Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencing

Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches

(2022) Martin Guilliams et al.   CELL

Squidpy: a scalable framework for spatial omics analysis

(2022) Giovanni Palla et al.   NATURE METHODS

Museum of spatial transcriptomics

(2022) Lambda Moses et al.   NATURE METHODS

Probabilistic harmonization and annotation of single‐cell transcriptomics data with deep generative models

(2021) Chenling Xu et al.   Molecular Systems Biology

Method of the Year: spatially resolved transcriptomics

(2021) Vivien Marx   NATURE METHODS

A machine learning method for the discovery of minimum marker gene combinations for cell type identification from single-cell RNA sequencing

(2021) Brian Aevermann et al.   GENOME RESEARCH

Joint cell segmentation and cell type annotation for spatial transcriptomics

(2021) Russell Littman et al.   Molecular Systems Biology

Spatial transcriptome profiling by MERFISH reveals fetal liver hematopoietic stem cell niche architecture

(2021) Yanfang Lu et al.   Cell Discovery

Spatially Resolved Transcriptomic Analysis of Acute Kidney Injury in a Female Murine Model

(2021) Eryn E. Dixon et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Cell segmentation in imaging-based spatial transcriptomics

(2021) Viktor Petukhov et al.   NATURE BIOTECHNOLOGY

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

(2021) Tommaso Biancalani et al.   NATURE METHODS

Efficient and precise single-cell reference atlas mapping with Symphony

(2021) Joyce B. Kang et al.   Nature Communications

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

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

Systematic comparison of single-cell and single-nucleus RNA-sequencing methods

(2020) Jiarui Ding et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Ageing hallmarks exhibit organ-specific temporal signatures

(2020) Nicholas Schaum et al.   NATURE

Multiplexed imaging of nucleome architectures in single cells of mammalian tissue

(2020) Miao Liu et al.   Nature Communications

Single Nucleus RNASeq Profiling of Mouse Lung: Reduced Dissociation Bias and Improved Rare Cell Type Detection Compared with Single Cell RNASeq

(2020) Jeffrey R. Koenitzer et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

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

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

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

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

Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression

(2019) Chenglong Xia et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2019) Ilya Korsunsky et al.   NATURE METHODS

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

(2018) Xiao Wang et al.   SCIENCE

Advantages of Single-Nucleus over Single-Cell RNA Sequencing of Adult Kidney: Rare Cell Types and Novel Cell States Revealed in Fibrosis

(2018) Haojia Wu et al.   JOURNAL OF THE AMERICAN SOCIETY OF NEPHROLOGY

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing

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

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

Validation of noise models for single-cell transcriptomics

(2014) Dominic Grün et al.   NATURE METHODS

Bayesian approach to single-cell differential expression analysis

(2014) Peter V Kharchenko et al.   NATURE METHODS

General properties of transcriptional time series in Escherichia coli

(2011) Lok-hang So et al.   NATURE GENETICS

Defining the Molecular Character of the Developing and Adult Kidney Podocyte

(2011) Eric W. Brunskill et al.   PLoS One