Exploring single cells in space and time during tissue development, homeostasis and regeneration

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

(2019) Samuel G. Rodriques et al.   SCIENCE

Characterization of cell fate probabilities in single-cell data with Palantir

(2019) Manu Setty et al.   NATURE BIOTECHNOLOGY

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

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

Identification of Enteroendocrine Regulators by Real-Time Single-Cell Differentiation Mapping

(2019) Helmuth Gehart et al.   CELL

Self-organization and symmetry breaking in intestinal organoid development

(2019) Denise Serra et al.   NATURE

The emergent landscape of the mouse gut endoderm at single-cell resolution

(2019) Sonja Nowotschin 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

Concepts and limitations for learning developmental trajectories from single cell genomics

(2019) Sophie Tritschler et al.   DEVELOPMENT

Mapping chromatin modifications at the single cell level

(2019) Connor H. Ludwig et al.   DEVELOPMENT

The evolving concept of cell identity in the single cell era

(2019) Samantha A. Morris   DEVELOPMENT

Defining Adult Stem Cells by Function, not by Phenotype

(2018) Hans Clevers et al.   Annual Review of Biochemistry

Hydrogel-Tissue Chemistry: Principles and Applications

(2018) Viviana Gradinaru et al.   Annual Review of Biophysics

Single-Cell Genomics: A Stepping Stone for Future Immunology Discoveries

(2018) Amir Giladi et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Single-Cell Transcriptomics Meets Lineage Tracing

(2018) Lennart Kester et al.   Cell Stem Cell

YAP/TAZ-Dependent Reprogramming of Colonic Epithelium Links ECM Remodeling to Tissue Regeneration

(2018) Shiro Yui et al.   Cell Stem Cell

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Clonal analysis of lineage fate in native haematopoiesis

(2018) Alejo E. Rodriguez-Fraticelli et al.   NATURE

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

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

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Fundamental limits on dynamic inference from single-cell snapshots

(2018) Caleb Weinreb et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms

(2018) Tsung-Li Liu et al.   SCIENCE

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

(2018) Xiao Wang et al.   SCIENCE

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Coordination of Cell Polarity, Mechanics and Fate in Tissue Self-organization

(2018) Esther Jeong Yoon Kim et al.   TRENDS IN CELL BIOLOGY

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

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

Unsupervised Trajectory Analysis of Single-Cell RNA-Seq and Imaging Data Reveals Alternative Tuft Cell Origins in the Gut

(2018) Charles A. Herring et al.   Cell Systems

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

Spatial Reconstruction of Single Enterocytes Uncovers Broad Zonation along the Intestinal Villus Axis

(2018) Andreas E. Moor et al.   CELL

Homeostatic Epidermal Stem Cell Self-Renewal Is Driven by Local Differentiation

(2018) Kailin R. Mesa et al.   Cell Stem Cell

Signaling in the stem cell niche: regulating cell fate, function and plasticity

(2018) Carlos Andrés Chacón-Martínez et al.   DEVELOPMENT

Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy

(2018) Chawin Ounkomol et al.   NATURE METHODS

Multiplexed protein maps link subcellular organization to cellular states

(2018) Gabriele Gut et al.   SCIENCE

In Toto Imaging and Reconstruction of Post-Implantation Mouse Development at the Single-Cell Level

(2018) Katie McDole et al.   CELL

From single cells to tissue self-organization

(2018) Aline Xavier da Silveira dos Santos et al.   FEBS Journal

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

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

Analysis of Single-Cell RNA-Seq Identifies Cell-Cell Communication Associated with Tumor Characteristics

(2018) Manu P. Kumar et al.   Cell Reports

Multivariate Control of Transcript to Protein Variability in Single Mammalian Cells

(2018) Doris Popovic et al.   Cell Systems

Hippo Signaling in the Liver Regulates Organ Size, Cell Fate, and Carcinogenesis

(2017) Sachin H. Patel et al.   GASTROENTEROLOGY

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

(2017) Yu Wang et al.   NANO LETTERS

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

From morphogen to morphogenesis and back

(2017) Darren Gilmour et al.   NATURE

Applying systems-level spectral imaging and analysis to reveal the organelle interactome

(2017) Alex M. Valm et al.   NATURE

Interplay between metabolic identities in the intestinal crypt supports stem cell function

(2017) Maria J. Rodríguez-Colman et al.   NATURE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Single-cell spatial reconstruction reveals global division of labour in the mammalian liver

(2017) Keren Bahar Halpern et al.   NATURE

Adhesion forces and cortical tension couple cell proliferation and differentiation to drive epidermal stratification

(2017) Yekaterina A. Miroshnikova et al.   NATURE CELL BIOLOGY

Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging

(2017) Francesco Cutrale et al.   NATURE METHODS

Profiling the transcriptome with RNA SPOTs

(2017) Chee-Huat Linus Eng et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq

(2017) Jun Chen et al.   Nature Protocols

Mechanobiology of YAP and TAZ in physiology and disease

(2017) Tito Panciera 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

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

(2017) Ed Lein et al.   SCIENCE

TheDrosophilaembryo at single-cell transcriptome resolution

(2017) Nikos Karaiskos et al.   SCIENCE

Mass Cytometry: Single Cells, Many Features

(2016) Matthew H. Spitzer et al.   CELL

On the Dependency of Cellular Protein Levels on mRNA Abundance

(2016) Yansheng Liu et al.   CELL

Replacement of Lost Lgr5-Positive Stem Cells through Plasticity of Their Enterocyte-Lineage Daughters

(2016) Paul W. Tetteh et al.   Cell Stem Cell

Induction of Expandable Tissue-Specific Stem/Progenitor Cells through Transient Expression of YAP/TAZ

(2016) Tito Panciera et al.   Cell Stem Cell

Integrin signalling regulates YAP and TAZ to control skin homeostasis

(2016) Ahmed Elbediwy 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

Integrated, multi-scale, spatial–temporal cell biology – A next step in the post genomic era

(2016) Rick Horwitz   METHODS

Gene‐specific correlation of RNA and protein levels in human cells and tissues

(2016) Fredrik Edfors et al.   Molecular Systems Biology

Designer matrices for intestinal stem cell and organoid culture

(2016) Nikolce Gjorevski et al.   NATURE

Revealing the vectors of cellular identity with single-cell genomics

(2016) Allon Wagner et al.   NATURE BIOTECHNOLOGY

Wishbone identifies bifurcating developmental trajectories from single-cell data

(2016) Manu Setty et al.   NATURE BIOTECHNOLOGY

Multi-target spectrally resolved fluorescence lifetime imaging microscopy

(2016) Thomas Niehörster et al.   NATURE METHODS

Nanoscale imaging of RNA with expansion microscopy

(2016) Fei Chen et al.   NATURE METHODS

Diffusion pseudotime robustly reconstructs lineage branching

(2016) Laleh Haghverdi et al.   NATURE METHODS

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

(2016) Sheel Shah et al.   NEURON

SLICE: determining cell differentiation and lineage based on single cell entropy

(2016) Minzhe Guo et al.   NUCLEIC ACIDS RESEARCH

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

Continuous genetic recording with self-targeting CRISPR-Cas in human cells

(2016) S. D. Perli et al.   SCIENCE

Light-sheet imaging of mammalian development

(2016) Gustavo de Medeiros et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Mpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development

(2016) Jinmiao Chen et al.   Nature Communications

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

(2016) Susanne Nichterwitz et al.   Nature Communications

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements

(2016) Sahand Hormoz et al.   Cell Systems

Control of Transcript Variability in Single Mammalian Cells

(2015) Nico Battich 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

Single-Cell RNA-Seq with Waterfall Reveals Molecular Cascades underlying Adult Neurogenesis

(2015) Jaehoon Shin et al.   Cell Stem Cell

Stem Cell Heterogeneity and Plasticity in Epithelia

(2015) Giacomo Donati et al.   Cell Stem Cell

Cell shape and the microenvironment regulate nuclear translocation of NF- B in breast epithelial and tumor cells

