer, part 3
- (2011) Steven I. Hajdu CANCER
- Hallmarks of Cancer: The Next Generation
- (2011) Douglas Hanahan et al. CELL
- RNAscope
- (2011) Fay Wang et al. JOURNAL OF MOLECULAR DIAGNOSTICS
- RGB marking facilitates multicolor clonal cell tracking
- (2011) Kristoffer Weber et al. NATURE MEDICINE
- Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum
- (2011) S. C. Bendall et al. SCIENCE
- Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells
- (2010) Hugo J. Snippert et al. CELL
- In situ detection and genotyping of individual mRNA molecules
- (2010) Chatarina Larsson et al. NATURE METHODS
- A Multicolor Panel of Novel Lentiviral “Gene Ontology” (LeGO) Vectors for Functional Gene Analysis
- (2008) Kristoffer Weber et al. MOLECULAR THERAPY
- Imaging individual mRNA molecules using multiple singly labeled probes
- (2008) Arjun Raj et al. NATURE METHODS
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