Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding

Spatial components of molecular tissue biology

(2022) Giovanni Palla et al.   NATURE BIOTECHNOLOGY

Cell2location maps fine-grained cell types in spatial transcriptomics

(2022) Vitalii Kleshchevnikov et al.   NATURE BIOTECHNOLOGY

Mechanistic flexibility of the retrosplenial cortex enables its contribution to spatial cognition

(2022) Martin Stacho et al.   TRENDS IN NEUROSCIENCES

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

(2022) Ao Chen et al.   CELL

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

(2022) Kangning Dong et al.   Nature Communications

High-plex imaging of RNA and proteins at subcellular resolution in fixed tissue by spatial molecular imaging

(2022) Shanshan He et al.   NATURE BIOTECHNOLOGY

Spatially resolved transcriptomics adds a new dimension to genomics

(2021) Ludvig Larsson et al.   NATURE METHODS

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

Semi-supervised adversarial neural networks for single-cell classification

(2021) Jacob C. Kimmel et al.   GENOME RESEARCH

Robust decomposition of cell type mixtures in spatial transcriptomics

(2021) Dylan M. Cable et al.   NATURE BIOTECHNOLOGY

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

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

SPOTlight: seeded NMF regression to deconvolute spatial transcriptomics spots with single-cell transcriptomes

(2021) Marc Elosua-Bayes et al.   NUCLEIC ACIDS RESEARCH

A taxonomy of transcriptomic cell types across the isocortex and hippocampal formation

(2021) Zizhen Yao et al.   CELL

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

(2021) Akira Cortal et al.   NATURE BIOTECHNOLOGY

Computational principles and challenges in single-cell data integration

(2021) Ricard Argelaguet et al.   NATURE BIOTECHNOLOGY

Hotspot identifies informative gene modules across modalities of single-cell genomics

(2021) David DeTomaso et al.   Cell Systems

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 omics and multiplexed imaging to explore cancer biology

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

The triumphs and limitations of computational methods for scRNA-seq

(2021) Peter V. Kharchenko   NATURE METHODS

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

(2021) Zoe A. Clarke et al.   Nature Protocols

Integrating single-cell and spatial transcriptomics to elucidate intercellular tissue dynamics

(2021) Sophia K. Longo et al.   NATURE REVIEWS GENETICS

Dynamic activity of interpeduncular nucleus GABAergic neurons controls expression of nicotine withdrawal in male mice

(2021) Paul M. Klenowski et al.   NEUROPSYCHOPHARMACOLOGY

scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network

(2021) Xin Shao et al.   NUCLEIC ACIDS RESEARCH

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

(2021) Zizhen Yao et al.   NATURE

A multimodal cell census and atlas of the mammalian primary motor cortex

(2021) et al.   NATURE

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

(2021) Meng Zhang et al.   NATURE

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

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

(2021) Tommaso Biancalani et al.   NATURE METHODS

The dorsal raphe nucleus in the control of energy balance

(2021) Varun M. Bhave et al.   TRENDS IN NEUROSCIENCES

Dissecting mammalian spermatogenesis using spatial transcriptomics

(2021) Haiqi Chen et al.   Cell Reports

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

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

(2020) Quanxin Wang et al.   CELL

The retrosplenial cortex and long-term spatial memory: from the cell to the network

(2020) Michal M Milczarek et al.   Current Opinion in Behavioral Sciences

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders

(2020) Devika Agarwal et al.   Nature Communications

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

Common cell type nomenclature for the mammalian brain

(2020) Jeremy A Miller et al.   eLife

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

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

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

A Comprehensive Roadmap of Murine Spermatogenesis Defined by Single-Cell RNA-Seq

(2018) Christopher Daniel Green et al.   DEVELOPMENTAL CELL

The adult human testis transcriptional cell atlas

(2018) Jingtao Guo et al.   CELL RESEARCH

Shared and distinct transcriptomic cell types across neocortical areas

(2018) Bosiljka Tasic et al.   NATURE

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

An interactive framework for whole-brain maps at cellular resolution

(2017) Daniel Fürth et al.   NATURE NEUROSCIENCE

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Adult mouse cortical cell taxonomy revealed by single cell transcriptomics

(2016) Bosiljka Tasic et al.   NATURE NEUROSCIENCE

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

(2016) P. L. Stahl et al.   SCIENCE

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS