Publications
T-cell dysfunction in the glioblastoma microenvironment is mediated by myeloid cells releasing interleukin-10
Nature Communications, 2022
Technology:
IMC, Visium
Species:
Human
Tissue:
Brain
Disease:
Glioblastoma
Breast tumor microenvironment structures are associated with genomic features and clinical outcome
Nature Genetics, 2022
Technology:
IMC
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy
Science Immunology, 2022
Technology:
IMC
Species:
Human
Tissue:
Skin
Disease:
Melanoma
Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma
Cell, 2022
Technology:
MIBI
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Reproducible, high-dimensional imaging in archival human tissue by multiplexed ion beam imaging by time-of-flight (MIBI-TOF)
Laboratory Investigation, 2022
Technology:
MIBI
Species:
Human
Tissue:
Mixed
Disease:
Cancer
Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis
Developmental Cell, 2022
Technology:
Stereo-seq
Species:
Zebra Fish
Tissue:
Embryo
Disease:
Normal
The single-cell stereo-seq reveals region-specific cell subtypes and transcriptome profiling in Arabidopsis leaves
Developmental Cell, 2022
Technology:
Stereo-seq
Species:
Arabidopsis Leaves
Tissue:
Plant
Disease:
Normal
High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae
Developmental Cell, 2022
Technology:
Stereo-seq
Species:
Fruit Fly
Tissue:
Embryo
Disease:
Normal
MEK inhibition suppresses metastatic progression of <i>KRAS</i> ‐mutated gastric cancer
Cancer Science, 2022
Technology:
Visium
Species:
Mouse
Tissue:
Stomach
Disease:
Gastric Cancer
Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches
Cell, 2022
Technology:
Visium
Species:
Mouse, Human
Tissue:
Liver
Disease:
Obesity
Spatial CRISPR genomics identifies regulators of the tumor microenvironment
Cell, 2022
Technology:
Visium
Species:
Mouse
Tissue:
Lung
Disease:
Lung Cancer
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics
Nature Neuroscience, 2022
Technology:
Visium
Species:
Mouse
Tissue:
Brain
Disease:
Normal
Human distal lung maps and lineage hierarchies reveal a bipotent progenitor
Nature, 2022
Technology:
Visium
Species:
Human
Tissue:
Lung
Disease:
Normal
Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays
Cell, 2022
Technology:
Stereo-seq
Species:
Mouse
Tissue:
Embryo
Disease:
Normal
The spatial transcriptomic landscape of the healing mouse intestine following damage
Nature Communications, 2022
Technology:
Visium
Species:
Mouse
Tissue:
Colon
Disease:
Normal
Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH
Science, 2022
Technology:
MERFISH
Species:
Mouse, Human
Tissue:
Cortex
Disease:
Normal
The spatiotemporal program of zonal liver regeneration following acute injury
Cell Stem Cell, 2022
Technology:
Visium
Species:
Mouse
Tissue:
Liver
Disease:
Acute Injury
Spatial profiling of chromatin accessibility in mouse and human tissues
Nature, 2022
Technology:
spatial-ATAC-seq
Species:
Human, Mouse
Tissue:
Tonsil, Brain, Embryo
Disease:
Normal
An N-Cadherin 2 expressing epithelial cell subpopulation predicts response to surgery, chemotherapy and immunotherapy in bladder cancer
Nature Communications, 2021
Technology:
CODEX
Species:
Human
Tissue:
Bladder
Disease:
Bladder Cancer
CODEX multiplexed tissue imaging with DNA-conjugated antibodies
Nature Protocols, 2021
Technology:
CODEX
Species:
Human
Tissue:
Tonsil
Disease:
Normal
Imaging mass cytometry for high-dimensional tissue profiling in the eye
BMC Ophthalmology, 2021
Technology:
IMC
Species:
Human
Tissue:
Eye
Disease:
Conjunctival Melanoma
Characterisation of tumour microenvironment remodelling following oncogene inhibition in preclinical studies with imaging mass cytometry
Nature Communications, 2021
Technology:
IMC
Species:
Mouse
Tissue:
Lung
Disease:
Lung Cancer
The spatial landscape of lung pathology during COVID-19 progression
Nature, 2021
Technology:
IMC
Species:
Human
Tissue:
Lung
Disease:
COVID-19
Three-dimensional imaging mass cytometry for highly multiplexed molecular and cellular mapping of tissues and the tumor microenvironment
Nature Cancer, 2021
Technology:
IMC
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH
Nature, 2021
Technology:
MERFISH
Species:
Mouse
Tissue:
Motor Cortex
Disease:
Normal
Multiplexed imaging analysis of the tumor-immune microenvironment reveals predictors of outcome in triple-negative breast cancer
Communications Biology, 2021
Technology:
MIBI
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Embryo-scale, single-cell spatial transcriptomics
Science, 2021
Technology:
sci-Space
Species:
Mouse
Tissue:
Embryo
Disease:
Normal
Microscopic examination of spatial transcriptome using Seq-Scope
Cell, 2021
Technology:
seq-scope
Species:
Mouse
Tissue:
Liver, Colon
Disease:
Normal
Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis
Nature Biotechnology, 2021
Technology:
seqFISH
Species:
Mouse
Tissue:
Embryo
Disease:
Normal
Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin
Cell Metabolism, 2021
Technology:
Visium
Species:
Human
Tissue:
Skin
Disease:
Obesity
Spatiotemporal analysis of human intestinal development at single-cell resolution
Cell, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Intestine
Disease:
Normal
The spatial RNA integrity number assay for in situ evaluation of transcriptome quality
Communications Biology, 2021
Technology:
Visium
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Single‐Cell, Single‐Nucleus, and Spatial RNA Sequencing of the Human Liver Identifies Cholangiocyte and Mesenchymal Heterogeneity
Hepatology Communications, 2021
Technology:
Visium
Species:
Human
Tissue:
Liver
Disease:
Normal
Integration of spatial and single-cell transcriptomics localizes epithelial cell–immune cross-talk in kidney injury
JCI Insight, 2021
Technology:
Visium
Species:
Human, Mouse
Tissue:
Kidney
Disease:
Kidney Injury
Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model
Journal of the American Society of Nephrology, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Kidney
Disease:
Kidney Injury
Super-resolved spatial transcriptomics by deep data fusion
Nature Biotechnology, 2021
Technology:
Visium
Species:
Human
Tissue:
Skin, Ileum
Disease:
Squamous cell carcinoma, Normal
Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions
Nature Communications, 2021
Technology:
Visium
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain
Nature Communications, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Postnatal Brain
Disease:
Normal
Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface
Nature Communications, 2021
Technology:
Visium
Species:
Zebra Fish
Tissue:
Whole Body (Transverse)
Disease:
Normal
A coordinated progression of progenitor cell states initiates urinary tract development
Nature Communications, 2021
Technology:
Visium
Species:
Human
Tissue:
Kidney
Disease:
Normal
Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver
Nature Communications, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Liver
Disease:
Normal
A single-cell and spatially resolved atlas of human breast cancers
Nature Genetics, 2021
Technology:
Visium
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Lineage recording in human cerebral organoids
Nature Methods, 2021
Technology:
Visium
Species:
Human
Tissue:
Organoid
Disease:
Normal
Neuroinflammatory astrocyte subtypes in the mouse brain
Nature Neuroscience, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Brain
Disease:
Inflammatory
Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex
Nature Neuroscience, 2021
Technology:
Visium
Species:
Human
Tissue:
Dorsolateral prefrontal cortex
Disease:
Normal
Dietary palmitic acid promotes a prometastatic memory via Schwann cells
Nature, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Brain
Disease:
Cancer
Spatial transcriptomics reveals a role for sensory nerves in preserving cranial suture patency through modulation of BMP/TGF-β signaling
Proceedings of the National Academy of Sciences, 2021
Technology:
Visium
Species:
Mouse
Tissue:
Bone
Disease:
Normal
Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front
Cell, 2020
Technology:
CODEX
Species:
Human
Tissue:
Colon
Disease:
Colorectal Cancer
HSF1 phase transition mediates stress adaptation and cell fate decisions
Nature Cell Biology, 2020
Technology:
CyCIF
Species:
Human
Tissue:
Colon
Disease:
Colon Cancer
High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue
Cell, 2020
Technology:
DBiT-seq
Species:
Mouse
Tissue:
Embryo
Disease:
Normal
Imaging mass cytometry and multiplatform genomics define the phenogenomic landscape of breast cancer
Nature Cancer, 2020
Technology:
IMC
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
The single-cell pathology landscape of breast cancer
Nature, 2020
Technology:
IMC
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Single-cell metabolic profiling of human cytotoxic T cells
