Spatial omics and multiplexed imaging to explore cancer biology

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