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

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Lung regeneration by multipotent stem cells residing at the bronchioalveolar-duct junction

(2019) Qiaozhen Liu et al.   NATURE GENETICS

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

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

Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues

(2019) Meng Jiang et al.   RNA

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules

(2019) Salvatore A. E. Marras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

(2019) Juan C. Caicedo et al.   NATURE METHODS

Human lung branching morphogenesis is orchestrated by the spatiotemporal distribution of ACTA2, SOX2, and SOX9

(2018) Soula Danopoulos et al.   AMERICAN JOURNAL OF PHYSIOLOGY-LUNG CELLULAR AND MOLECULAR PHYSIOLOGY

Ager-CreERT2: A New Genetic Tool for Studying Lung Alveolar Development, Homeostasis, and Repair

(2018) Mei-I Chung et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Myoepithelial Cells of Submucosal Glands Can Function as Reserve Stem Cells to Regenerate Airways after Injury

(2018) Aleksandra Tata et al.   Cell Stem Cell

Placing RNA in context and space - methods for spatially resolved transcriptomics

(2018) Carina Strell et al.   FEBS Journal

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

(2018) Xiao Wang et al.   SCIENCE

Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells

(2018) Ahmad N. Nabhan et al.   SCIENCE

RNase H-assisted RNA-primed rolling circle amplification for targeted RNA sequence detection

(2018) Hirokazu Takahashi et al.   Scientific Reports

CellProfiler 3.0: Next-generation image processing for biology

(2018) Claire McQuin et al.   PLOS BIOLOGY

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

(2018) Monica Nagendran et al.   eLife

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

A revised airway epithelial hierarchy includes CFTR-expressing ionocytes

(2018) Daniel T. Montoro et al.   NATURE

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

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Spatial organization of the somatosensory cortex revealed by osmFISH

(2018) Simone Codeluppi et al.   NATURE METHODS

Chimeric padlock and iLock probes for increased efficiency of targeted RNA detection

(2018) Tomasz Krzywkowski et al.   RNA

Preexisting endothelial cells mediate cardiac neovascularization after injury

(2017) Lingjuan He et al.   JOURNAL OF CLINICAL INVESTIGATION

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

Fidelity of RNA templated end-joining by chlorella virus DNA ligase and a novel iLock assay with improved direct RNA detection accuracy

(2017) Tomasz Krzywkowski et al.   NUCLEIC ACIDS RESEARCH

Transcription factor Etv5 is essential for the maintenance of alveolar type II cells

(2017) Zhen Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Human embryonic lung epithelial tips are multipotent progenitors that can be expanded in vitro as long-term self-renewing organoids

(2017) Marko Z Nikolić et al.   eLife

The Origins and Functions of Tissue-Resident Macrophages in Kidney Development

(2017) David A. D. Munro et al.   Frontiers in Physiology

Promoter Specificity and Efficacy in Conditional and Inducible Transgenic Targeting of Lung Macrophages

(2017) Alexandra L. McCubbrey et al.   Frontiers in Immunology

Mapping a multiplexed zoo of mRNA expression

(2016) Harry M. T. Choi et al.   DEVELOPMENT

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

(2016) Sheel Shah et al.   DEVELOPMENT

In Situ Transcription Profiling of Single Cells Reveals Spatial Organization of Cells in the Mouse Hippocampus

(2016) Sheel Shah et al.   NEURON

Efficient in situ detection of mRNAs using the Chlorella virus DNA ligase for padlock probe ligation

(2016) Nils Schneider et al.   RNA

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

Progenitor Cells in Proximal Airway Epithelial Development and Regeneration

(2014) Thomas J. Lynch et al.   JOURNAL OF CELLULAR BIOCHEMISTRY

Comparative analysis of the efficiency and specificity of myeloid-Cre deleting strains using ROSA-EYFP reporter mice

(2014) Clare L. Abram et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Alveolar progenitor and stem cells in lung development, renewal and cancer

(2014) Tushar J. Desai et al.   NATURE

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Type 2 alveolar cells are stem cells in adult lung

(2013) Christina E. Barkauskas et al.   JOURNAL OF CLINICAL INVESTIGATION

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Surfactant Protein–C Chromatin-Bound Green Fluorescence Protein Reporter Mice Reveal Heterogeneity of Surfactant Protein C–Expressing Lung Cells

(2012) Joo-Hyeon Lee et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

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

(2012) Johannes Schindelin et al.   NATURE METHODS

Integrin α6β4 identifies an adult distal lung epithelial population with regenerative potential in mice

(2011) Harold A. Chapman et al.   JOURNAL OF CLINICAL INVESTIGATION

RNAscope

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

Globally optimal stitching of tiled 3D microscopic image acquisitions

(2009) S. Preibisch et al.   BIOINFORMATICS

The role of hypoxia and neurogenic genes (Mash-1 and Prox-1) in the developmental programming and maturation of pulmonary neuroendocrine cells in fetal mouse lung

(2009) Suzanne McGovern et al.   LABORATORY INVESTIGATION

A robust and high-throughput Cre reporting and characterization system for the whole mouse brain

(2009) Linda Madisen et al.   NATURE NEUROSCIENCE

The branching programme of mouse lung development

(2008) Ross J. Metzger et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS