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

CytoMAP: A Spatial Analysis Toolbox Reveals Features of Myeloid Cell Organization in Lymphoid Tissues

(2020) Caleb R. Stoltzfus et al.   Cell Reports

Vitamin D Is Required for ILC3 Derived IL-22 and Protection From Citrobacter rodentium Infection

(2019) Yang-Ding Lin et al.   Frontiers in Immunology

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

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

MULTI-seq: sample multiplexing for single-cell RNA sequencing using lipid-tagged indices

(2019) Christopher S. McGinnis et al.   NATURE METHODS

Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets

(2019) Frédéric Pont et al.   NUCLEIC ACIDS RESEARCH

Epigenetic signature of PD-1+ TCF1+ CD8 T cells that act as resource cells during chronic viral infection and respond to PD-1 blockade

(2019) Rohit R. Jadhav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-definition spatial transcriptomics for in situ tissue profiling

(2019) Sanja Vickovic et al.   NATURE METHODS

TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision

(2019) Zeyu Chen et al.   IMMUNITY

Single-cell gene expression reveals a landscape of regulatory T cell phenotypes shaped by the TCR

(2018) David Zemmour et al.   NATURE IMMUNOLOGY

Diverse Functions of Macrophages in Different Tumor Microenvironments

(2018) Ming Yang et al.   CANCER RESEARCH

Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging

(2018) Yury Goltsev et al.   CELL

CCR5-Dependent Homing of T Regulatory Cells to the Tumor Microenvironment Contributes to Skin Squamous Cell Carcinoma Development

(2017) Carine Ervolino de Oliveira et al.   MOLECULAR CANCER THERAPEUTICS

Tissue-scale coordination of cellular behaviour promotes epidermal wound repair in live mice

(2017) Sangbum Park et al.   NATURE CELL BIOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

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

(2017) Chiara Medaglia et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Tumor macrophages are pivotal constructors of tumor collagenous matrix

(2016) Ran Afik et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy

(2016) Se Jin Im et al.   NATURE

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

(2016) P. L. Stahl et al.   SCIENCE

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

(2015) Evan Z. Macosko et al.   CELL

Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells

(2015) Monika S. Kowalczyk et al.   GENOME RESEARCH

The Transcription Factor KLF2 Restrains CD4 + T Follicular Helper Cell Differentiation

(2015) June-Yong Lee et al.   IMMUNITY

ICOS maintains the T follicular helper cell phenotype by down-regulating Krüppel-like factor 2

(2015) Jan P. Weber et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Wound healing revised: A novel reepithelialization mechanism revealed by in vitro and in silico models

(2014) Kai Safferling et al.   JOURNAL OF CELL BIOLOGY

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

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

The cellular and molecular origin of tumor-associated macrophages

(2014) R. A. Franklin 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

SERPINE1: A Molecular Switch in the Proliferation-Migration Dichotomy in Wound-“Activated” Keratinocytes

(2014) Tessa M. Simone et al.   Advances in Wound Care

Optochemical control of RNA interference in mammalian cells

(2013) Jeane M. Govan et al.   NUCLEIC ACIDS RESEARCH

Smooth Muscle α Actin (Acta2) and Myofibroblast Function during Hepatic Wound Healing

(2013) Don C. Rockey et al.   PLoS One

CXCR6 and CCR5 Localize T Lymphocyte Subsets in Nasopharyngeal Carcinoma

(2012) Greg Parsonage et al.   AMERICAN JOURNAL OF PATHOLOGY

Marginating Dendritic Cells of the Tumor Microenvironment Cross-Present Tumor Antigens and Stably Engage Tumor-Specific T Cells

(2012) John J. Engelhardt et al.   CANCER CELL

CCR5 in cancer immunotherapy: More than an “attractive” receptor for T cells

(2012) Alicia González-Martín et al.   OncoImmunology

Phenotypic and functional plasticity of cells of innate immunity: macrophages, mast cells and neutrophils

(2011) Stephen J Galli et al.   NATURE IMMUNOLOGY

Different Tumor Microenvironments Contain Functionally Distinct Subsets of Macrophages Derived from Ly6C(high) Monocytes

(2010) K. Movahedi et al.   CANCER RESEARCH

Light activation as a method of regulating and studying gene expression

(2009) Alexander Deiters   CURRENT OPINION IN CHEMICAL BIOLOGY