Single-cell transcriptomics to explore the immune system in health and disease

Computational approaches for interpreting scRNA-seq data

(2017) Raghd Rostom et al.   FEBS LETTERS

Single-cell transcriptome analysis of fish immune cells provides insight into the evolution of vertebrate immune cell types

(2017) Santiago J. Carmona et al.   GENOME RESEARCH

Immunology: The patterns of T-cell target recognition

(2017) Sai T. Reddy   NATURE

Quantifiable predictive features define epitope-specific T cell receptor repertoires

(2017) Pradyot Dash et al.   NATURE

Identifying specificity groups in the T cell receptor repertoire

(2017) Jacob Glanville et al.   NATURE

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

Aging increases cell-to-cell transcriptional variability upon immune stimulation

(2017) Celia Pilar Martinez-Jimenez et al.   SCIENCE

Mapping the human DC lineage through the integration of high-dimensional techniques

(2017) Peter See et al.   SCIENCE

Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq

(2017) Andrew S. Venteicher et al.   SCIENCE

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

(2017) Ed Lein et al.   SCIENCE

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

(2016) Meital Gury-BenAri et al.   CELL

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Distinct Gene Module for Dysfunction Uncoupled from Activation in Tumor-Infiltrating T Cells

(2016) Meromit Singer et al.   CELL

Linking the T cell receptor to the single cell transcriptome in antigen-specific human T cells

(2016) Auda A Eltahla et al.   IMMUNOLOGY AND CELL BIOLOGY

Single-cell RNA-seq identifies a PD-1hi ILC progenitor and defines its development pathway

(2016) Yong Yu 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

The heterogeneity of human CD127+ innate lymphoid cells revealed by single-cell RNA sequencing

(2016) Åsa K Björklund et al.   NATURE IMMUNOLOGY

Evidence of innate lymphoid cell redundancy in humans

(2016) Frédéric Vély et al.   NATURE IMMUNOLOGY

The role of the local environment and epigenetics in shaping macrophage identity and their effect on tissue homeostasis

(2016) Ido Amit et al.   NATURE IMMUNOLOGY

Tissue biology perspective on macrophages

(2016) Yasutaka Okabe et al.   NATURE IMMUNOLOGY

Highly multiplexed simultaneous detection of RNAs and proteins in single cells

(2016) Andreas P Frei et al.   NATURE METHODS

T cell fate and clonality inference from single-cell transcriptomes

(2016) Michael J T Stubbington et al.   NATURE METHODS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Single-Cell RNA-Sequencing Reveals a Continuous Spectrum of Differentiation in Hematopoietic Cells

(2016) Iain C. Macaulay et al.   Cell Reports

Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications

(2016) Bernd Bodenmiller   Cell Systems

Single-cell RNA-seq ties macrophage polarization to growth rate of intracellular Salmonella

(2016) Antoine-Emmanuel Saliba et al.   Nature Microbiology

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity

(2015) Jellert T. Gaublomme et al.   CELL

CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity

(2015) Chao Wang et al.   CELL

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses

(2015) Roi Avraham et al.   CELL

Combined Single-Cell Functional and Gene Expression Analysis Resolves Heterogeneity within Stem Cell Populations

(2015) Nicola K. Wilson et al.   Cell Stem Cell

Circulating precursors of human CD1c+and CD141+dendritic cells

(2015) Gaëlle Breton et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Computational assignment of cell-cycle stage from single-cell transcriptome data

(2015) Antonio Scialdone et al.   METHODS

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

The biology of innate lymphoid cells

(2015) David Artis et al.   NATURE

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Oscope identifies oscillatory genes in unsynchronized single-cell RNA-seq experiments

(2015) Ning Leng et al.   NATURE METHODS

Innate lymphoid cells: A new paradigm in immunology

(2015) G. Eberl et al.   SCIENCE

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

(2014) Sean C. Bendall et al.   CELL

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

(2014) Alex K. Shalek et al.   NATURE

Linking T-cell receptor sequence to functional phenotype at the single-cell level

(2014) Arnold Han et al.   NATURE BIOTECHNOLOGY

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

(2014) Charlotte Giesen et al.   NATURE METHODS

Single-Cell RNA Sequencing Reveals T Helper Cells Synthesizing Steroids De Novo to Contribute to Immune Homeostasis

(2014) Bidesh Mahata et al.   Cell Reports

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Immunity in the tissues

(2013)   NATURE IMMUNOLOGY

Immunological Genome Project and systems immunology

(2013) Tal Shay et al.   TRENDS IN IMMUNOLOGY

A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst

(2012) F. Buettner et al.   BIOINFORMATICS

Mass Cytometry: Technique for Real Time Single Cell Multitarget Immunoassay Based on Inductively Coupled Plasma Time-of-Flight Mass Spectrometry

(2009) Dmitry R. Bandura et al.   ANALYTICAL CHEMISTRY