Alignment and integration of spatial transcriptomics data

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

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

Spatial transcriptomics at subspot resolution with BayesSpace

(2021) Edward Zhao et al.   NATURE BIOTECHNOLOGY

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

(2021) Tommaso Biancalani et al.   NATURE METHODS

Spatial deconvolution of HER2-positive breast cancer delineates tumor-associated cell type interactions

(2021) Alma Andersson et al.   Nature Communications

netNMF-sc: leveraging gene–gene interactions for imputation and dimensionality reduction in single-cell expression analysis

(2020) Rebecca Elyanow et al.   GENOME RESEARCH

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

(2020) Reuben Moncada et al.   NATURE BIOTECHNOLOGY

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

(2020) Zixuan Cang et al.   Nature Communications

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

BATMAN: Fast and Accurate Integration of Single-Cell RNA-Seq Datasets via Minimum-Weight Matching

(2020) Igor Mandric et al.   iScience

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

(2020) Andrew L. Ji et al.   CELL

STARCH: Copy number and clone inference from spatial transcriptomics data

(2020) Rebecca Elyanow et al.   PHYSICAL BIOLOGY

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

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

McImpute: Matrix Completion Based Imputation for Single Cell RNA-seq Data

(2019) Aanchal Mongia et al.   Frontiers in Genetics

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Probabilistic Count Matrix Factorization for Single Cell Expression Data Analysis

(2019) G Durif et al.   BIOINFORMATICS

Efficient integration of heterogeneous single-cell transcriptomes using Scanorama

(2019) Brian Hie et al.   NATURE BIOTECHNOLOGY

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Modeling Spatial Correlation of Transcripts with Application to Developing Pancreas

(2019) Ruishan Liu et al.   Scientific Reports

Modeling Cell-Cell Interactions from Spatial Molecular Data with Spatial Variance Component Analysis

(2019) Damien Arnol et al.   Cell Reports

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

(2018) Laleh Haghverdi et al.   NATURE BIOTECHNOLOGY

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

(2018) Emelie Berglund et al.   Nature Communications

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics

(2018) Anna Lundmark et al.   Scientific Reports

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue

(2017) Michaela Asp et al.   Scientific Reports

Detecting heterogeneity in single-cell RNA-Seq data by non-negative matrix factorization

(2017) Xun Zhu et al.   PeerJ

Robust classification of single-cell transcriptome data by nonnegative matrix factorization

(2016) Chunxuan Shao et al.   BIOINFORMATICS

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

(2016) P. L. Stahl et al.   SCIENCE