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

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

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

A joint deep learning model enables simultaneous batch effect correction, denoising, and clustering in single-cell transcriptomics

(2021) Justin Lakkis et al.   GENOME RESEARCH

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

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

Deep learning enables accurate clustering with batch effect removal in single-cell RNA-seq analysis

(2020) Xiangjie Li et al.   Nature Communications

KRT17 Functions as a Tumor Promoter and Regulates Proliferation, Migration and Invasion in Pancreatic Cancer via mTOR/S6k1 Pathway

(2020) Ding Li et al.   Cancer Management and Research

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

(2020) Wei-Ting Chen et al.   CELL

Spage2vec: Unsupervised representation of localized spatial gene expression signatures

(2020) Gabriele Partel et al.   FEBS Journal

SpaGE: Spatial Gene Enhancement using scRNA-seq

(2020) Tamim Abdelaal et al.   NUCLEIC ACIDS RESEARCH

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

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

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

Identification of Matrix Metalloproteinase 11 as a Prognostic Biomarker in Pancreatic Cancer

(2019) JUNGWHOI LEE et al.   ANTICANCER RESEARCH

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

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Identification of spatially associated subpopulations by combining scRNAseq and sequential fluorescence in situ hybridization data

(2018) Qian Zhu et al.   NATURE BIOTECHNOLOGY

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

(2016) Ye Zhang et al.   NEURON

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

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

Fast unfolding of communities in large networks

(2008) Vincent D Blondel et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT