High-resolution alignment of single-cell and spatial transcriptomes with CytoSPACE

Cell2location maps fine-grained cell types in spatial transcriptomics

(2022) Vitalii Kleshchevnikov et al.   NATURE BIOTECHNOLOGY

Tissue-resident FOLR2+ macrophages associate with CD8+ T cell infiltration in human breast cancer

(2022) Rodrigo Nalio Ramos et al.   CELL

Spatial charting of single-cell transcriptomes in tissues

(2022) Runmin Wei et al.   NATURE BIOTECHNOLOGY

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

DEEPsc: A Deep Learning-Based Map Connecting Single-Cell Transcriptomics and Spatial Imaging Data

(2021) Floyd Maseda et al.   Frontiers in Genetics

Integration of spatial and single cell transcriptomics localizes epithelial-immune cross-talk in kidney injury

(2021) Ricardo Melo Ferreira et al.   JCI Insight

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

Spatially confined sub-tumor microenvironments in pancreatic cancer

(2021) Barbara T. Grünwald et al.   CELL

Atlas of clinically distinct cell states and ecosystems across human solid tumors

(2021) Bogdan A. Luca et al.   CELL

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

(2021) Tommaso Biancalani et al.   NATURE METHODS

Pan-cancer single-cell landscape of tumor-infiltrating T cells

(2021) Liangtao Zheng et al.   SCIENCE

The single-cell pathology landscape of breast cancer

(2020) Hartland W. Jackson et al.   NATURE

Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

Single-cell transcriptional diversity is a hallmark of developmental potential

(2020) Gunsagar S. Gulati et al.   SCIENCE

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

(2020) Hae-Ock Lee et al.   NATURE GENETICS

Inferring spatial and signaling relationships between cells from single cell transcriptomic data

(2020) Zixuan Cang et al.   Nature Communications

SpaGE: Spatial Gene Enhancement using scRNA-seq

(2020) Tamim Abdelaal et al.   NUCLEIC ACIDS RESEARCH

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

Analysis of the three dimensional structure of the kidney glomerulus capillary network

(2020) Mark Terasaki et al.   Scientific Reports

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

Determining cell type abundance and expression from bulk tissues with digital cytometry

(2019) Aaron M. Newman et al.   NATURE BIOTECHNOLOGY

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

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

Single-Cell Profiling Reveals Sex, Lineage, and Regional Diversity in the Mouse Kidney

(2019) Andrew Ransick et al.   DEVELOPMENTAL CELL

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Identification of spatial expression trends in single-cell gene expression data

(2018) Daniel Edsgärd et al.   NATURE METHODS

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

Spatially resolved transcriptomics enables dissection of genetic heterogeneity in stage III cutaneous malignant melanoma

(2018) Kim Thrane et al.   CANCER RESEARCH

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders 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

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

(2018) Keren Bahar Halpern et al.   NATURE BIOTECHNOLOGY

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

(2017) Keren Bahar Halpern et al.   NATURE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Single Mammalian Cells Compensate for Differences in Cellular Volume and DNA Copy Number through Independent Global Transcriptional Mechanisms

(2015) Olivia Padovan-Merhar et al.   MOLECULAR CELL