(2015) J. E. Sero et al.   Molecular Systems Biology

Cell-intrinsic adaptation of lipid composition to local crowding drives social behaviour

(2015) Mathieu Frechin et al.   NATURE

Reproducibility crisis: Blame it on the antibodies

(2015) Monya Baker   NATURE

Yap-dependent reprogramming of Lgr5+ stem cells drives intestinal regeneration and cancer

(2015) Alex Gregorieff et al.   NATURE

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

Network plasticity of pluripotency transcription factors in embryonic stem cells

(2015) Adam Filipczyk et al.   NATURE CELL BIOLOGY

Guide to light-sheet microscopy for adventurous biologists

(2015) Emmanuel G Reynaud et al.   NATURE METHODS

Trajectories of cell-cycle progression from fixed cell populations

(2015) Gabriele Gut et al.   NATURE METHODS

Inverted light-sheet microscope for imaging mouse pre-implantation development

(2015) Petr Strnad et al.   NATURE METHODS

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

What is an adult stem cell?

(2015) H. Clevers   SCIENCE

Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice

(2015) Yuka Morikawa et al.   Science Signaling

Plasticity within stem cell hierarchies in mammalian epithelia

(2015) Paul W. Tetteh et al.   TRENDS IN CELL BIOLOGY

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

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

Actin cytoskeletal remodeling with protrusion formation is essential for heart regeneration in Hippo-deficient mice

(2015) Yuka Morikawa et al.   Science Signaling

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

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

Transit-Amplifying Cells Orchestrate Stem Cell Activity and Tissue Regeneration

(2014) Ya-Chieh Hsu et al.   CELL

A Hierarchical Map of Regulatory Genetic Interactions in Membrane Trafficking

(2014) Prisca Liberali et al.   CELL

Single-Cell Trajectory Detection Uncovers Progression and Regulatory Coordination in Human B Cell Development

(2014) Sean C. Bendall et al.   CELL

Rethinking Differentiation: Stem Cells, Regeneration, and Plasticity

(2014) Alejandro Sánchez Alvarado et al.   CELL

Yap Tunes Airway Epithelial Size and Architecture by Regulating the Identity, Maintenance, and Self-Renewal of Stem Cells

(2014) Rui Zhao et al.   DEVELOPMENTAL CELL

Elution of High-affinity (>10-9 KD) Antibodies from Tissue Sections

(2014) Rossella Gendusa et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Intestinal crypt homeostasis revealed at single-stem-cell level by in vivo live imaging

(2014) Laila Ritsma et al.   NATURE

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

Spatially resolved transcriptomics and beyond

(2014) Nicola Crosetto et al.   NATURE REVIEWS GENETICS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

The Cell-Cycle State of Stem Cells Determines Cell Fate Propensity

(2013) Siim Pauklin et al.   CELL

The Intestinal Crypt, A Prototype Stem Cell Compartment

(2013) Hans Clevers   CELL

Differentiated Troy+ Chief Cells Act as Reserve Stem Cells to Generate All Lineages of the Stomach Epithelium

(2013) Daniel E. Stange et al.   CELL

The Epidermis Comprises Autonomous Compartments Maintained by Distinct Stem Cell Populations

(2013) Mahalia E. Page et al.   Cell Stem Cell

Robust cellular reprogramming occurs spontaneously during liver regeneration

(2013) K. Yanger et al.   GENES & DEVELOPMENT

Epithelial mechanobiology, skin wound healing, and the stem cell niche

(2013) Nicholas D. Evans et al.   Journal of the Mechanical Behavior of Biomedical Materials

Intestinal label-retaining cells are secretory precursors expressing Lgr5

(2013) Simon J. A. Buczacki et al.   NATURE

Dedifferentiation of committed epithelial cells into stem cells in vivo

(2013) Purushothama Rao Tata et al.   NATURE

Cytosystems dynamics in self-organization of tissue architecture

(2013) Yoshiki Sasai   NATURE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Image-based transcriptomics in thousands of single human cells at single-molecule resolution

(2013) Nico Battich et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

Calcium Dynamics in Root Cells of Arabidopsis thaliana Visualized with Selective Plane Illumination Microscopy

(2013) Alex Costa et al.   PLoS One

Hippo pathway effector Yap promotes cardiac regeneration

(2013) Mei Xin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Growing Self-Organizing Mini-Guts from a Single Intestinal Stem Cell: Mechanism and Applications

(2013) T. Sato et al.   SCIENCE

The Circadian Molecular Clock Regulates Adult Hippocampal Neurogenesis by Controlling the Timing of Cell-Cycle Entry and Exit

(2013) Pascale Bouchard-Cannon et al.   Cell Reports

Designing Synthetic Regulatory Networks Capable of Self-Organizing Cell Polarization

(2012) Angela H. Chau et al.   CELL

Quantitative Analysis of Embryogenesis: A Perspective for Light Sheet Microscopy

(2012) Burkhard Höckendorf et al.   DEVELOPMENTAL CELL

Single-cell analysis of population context advances RNAi screening at multiple levels

(2012) Berend Snijder et al.   Molecular Systems Biology

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Dll1+ secretory progenitor cells revert to stem cells upon crypt damage

(2012) Johan H. van Es et al.   NATURE CELL BIOLOGY

Single-cell systems biology by super-resolution imaging and combinatorial labeling

(2012) Eric Lubeck et al.   NATURE METHODS

Using Cell-to-Cell Variability--A New Era in Molecular Biology

(2012) L. Pelkmans   SCIENCE

Hippo signaling in mammalian stem cells

(2012) Annie M. Tremblay et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

A short G1 phase is an intrinsic determinant of naïve embryonic stem cell pluripotency

(2012) Diana Coronado et al.   Stem Cell Research

CEL-Seq: Single-Cell RNA-Seq by Multiplexed Linear Amplification

(2012) Tamar Hashimshony et al.   Cell Reports

Yap1 Acts Downstream of α-Catenin to Control Epidermal Proliferation

(2011) Karin Schlegelmilch et al.   CELL

Dll1- and Dll4-Mediated Notch Signaling Are Required for Homeostasis of Intestinal Stem Cells

(2011) Luca Pellegrinet et al.   GASTROENTEROLOGY

A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable

(2011) Hua Tian et al.   NATURE

Role of YAP/TAZ in mechanotransduction

(2011) Sirio Dupont et al.   NATURE

Origins of regulated cell-to-cell variability

(2011) Berend Snijder et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Live cell division dynamics monitoring in 3D large spheroid tumor models using light sheet microscopy

(2011) Corinne Lorenzo et al.   Cell Division

Cellular Heterogeneity: Do Differences Make a Difference?

(2010) Steven J. Altschuler et al.   CELL

Cdks and cyclins link G1length and differentiation of embryonic, neural and hematopoietic stem cells

(2010) Christian Lange et al.   CELL CYCLE

Glucocorticoids and circadian clock control of cell proliferation: At the interface between three dynamic systems

(2010) Thomas Dickmeis et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Paneth cells constitute the niche for Lgr5 stem cells in intestinal crypts

(2010) Toshiro Sato et al.   NATURE

Cdk4/CyclinD1 Overexpression in Neural Stem Cells Shortens G1, Delays Neurogenesis, and Promotes the Generation and Expansion of Basal Progenitors

(2009) Christian Lange et al.   Cell Stem Cell

Liver regeneration: Alternative epithelial pathways

(2009) George K. Michalopoulos   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Antibody Elution Method for Multiple Immunohistochemistry on Primary Antibodies Raised in the Same Species and of the Same Subtype

(2009) Daniel Pirici et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Population context determines cell-to-cell variability in endocytosis and virus infection

(2009) Berend Snijder et al.   NATURE

Non-genetic origins of cell-to-cell variability in TRAIL-induced apoptosis

(2009) Sabrina L. Spencer et al.   NATURE

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS

From cells to organs: building polarized tissue

(2008) David M. Bryant et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY