SM-Omics is an automated platform for high-throughput spatial multi-omics

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

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

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues

(2020) Emelie Berglund et al.   BMC GENOMICS

SuperPlots: Communicating reproducibility and variability in cell biology

(2020) Samuel J. Lord et al.   JOURNAL OF CELL BIOLOGY

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

(2020) Christopher R. Merritt 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

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

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

(2019) Silas Maniatis et al.   SCIENCE

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

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

(2019) Michaela Asp et al.   CELL

ST Spot Detector: a web-based application for automatic spot and tissue detection for spatial Transcriptomics image datasets

(2018) Kim Wong et al.   BIOINFORMATICS

SpatialDE: identification of spatially variable genes

(2018) Valentine Svensson et al.   NATURE METHODS

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

(2018) Emelie Berglund et al.   Nature Communications

Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry

(2018) Daniel Schulz et al.   Cell Systems

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

Molecular Architecture of the Mouse Nervous System

(2018) Amit Zeisel et al.   CELL

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

(2018) Leeat Keren et al.   CELL

Neurotechnology to address big questions

(2018) Thomas Knöpfel   SCIENCE

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

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

(2018) Fredrik Salmén et al.   Nature Protocols

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

(2018) Jeffrey R. Moffitt et al.   SCIENCE

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Power analysis of single-cell RNA-sequencing experiments

(2017) Valentine Svensson et al.   NATURE METHODS

Massively parallel single-nucleus RNA-seq with DroNc-seq

(2017) Naomi Habib et al.   NATURE METHODS

The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing

(2017) Ed Lein et al.   SCIENCE

Identification of a peptide recognizing cerebrovascular changes in mouse models of Alzheimer’s disease

(2017) Aman P. Mann et al.   Nature Communications

Defining the consequences of genetic variation on a proteome-wide scale

(2016) Joel M. Chick et al.   NATURE

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

(2016) P. L. Stahl et al.   SCIENCE

Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons

(2016) Naomi Habib et al.   SCIENCE

Massive and parallel expression profiling using microarrayed single-cell sequencing

(2016) Sanja Vickovic et al.   Nature Communications

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells

(2016) Spyros Darmanis et al.   Cell Reports

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries

(2016) Anders Jemt et al.   Scientific Reports

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Dynamic profiling of the protein life cycle in response to pathogens

(2015) M. Jovanovic et al.   SCIENCE

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

High-Resolution Sequencing and Modeling Identifies Distinct Dynamic RNA Regulatory Strategies

(2014) Michal Rabani et al.   CELL

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

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

(2014) Charlotte Giesen et al.   NATURE METHODS

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

Neuronal organization of olfactory bulb circuits

(2014) Shin Nagayama et al.   Frontiers in Neural Circuits

scikit-image: image processing in Python

(2014) Stéfan van der Walt et al.   PeerJ

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

TagGD: Fast and Accurate Software for DNA Tag Generation and Demultiplexing

(2013) Paul Igor Costea et al.   PLoS One

Highly multiplexed single-cell analysis of formalin-fixed, paraffin-embedded cancer tissue

(2013) M. J. Gerdes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Accessories to the Crime: Functions of Cells Recruited to the Tumor Microenvironment

(2012) Douglas Hanahan et al.   CANCER CELL

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

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

(2012) Johannes Schindelin et al.   NATURE METHODS

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

(2011) Sheila Fisher et al.   GENOME BIOLOGY