Spatial components of molecular tissue biology

Spatially resolved transcriptomics in neuroscience

(2021) Jennie L. Close et al.   NATURE METHODS

Spatially resolved single-cell genomics and transcriptomics by imaging

(2021) Xiaowei Zhuang   NATURE METHODS

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

Multi-domain translation between single-cell imaging and sequencing data using autoencoders

(2021) Karren Dai Yang et al.   Nature Communications

sepal: Identifying Transcript Profiles with Spatial Patterns by Diffusion-based Modeling

(2021) Alma Anderson et al.   BIOINFORMATICS

Resolving organoid brain region identities by mapping single-cell genomic data to reference atlases

(2021) Jonas Simon Fleck et al.   Cell Stem Cell

Spatiotemporal dissection of the cell cycle with single-cell proteogenomics

(2021) Diana Mahdessian et al.   NATURE

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

BARcode DEmixing through Non-negative Spatial Regression (BarDensr)

(2021) Shuonan Chen et al.   PLoS Computational Biology

Single-cell transcriptomic analysis of mIHC images via antigen mapping

(2021) Kiya W. Govek et al.   Science Advances

Iterative single-cell multi-omic integration using online learning

(2021) Chao Gao et al.   NATURE BIOTECHNOLOGY

Spatial tissue profiling by imaging-free molecular tomography

(2021) Halima Hannah Schede et al.   NATURE BIOTECHNOLOGY

Compressed sensing for highly efficient imaging transcriptomics

(2021) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Computational principles and challenges in single-cell data integration

(2021) Ricard Argelaguet et al.   NATURE BIOTECHNOLOGY

Imaging cell lineage with a synthetic digital recording system

(2021) Ke-Huan K. Chow et al.   SCIENCE

Democratising deep learning for microscopy with ZeroCostDL4Mic

(2021) Lucas von Chamier et al.   Nature Communications

MAUI (MBI Analysis User Interface)—An image processing pipeline for Multiplexed Mass Based Imaging

(2021) Alex Baranski et al.   PLoS Computational Biology

Imputation of spatially-resolved transcriptomes by graph-regularized tensor completion

(2021) Zhuliu Li et al.   PLoS Computational Biology

sparrpowR: a flexible R package to estimate statistical power to identify spatial clustering of two groups and its application

(2021) Ian D. Buller et al.   International Journal of Health Geographics

SOMDE: A scalable method for identifying spatially variable genes with self-organizing map

(2021) Minsheng Hao et al.   BIOINFORMATICS

Non-parametric modelling of temporal and spatial counts data from RNA-seq experiments

(2021) Nuha BinTayyash et al.   BIOINFORMATICS

A convolutional neural network for common coordinate registration of high-resolution histology images

(2021) Aidan C Daly et al.   BIOINFORMATICS

Bayesian modeling of spatial molecular profiling data via Gaussian process

(2021) Qiwei Li et al.   BIOINFORMATICS

stPlus: a reference-based method for the accurate enhancement of spatial transcriptomics

(2021) Chen Shengquan et al.   BIOINFORMATICS

CoSTA: unsupervised convolutional neural network learning for spatial transcriptomics analysis

(2021) Yang Xu et al.   BMC BIOINFORMATICS

Spatially organized multicellular immune hubs in human colorectal cancer

(2021) Karin Pelka et al.   CELL

Likelihood-based deconvolution of bulk gene expression data using single-cell references

(2021) Dan D. Erdmann-Pham et al.   GENOME RESEARCH

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

Cell segmentation-free inference of cell types from in situ transcriptomics data

(2021) Jeongbin Park et al.   Nature Communications

LineageOT is a unified framework for lineage tracing and trajectory inference

(2021) Aden Forrow et al.   Nature Communications

Model-based prediction of spatial gene expression via generative linear mapping

(2021) Yasushi Okochi et al.   Nature Communications

AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution

(2021) Hananeh Aliee et al.   Cell Systems

Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data

(2021) Michael J. Geuenich et al.   Cell Systems

Clustering spatial transcriptomics data

(2021) Haotian Teng et al.   BIOINFORMATICS

A multi-scale map of cell structure fusing protein images and interactions

(2021) Yue Qin et al.   NATURE

Whole-cell organelle segmentation in volume electron microscopy

(2021) Larissa Heinrich et al.   NATURE

Single-cell transcriptomic characterization of a gastrulating human embryo

(2021) Richard C. V. Tyser et al.   NATURE

Super-resolved spatial transcriptomics by deep data fusion

(2021) Ludvig Bergenstråhle et al.   NATURE BIOTECHNOLOGY

Cell segmentation in imaging-based spatial transcriptomics

(2021) Viktor Petukhov et al.   NATURE BIOTECHNOLOGY

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

MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging

(2021) Denis Schapiro et al.   NATURE METHODS

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

(2021) Tommaso Biancalani et al.   NATURE METHODS

ClusterMap for multi-scale clustering analysis of spatial gene expression

(2021) Yichun He et al.   Nature Communications

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

(2021) Alma Andersson et al.   Nature Communications

scPower accelerates and optimizes the design of multi-sample single cell transcriptomic studies

(2021) Katharina T. Schmid et al.   Nature Communications

Hybrid Clustering of Single-Cell Gene Expression and Spatial Information via Integrated NMF and K-Means

(2021) Sooyoun Oh et al.   Frontiers in Genetics

Systematic genetics and single‐cell imaging reveal widespread morphological pleiotropy and cell‐to‐cell variability

(2020) Mojca Mattiazzi Usaj et al.   Molecular Systems Biology

Single-cell and spatial transcriptomics reveal somitogenesis in gastruloids

(2020) Susanne C. van den Brink et al.   NATURE

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

CellPhoneDB: inferring cell–cell communication from combined expression of multi-subunit ligand–receptor complexes

(2020) Mirjana Efremova et al.   Nature Protocols

Cell Atlas technologies and insights into tissue architecture

(2020) Anna Wilbrey-Clark et al.   BIOCHEMICAL JOURNAL

Spatially Resolved Transcriptomes—Next Generation Tools for Tissue Exploration

(2020) Michaela Asp et al.   BIOESSAYS

TissUUmaps: Interactive visualization of large-scale spatial gene expression and tissue morphology data

(2020) Leslie Solorzano et al.   BIOINFORMATICS

SpatialCPie: an R/Bioconductor package for spatial transcriptomics cluster evaluation

(2020) Joseph Bergenstråhle et al.   BMC BIOINFORMATICS

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

(2020) Zixuan Cang et al.   Nature Communications

Deep semantic segmentation of natural and medical images: a review

(2020) Saeid Asgari Taghanaki et al.   ARTIFICIAL INTELLIGENCE REVIEW

Seamless integration of image and molecular analysis for spatial transcriptomics workflows

(2020) Joseph Bergenstråhle et al.   BMC GENOMICS

Spatial molecular profiling: platforms, applications and analysis tools

(2020) Minzhe Zhang et al.   BRIEFINGS IN BIOINFORMATICS

Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front

(2020) Christian M. Schürch et al.   CELL

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

(2020) Wei-Ting Chen et al.   CELL

Single-cell genomics and spatial transcriptomics: discovery of novel cell states and cellular interactions in liver physiology and disease biology

(2020) Antonio Saviano et al.   JOURNAL OF HEPATOLOGY

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

(2020)   NATURE

Generalizing RNA velocity to transient cell states through dynamical modeling

(2020) Volker Bergen et al.   NATURE BIOTECHNOLOGY

Integrating spatial gene expression and breast tumour morphology via deep learning

(2020) Bryan He et al.   Nature Biomedical Engineering

Identifying signaling genes in spatial single cell expression data

(2020) Dongshunyi Li et al.   BIOINFORMATICS

Spage2vec: Unsupervised representation of localized spatial gene expression signatures

(2020) Gabriele Partel et al.   FEBS Journal

Enhancing scientific discoveries in molecular biology with deep generative models

(2020) Romain Lopez et al.   Molecular Systems Biology

Single-cell metabolic profiling of human cytotoxic T cells

(2020) Felix J. Hartmann et al.   NATURE BIOTECHNOLOGY

SpaGE: Spatial Gene Enhancement using scRNA-seq

(2020) Tamim Abdelaal et al.   NUCLEIC ACIDS RESEARCH

Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography

(2020) Alma Andersson et al.   Communications Biology

DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence

(2020) Qianqian Song et al.   BRIEFINGS IN BIOINFORMATICS

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

Cellpose: a generalist algorithm for cellular segmentation

(2020) Carsen Stringer et al.   NATURE METHODS

Single-cell RNA-seq denoising using a deep count autoencoder

(2019) Gökcen Eraslan et al.   Nature Communications

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

Not-so-supervised: a survey of semi-supervised, multi-instance, and transfer learning in medical image analysis

(2019) Veronika Cheplygina et al.   MEDICAL IMAGE ANALYSIS

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming

(2019) Geoffrey Schiebinger et al.   CELL

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics

(2019) Leif S. Ludwig et al.   CELL

Inferring population dynamics from single-cell RNA-sequencing time series data

(2019) David S. Fischer et al.   NATURE BIOTECHNOLOGY

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

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

Deep learning for cellular image analysis

(2019) Erick Moen et al.   NATURE METHODS

Deep learning: new computational modelling techniques for genomics

(2019) Gökcen Eraslan et al.   NATURE REVIEWS GENETICS

Spatial transcriptomics coming of age

(2019) Darren J. Burgess   NATURE REVIEWS GENETICS

Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization

(2019) Chong Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis

(2019) Christopher S. Smillie et al.   CELL

Atlas of Subcellular RNA Localization Revealed by APEX-Seq

(2019) Furqan M. Fazal et al.   CELL

Single-Cell Multi-omic Integration Compares and Contrasts Features of Brain Cell Identity

(2019) Joshua D. Welch et al.   CELL

Starfish enterprise: finding RNA patterns in single cells

(2019) Jeffrey M. Perkel   NATURE

BigStitcher: reconstructing high-resolution image datasets of cleared and expanded samples

(2019) David Hörl et al.   NATURE METHODS

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

ilastik: interactive machine learning for (bio)image analysis

(2019) Stuart Berg et al.   NATURE METHODS

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

Learning unsupervised feature representations for single cell microscopy images with paired cell inpainting

(2019) Alex X. Lu et al.   PLoS Computational Biology

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Probabilistic cell typing enables fine mapping of closely related cell types in situ

(2019) Xiaoyan Qian et al.   NATURE METHODS

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

(2019) Damien Arnol et al.   Cell Reports

SpaCell: integrating tissue morphology and spatial gene expression to predict disease cells

(2019) Xiao Tan et al.   BIOINFORMATICS

Toward a Common Coordinate Framework for the Human Body

(2019) Jennifer E. Rood et al.   CELL

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart

(2019) Michaela Asp et al.   CELL

Orchestrating single-cell analysis with Bioconductor

(2019) Robert A. Amezquita et al.   NATURE METHODS

NicheNet: modeling intercellular communication by linking ligands to target genes

(2019) Robin Browaeys et al.   NATURE METHODS

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

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

Mapping the physical network of cellular interactions

(2018) Jean-Charles Boisset et al.   NATURE METHODS

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

(2018) Emelie Berglund et al.   Nature Communications

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

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

(2018) Keren Bahar Halpern et al.   NATURE BIOTECHNOLOGY

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut 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

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Deep generative modeling for single-cell transcriptomics

(2018) Romain Lopez et al.   NATURE METHODS

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections

(2018) Fredrik Salmén et al.   Nature Protocols

Data-analysis strategies for image-based cell profiling

(2017) Juan C Caicedo et al.   NATURE METHODS

histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data

(2017) Denis Schapiro et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Mechanobiology of collective cell behaviours

(2017) Benoit Ladoux et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Mechanical forces direct stem cell behaviour in development and regeneration

(2017) Kyle H. Vining et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Spatial reconstruction of immune niches by combining photoactivatable reporters and scRNA-seq

(2017) Chiara Medaglia et al.   SCIENCE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Metabolic zonation of the liver: The oxygen gradient revisited

(2017) Thomas Kietzmann   Redox Biology

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Tissue biology perspective on macrophages

(2016) Yasutaka Okabe et al.   NATURE IMMUNOLOGY

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

(2016) P. L. Stahl et al.   SCIENCE

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

(2015) Kaia Achim et al.   NATURE BIOTECHNOLOGY

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

rSPACE: Spatially based power analysis for conservation and ecology

(2015) Martha M. Ellis et al.   Methods in Ecology and Evolution

Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry

(2014) Charlotte Giesen et al.   NATURE METHODS

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

The tumor microenvironment at a glance

(2013) F. R. Balkwill et al.   JOURNAL OF CELL SCIENCE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

Morphogen Gradients: From Generation to Interpretation

(2011) Katherine W. Rogers et al.   Annual Review of Cell and Developmental Biology

mRNA Localization: Gene Expression in the Spatial Dimension

(2009) Kelsey C. Martin et al.   CELL