Nature Biotechnology, 2020
Technology:
MIBI
Species:
Human
Tissue:
Colon
Disease:
Colon Cancer
Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease
Cell, 2020
Technology:
Visium
Species:
Mouse
Tissue:
Brain
Disease:
Alzheimer
Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma
Cell, 2020
Technology:
Visium
Species:
Human
Tissue:
Skin
Disease:
Squamous Cell Carcinoma
Spatial Transcriptomics Reveals Genes Associated with Dysregulated Mitochondrial Functions and Stress Signaling in Alzheimer Disease
iScience, 2020
Technology:
Visium
Species:
Mouse
Tissue:
Hippocampus, Olfactory Bulb
Disease:
Alzheimer
Integrating spatial gene expression and breast tumour morphology via deep learning
Nature Biomedical Engineering, 2020
Technology:
Visium
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas
Nature Biotechnology, 2020
Technology:
Visium
Species:
Human
Tissue:
Pancreas
Disease:
Pancreatic Cancer
Molecular atlas of the adult mouse brain
Science Advances, 2020
Technology:
Visium
Species:
Mouse
Tissue:
Brain
Disease:
Normal
Qualifying antibodies for image-based immune profiling and multiplexed tissue imaging
Nature Protocols, 2019
Technology:
CyCIF
Species:
Human
Tissue:
Tonsil, Mixed
Disease:
Normal, Lung Cancer
A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry
Cell Metabolism, 2019
Technology:
IMC
Species:
Human
Tissue:
Pancreas
Disease:
Diabetes
Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression
Proceedings of the National Academy of Sciences, 2019
Technology:
MERFISH
Species:
Human
Tissue:
U2-Cell
Disease:
Osteosarcoma
Probabilistic cell typing enables fine mapping of closely related cell types in situ
Nature Methods, 2019
Technology:
pciSeq
Species:
Mouse
Tissue:
Hippocampal
Disease:
Normal
Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+
Nature, 2019
Technology:
seqFISH
Species:
Mouse
Tissue:
Olfactory Bulb, Cortex
Disease:
Normal
Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution
Science, 2019
Technology:
Slide-seq
Species:
Mouse
Tissue:
Cerebellum
Disease:
Normal
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart
Cell, 2019
Technology:
Visium
Species:
Human
Tissue:
Heart
Disease:
Normal
Profiling of the plasma proteome across different stages of human heart failure
Nature Communications, 2019
Technology:
Visium
Species:
Human
Tissue:
Heart
Disease:
Normal
Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis
Science, 2019
Technology:
Visium
Species:
Human, Mouse
Tissue:
Spinal Cord
Disease:
Amyotrophic lateral sclerosis
Exploring inflammatory signatures in arthritic joint biopsies with Spatial Transcriptomics
Scientific Reports, 2019
Technology:
Visium
Species:
Human
Tissue:
Joint
Disease:
Arthritic joint
Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging
Cell, 2018
Technology:
CODEX
Species:
Mouse
Tissue:
Spleen
Disease:
Systemic Autoimmune
Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes
eLife, 2018
Technology:
CyCIF
Species:
Human
Tissue:
Pancreas, Mixed, Brain
Disease:
Pancreatic Cancer, Cancer, Glioblastoma
Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region
Science, 2018
Technology:
MERFISH
Species:
Mouse
Tissue:
Hypothalamic Preoptic
Disease:
Normal
A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging
Cell, 2018
Technology:
MIBI
Species:
Human
Tissue:
Breast
Disease:
Breast Cancer
Spatial organization of the somatosensory cortex revealed by osmFISH
Nature Methods, 2018
Technology:
osmFISH
Species:
Mouse
Tissue:
Somatosensory cortex
Disease:
Normal
Three-dimensional intact-tissue sequencing of single-cell transcriptional states
Science, 2018
Technology:
STARmap
Species:
Mouse
Tissue:
Medial Prefrontal Cortex, Visual Cortex
Disease:
Normal
Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage III cutaneous malignant melanoma
Cancer Research, 2018
Technology:
Visium
Species:
Human
Tissue:
Lymph Node
Disease:
Cutaneous malignant melanoma
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity
Nature Communications, 2018
Technology:
Visium
Species:
Human
Tissue:
Prostate
Disease:
Prostate Cancer
Spatial detection of fetal marker genes expressed at low level in adult human heart tissue
Scientific Reports, 2017
Technology:
Visium
Species:
Human
Tissue:
Heart
Disease:
Normal
In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus
Neuron, 2016
Technology:
seqFISH
Species:
Mouse
Tissue:
Hippocampus
Disease:
Normal