SODB facilitates comprehensive exploration of spatial omics data

Transition to invasive breast cancer is associated with progressive changes in the structure and composition of tumor stroma

(2022) Tyler Risom et al.   CELL

Seven technologies to watch in 2022

(2022) Michael Eisenstein   NATURE

Spatial components of molecular tissue biology

(2022) Giovanni Palla et al.   NATURE BIOTECHNOLOGY

Squidpy: a scalable framework for spatial omics analysis

(2022) Giovanni Palla et al.   NATURE METHODS

SM-Omics is an automated platform for high-throughput spatial multi-omics

(2022) S. Vickovic et al.   Nature Communications

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

(2022) Ao Chen et al.   CELL

Spatiotemporal mapping of gene expression landscapes and developmental trajectories during zebrafish embryogenesis

(2022) Chang Liu et al.   DEVELOPMENTAL CELL

High-resolution 3D spatiotemporal transcriptomic maps of developing Drosophila embryos and larvae

(2022) Mingyue Wang et al.   DEVELOPMENTAL CELL

Breast tumor microenvironment structures are associated with genomic features and clinical outcome

(2022) Esther Danenberg et al.   NATURE GENETICS

Museum of spatial transcriptomics

(2022) Lambda Moses et al.   NATURE METHODS

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

(2022) Bin Li et al.   NATURE METHODS

Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder

(2022) Kangning Dong et al.   Nature Communications

High-resolution Slide-seqV2 spatial transcriptomics enables discovery of disease-specific cell neighborhoods and pathways

(2022) Jamie L. Marshall et al.   iScience

Deciphering tissue structure and function using spatial transcriptomics

(2022) Benjamin L. Walker et al.   Communications Biology

The emerging landscape of spatial profiling technologies

(2022) Jeffrey R. Moffitt et al.   NATURE REVIEWS GENETICS

Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

(2022) Rongxin Fang et al.   SCIENCE

Identifying multicellular spatiotemporal organization of cells with SpaceFlow

(2022) Honglei Ren et al.   Nature Communications

Spatial transcriptome unveils a discontinuous inflammatory pattern in proficient mismatch repair colorectal adenocarcinoma

(2022) Rongxin Zhang et al.   Fundamental Research

Spatiotemporal analysis of human intestinal development at single-cell resolution

(2021) David Fawkner-Corbett et al.   CELL

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics

(2021) Michael J. Taylor et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex

(2021) Kristen R. Maynard et al.   NATURE NEUROSCIENCE

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis

(2021) Madhav Mantri et al.   Nature Communications

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

Integration of spatial and single-cell transcriptomic data elucidates mouse organogenesis

(2021) T. Lohoff et al.   NATURE BIOTECHNOLOGY

A single-cell and spatially resolved atlas of human breast cancers

(2021) Sunny Z. Wu et al.   NATURE GENETICS

Spatial omics and multiplexed imaging to explore cancer biology

(2021) Sabrina M. Lewis et al.   NATURE METHODS

SpaceM reveals metabolic states of single cells

(2021) Luca Rappez et al.   NATURE METHODS

Embryo-scale, single-cell spatial transcriptomics

(2021) Sanjay R. Srivatsan et al.   SCIENCE

Peak learning of mass spectrometry imaging data using artificial neural networks

(2021) Walid M. Abdelmoula et al.   Nature Communications

EASI-FISH for thick tissue defines lateral hypothalamus spatio-molecular organization

(2021) Yuhan Wang et al.   CELL

Advances in spatial transcriptomic data analysis

(2021) Ruben Dries et al.   GENOME RESEARCH

Spatial genomics enables multi-modal study of clonal heterogeneity in tissues

(2021) Tongtong Zhao et al.   NATURE

Spatially resolved cell atlas of the mouse primary motor cortex by MERFISH

(2021) Meng Zhang et al.   NATURE

SEAM is a spatial single nuclear metabolomics method for dissecting tissue microenvironment

(2021) Zhiyuan Yuan et al.   NATURE METHODS

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

(2021) John W. Hickey et al.   NATURE METHODS

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

(2021) Jian Hu et al.   NATURE METHODS

Joint single-cell measurements of nuclear proteins and RNA in vivo

(2021) Hattie Chung et al.   NATURE METHODS

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

(2021) Tommaso Biancalani et al.   NATURE METHODS

Decoding molecular and cellular heterogeneity of mouse nucleus accumbens

(2021) Renchao Chen et al.   NATURE NEUROSCIENCE

Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver

(2021) Franziska Hildebrandt et al.   Nature Communications

Spatially resolved transcriptomics reveals the architecture of the tumor-microenvironment interface

(2021) Miranda V. Hunter et al.   Nature Communications

Dissecting mammalian spermatogenesis using spatial transcriptomics

(2021) Haiqi Chen et al.   Cell Reports

Comprehensive analysis of spatial architecture in primary liver cancer

(2021) Rui Wu et al.   Science Advances

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas

(2020) Quanxin Wang et al.   CELL

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt et al.   NATURE BIOTECHNOLOGY

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma

(2020) Andrew L. Ji et al.   CELL

Spatial Transcriptomics and In Situ Sequencing to Study Alzheimer’s Disease

(2020) Wei-Ting Chen et al.   CELL

Highly specific multiplexed RNA imaging in tissues with split-FISH

(2020) Jolene Jie Lin Goh et al.   NATURE METHODS

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

Single-cell metabolic profiling of human cytotoxic T cells

(2020) Felix J. Hartmann et al.   NATURE BIOTECHNOLOGY

High-Spatial-Resolution Multi-Omics Sequencing via Deterministic Barcoding in Tissue

(2020) Yang Liu et al.   CELL

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

(2020) Robert R. Stickels et al.   NATURE BIOTECHNOLOGY

Spatial proteomics: a powerful discovery tool for cell biology

(2019) Emma Lundberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

A Map of Human Type 1 Diabetes Progression by Imaging Mass Cytometry

(2019) Nicolas Damond et al.   Cell Metabolism

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

MIBI-TOF: A multiplexed imaging platform relates cellular phenotypes and tissue structure

(2019) Leeat Keren et al.   Science Advances

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

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

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

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

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Spatially resolved metabolomics to discover tumor-associated metabolic alterations

(2018) Chenglong Sun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

The 3D OrbiSIMS—label-free metabolic imaging with subcellular lateral resolution and high mass-resolving power

(2017) Melissa K Passarelli et al.   NATURE METHODS

FDR-controlled metabolite annotation for high-resolution imaging mass spectrometry

(2016) Andrew Palmer et al.   NATURE METHODS

High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization

(2016) Jeffrey R. Moffitt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics

(2016) P. L. Stahl et al.   SCIENCE

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS