Enablers and challenges of spatial omics, a melting pot of technologies

Integrated intracellular organization and its variations in human iPS cells

(2023) Matheus P. Viana et al.   NATURE

Integration of whole transcriptome spatial profiling with protein markers

(2023) Nir Ben-Chetrit et al.   NATURE BIOTECHNOLOGY

Screening cell–cell communication in spatial transcriptomics via collective optimal transport

(2023) Zixuan Cang et al.   NATURE METHODS

Current Progress in Expansion Microscopy: Chemical Strategies and Applications

(2023) Gang Wen et al.   Chemical Reviews

Microbial Pathogenesis in the Era of Spatial Omics

(2023) Samantha Lempke et al.   INFECTION AND IMMUNITY

Spatial epigenome–transcriptome co-profiling of mammalian tissues

(2023) Di Zhang et al.   NATURE

High-plex protein and whole transcriptome co-mapping at cellular resolution with spatial CITE-seq

(2023) Yang Liu et al.   NATURE BIOTECHNOLOGY

Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution

(2023) Sarah M. Mangiameli et al.   NATURE METHODS

Best practices for single-cell analysis across modalities

(2023) Lukas Heumos et al.   NATURE REVIEWS GENETICS

Spatial profiling of microbial communities by sequential FISH with error-robust encoding

(2023) Zhaohui Cao et al.   Nature Communications

MALDI HiPLEX-IHC: multiomic and multimodal imaging of targeted intact proteins in tissues

(2023) Mark J. Lim et al.   Frontiers in Chemistry

High-plex immunofluorescence imaging and traditional histology of the same tissue section for discovering image-based biomarkers

(2023) Jia-Ren Lin et al.   Nature Cancer

OME-Zarr: a cloud-optimized bioimaging file format with international community support

(2023) Josh Moore et al.   HISTOCHEMISTRY AND CELL BIOLOGY

Spatial components of molecular tissue biology

(2022) Giovanni Palla et al.   NATURE BIOTECHNOLOGY

Spatially resolved isotope tracing reveals tissue metabolic activity

(2022) Lin Wang et al.   NATURE METHODS

Squidpy: a scalable framework for spatial omics analysis

(2022) Giovanni Palla et al.   NATURE METHODS

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

(2022) S. Vickovic et al.   Nature Communications

Clinical challenges of tissue preparation for spatial transcriptome

(2022) Xiaoxia Liu et al.   Clinical and Translational Medicine

SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor

(2022) Dario Righelli et al.   BIOINFORMATICS

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

(2022) Ao Chen et al.   CELL

Deep Visual Proteomics defines single-cell identity and heterogeneity

(2022) Andreas Mund et al.   NATURE BIOTECHNOLOGY

Publisher Correction: Museum of spatial transcriptomics

(2022) Lambda Moses et al.   NATURE METHODS

MITI minimum information guidelines for highly multiplexed tissue images

(2022) Denis Schapiro et al.   NATURE METHODS

Benchmarking spatial and single-cell transcriptomics integration methods for transcript distribution prediction and cell type deconvolution

(2022) Bin Li et al.   NATURE METHODS

PICASSO allows ultra-multiplexed fluorescence imaging of spatially overlapping proteins without reference spectra measurements

(2022) Junyoung Seo et al.   Nature Communications

Direct RNA targeted in situ sequencing for transcriptomic profiling in tissue

(2022) Hower Lee et al.   Scientific Reports

Integrating knowledge and omics to decipher mechanisms via large‐scale models of signaling networks

(2022) Martin Garrido‐Rodriguez et al.   Molecular Systems Biology

Live-seq enables temporal transcriptomic recording of single cells

(2022) Wanze Chen et al.   NATURE

Spatial profiling of chromatin accessibility in mouse and human tissues

(2022) Yanxiang Deng et al.   NATURE

Spatial multi-omic map of human myocardial infarction

(2022) Christoph Kuppe et al.   NATURE

Single-cell roadmap of human gonadal development

(2022) Luz Garcia-Alonso et al.   NATURE

The emerging landscape of spatial profiling technologies

(2022) Jeffrey R. Moffitt et al.   NATURE REVIEWS GENETICS

Spatially resolved epigenomic profiling of single cells in complex tissues

(2022) Tian Lu et al.   CELL

Modeling intercellular communication in tissues using spatial graphs of cells

(2022) David S. Fischer et al.   NATURE BIOTECHNOLOGY

ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ

(2022) Ian Dardani et al.   NATURE METHODS

Light-Seq: light-directed in situ barcoding of biomolecules in fixed cells and tissues for spatially indexed sequencing

(2022) Jocelyn Y. Kishi et al.   NATURE METHODS

Spatial proteomics in three-dimensional intact specimens

(2022) Harsharan Singh Bhatia et al.   CELL

Polony gels enable amplifiable DNA stamping and spatial transcriptomics of chronic pain

(2022) Xiaonan Fu et al.   CELL

Image-seq: spatially resolved single-cell sequencing guided by in situ and in vivo imaging

(2022) Christa Haase et al.   NATURE METHODS

UnMICST: Deep learning with real augmentation for robust segmentation of highly multiplexed images of human tissues

(2022) Clarence Yapp et al.   Communications Biology

The Tumor Profiler Study: integrated, multi-omic, functional tumor profiling for clinical decision support

(2021) Anja Irmisch et al.   CANCER CELL

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

Rationale and design of the Kidney Precision Medicine Project

(2021) Ian H. de Boer et al.   KIDNEY INTERNATIONAL

Integrated spatial genomics reveals global architecture of single nuclei

(2021) Yodai Takei 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

Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems

(2021) Shahar Alon et al.   SCIENCE

The spatial landscape of lung pathology during COVID-19 progression

(2021) André F. Rendeiro et al.   NATURE

Computational principles and challenges in single-cell data integration

(2021) Ricard Argelaguet et al.   NATURE BIOTECHNOLOGY

Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses

(2021) Songlei Liu et al.   NUCLEIC ACIDS RESEARCH

Microscopic examination of spatial transcriptome using Seq-Scope

(2021) Chun-Seok Cho et al.   CELL

Applications and continued evolution of glycan imaging mass spectrometry

(2021) Colin T. McDowell et al.   MASS SPECTROMETRY REVIEWS

A proximity-dependent biotinylation map of a human cell

(2021) Christopher D. Go et al.   NATURE

Exploring tissue architecture using spatial transcriptomics

(2021) Anjali Rao et al.   NATURE

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

Spatial omics and multiplexed imaging to explore cancer biology

(2021) Sabrina M. Lewis et al.   NATURE METHODS

Metabolomic profiling of single enlarged lysosomes

(2021) Hongying Zhu et al.   NATURE METHODS

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

(2021) Jeongbin Park et al.   Nature Communications

Subcellular localization of biomolecules and drug distribution by high-definition ion beam imaging

(2021) Xavier Rovira-Clavé et al.   Nature Communications

High-throughput single-cell epigenomic profiling by targeted insertion of promoters (TIP-seq)

(2021) Daniel A. Bartlett et al.   JOURNAL OF CELL BIOLOGY

Super-resolved spatial transcriptomics by deep data fusion

(2021) Ludvig Bergenstråhle et al.   NATURE BIOTECHNOLOGY

Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning

(2021) Noah F. Greenwald et al.   NATURE BIOTECHNOLOGY

Cell segmentation in imaging-based spatial transcriptomics

(2021) Viktor Petukhov et al.   NATURE BIOTECHNOLOGY

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Spatial mapping of protein composition and tissue organization: a primer for multiplexed antibody-based imaging

(2021) John W. Hickey et al.   NATURE METHODS

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

Single-cell nuclear architecture across cell types in the mouse brain

(2021) Yodai Takei et al.   SCIENCE

Toward modeling metabolic state from single-cell transcriptomics

(2021) Karin Hrovatin et al.   Molecular Metabolism

B cells and tertiary lymphoid structures promote immunotherapy response

(2020) Beth A. Helmink et al.   NATURE

Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies

(2020) Shiquan Sun et al.   NATURE METHODS

Spatial metabolomics of in situ host–microbe interactions at the micrometre scale

(2020) Benedikt Geier et al.   Nature Microbiology

The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution

(2020) Orit Rozenblatt-Rosen et al.   CELL

Multiplex digital spatial profiling of proteins and RNA in fixed tissue

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

OligoMinerApp: a web-server application for the design of genome-scale oligonucleotide in situ hybridization probes through the flexible OligoMiner environment

(2020) Marco Passaro et al.   NUCLEIC ACIDS RESEARCH

Metabolomics and mass spectrometry imaging reveal channeled de novo purine synthesis in cells

(2020) Vidhi Pareek et al.   SCIENCE

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

(2020) Zixuan Cang et al.   Nature Communications

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

(2020) Christian M. Schürch et al.   CELL

The cell biologist's guide to super-resolution microscopy

(2020) Guillaume Jacquemet et al.   JOURNAL OF CELL SCIENCE

3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing

(2020) Huy Q. Nguyen et al.   NATURE METHODS

ZipSeq: barcoding for real-time mapping of single cell transcriptomes

(2020) Kenneth H. Hu et al.   NATURE METHODS

Investigating higher-order interactions in single-cell data with scHOT

(2020) Shila Ghazanfar et al.   NATURE METHODS

Spatially resolved analysis of FFPE tissue proteomes by quantitative mass spectrometry

(2020) Katarzyna Buczak et al.   Nature Protocols

Molecular atlas of the adult mouse brain

(2020) Cantin Ortiz et al.   Science Advances

Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin

(2020) Jun-Han Su et al.   CELL

Enhancing scientific discoveries in molecular biology with deep generative models

(2020) Romain Lopez et al.   Molecular Systems Biology

LifeTime and improving European healthcare through cell-based interceptive medicine

(2020) Nikolaus Rajewsky et al.   NATURE

An Optimized Mouse Brain Atlas for Automated Mapping and Quantification of Neuronal Activity Using iDISCO+ and Light Sheet Fluorescence Microscopy

(2020) Johanna Perens et al.   NEUROINFORMATICS

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

(2020) Daniel Gyllborg et al.   NUCLEIC ACIDS RESEARCH

DNA‐Barcoded Fluorescence Microscopy for Spatial Omics

(2020) Florian Schueder et al.   PROTEOMICS

Raman-guided subcellular pharmaco-metabolomics for metastatic melanoma cells

(2020) Jiajun Du et al.   Nature Communications

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

(2020) Alma Andersson et al.   Communications Biology

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data

(2020) Jovan Tanevski et al.   Life Science Alliance

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

ProbeDealer is a convenient tool for designing probes for highly multiplexed fluorescence in situ hybridization

(2020) Mengwei Hu et al.   Scientific Reports

SCRINSHOT enables spatial mapping of cell states in tissue sections with single-cell resolution

(2020) Alexandros Sountoulidis et al.   PLOS BIOLOGY

Slide-seq: A scalable technology for measuring genome-wide expression at high spatial resolution

(2019) Samuel G. Rodriques et al.   SCIENCE

Immune and genomic correlates of response to anti-PD-1 immunotherapy in glioblastoma

(2019) Junfei Zhao et al.   NATURE MEDICINE

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

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

Visualizing DNA folding and RNA in embryos at single-cell resolution

(2019) Leslie J. Mateo et al.   NATURE

SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues

(2019) Jocelyn Y. Kishi et al.   NATURE METHODS

DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction

(2019) Joshua A. Weinstein et al.   CELL

Gene expression atlas of a developing tissue by single cell expression correlation analysis

(2019) Josephine Bageritz et al.   NATURE METHODS

Multiplexed detection of RNA using MERFISH and branched DNA amplification

(2019) Chenglong Xia et al.   Scientific Reports

Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues

(2019) Sinem K. Saka et al.   NATURE BIOTECHNOLOGY

Transmission-mode MALDI-2 mass spectrometry imaging of cells and tissues at subcellular resolution

(2019) M. Niehaus et al.   NATURE METHODS

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

A computational framework for DNA sequencing microscopy

(2019) Ian T. Hoffecker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

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

(2019) Damien Arnol et al.   Cell Reports

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Single-Cell Analysis Using Hyperspectral Imaging Modalities

(2018) Nishir Mehta et al.   JOURNAL OF BIOMECHANICAL ENGINEERING-TRANSACTIONS OF THE ASME

Spatially resolved proteome mapping of laser capture microdissected tissue with automated sample transfer to nanodroplets

(2018) Ying Zhu et al.   MOLECULAR & CELLULAR PROTEOMICS

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

OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes

(2018) Brian J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Xiao Wang et al.   SCIENCE

Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy

(2018) Guiping Wang et al.   Scientific Reports

Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes

(2018) Jia-Ren Lin et al.   eLife

Automated cell-type classification in intact tissues by single-cell molecular profiling

(2018) Monica Nagendran et al.   eLife

Spatially Resolved Proteome Profiling of

(2018) Yiran Liang et al.   ANALYTICAL CHEMISTRY

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev 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

Stellaris™ fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection

(2018) Arturo Orjalo et al.   NATURE METHODS

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

Advances in mass spectrometry imaging enabling observation of localised lipid biochemistry within tissues

(2018) Andrew P. Bowman et al.   TRAC-TRENDS IN ANALYTICAL CHEMISTRY

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Protection of tissue physicochemical properties using polyfunctional crosslinkers

(2018) Young-Gyun Park et al.   NATURE BIOTECHNOLOGY

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

(2018) Guy Nir et al.   PLoS Genetics

Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues

(2017) Yu Wang et al.   NANO LETTERS

Super-multiplex vibrational imaging

(2017) Lu Wei et al.   NATURE

Glucose feeds the TCA cycle via circulating lactate

(2017) Sheng Hui et al.   NATURE

The 4D nucleome project

(2017) Job Dekker et al.   NATURE

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

(2017) Denis Schapiro et al.   NATURE METHODS

Using hyperLOPIT to perform high-resolution mapping of the spatial proteome

(2017) Claire M Mulvey et al.   Nature Protocols

Editorial Note to: In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2017) Sheel Shah et al.   NEURON

A subcellular map of the human proteome

(2017) Peter J. Thul et al.   SCIENCE

DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging

(2017) Sarit S. Agasti et al.   Chemical Science

Synthetic DNA Synthesis and Assembly: Putting the Synthetic in Synthetic Biology

(2017) Randall A. Hughes et al.   Cold Spring Harbor Perspectives in Biology

A DNA nanoscope via auto-cycling proximity recording

(2017) Thomas E. Schaus et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Absolute Quantification of Matrix Metabolites Reveals the Dynamics of Mitochondrial Metabolism

(2016) Walter W. Chen et al.   CELL

Where imaging mass spectrometry stands: here are the numbers

(2016) Andrew Palmer et al.   Metabolomics

Multiplexed and scalable super-resolution imaging of three-dimensional protein localization in size-adjustable tissues

(2016) Taeyun Ku et al.   NATURE BIOTECHNOLOGY

Shrinkage-mediated imaging of entire organs and organisms using uDISCO

(2016) Chenchen Pan et al.   NATURE METHODS

ATAC-see reveals the accessible genome by transposase-mediated imaging and sequencing

(2016) Xingqi Chen et al.   NATURE METHODS

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

Next-generation technologies for spatial proteomics: Integrating ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis

(2016) Jeffrey M. Spraggins et al.   PROTEOMICS

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

(2016) P. L. Stahl et al.   SCIENCE

Spatial organization of chromatin domains and compartments in single chromosomes

(2016) Siyuan Wang et al.   SCIENCE

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

(2016) Susanne Nichterwitz et al.   Nature Communications

Serial 3D Imaging Mass Spectrometry at Its Tipping Point

(2015) Andrew D. Palmer et al.   ANALYTICAL CHEMISTRY

Simple, Scalable Proteomic Imaging for High-Dimensional Profiling of Intact Systems

(2015) Evan Murray et al.   CELL

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

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

Molecular cartography of the human skin surface in 3D

(2015) Amina Bouslimani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Highly multiplexed imaging of single cells using a high-throughput cyclic immunofluorescence method

(2015) Jia-Ren Lin et al.   Nature Communications

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes

(2015) Brian J. Beliveau et al.   Nature Communications

Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability

(2014) Harry M. T. Choi et al.   ACS Nano

Multiplexed ion beam imaging of human breast tumors

(2014) Michael Angelo et al.   NATURE MEDICINE

Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT

(2014) Ralf Jungmann et al.   NATURE METHODS

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

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

CLARITY for mapping the nervous system

(2013) Kwanghun Chung et al.   NATURE METHODS

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

Mass spectrometry imaging for in situ kinetic histochemistry

(2013) Katherine B. Louie et al.   Scientific Reports

Histo-Cytometry: A Method for Highly Multiplex Quantitative Tissue Imaging Analysis Applied to Dendritic Cell Subset Microanatomy in Lymph Nodes

(2012) Michael Y. Gerner et al.   IMMUNITY

Multi-isotope imaging mass spectrometry quantifies stem cell division and metabolism

(2012) Matthew L. Steinhauser et al.   NATURE

Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes

(2012) B. J. Beliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNAscope

(2011) Fay Wang et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

NUPACK: Analysis and design of nucleic acid systems

(2010) Joseph N. Zadeh et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY