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

CD8 + T Cells Orchestrate pDC-XCR1 + Dendritic Cell Spatial and Functional Cooperativity to Optimize Priming

(2017) Anna Brewitz et al.   IMMUNITY

Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance

(2017) Sydney M. Shaffer et al.   NATURE

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

(2017) Keren Bahar Halpern et al.   NATURE

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

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

(2016) Meital Gury-BenAri et al.   CELL

Tissue Repair: How to Inflame Your Neighbours

(2016) Pascal Meier et al.   CURRENT BIOLOGY

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

(2016) P. L. Stahl et al.   SCIENCE

Visualizing antibody affinity maturation in germinal centers

(2016) J. M. J. Tas et al.   SCIENCE

Virus-specific antibodies allow viral replication in the marginal zone, thereby promoting CD8+ T-cell priming and viral control

(2016) Vikas Duhan et al.   Scientific Reports

Robust Anti-viral Immunity Requires Multiple Distinct T Cell-Dendritic Cell Interactions

(2015) Sarah Eickhoff et al.   CELL

Immunosurveillance of the Liver by Intravascular Effector CD8 + T Cells

(2015) Luca G. Guidotti et al.   CELL

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine 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

CD8 T Cells Enter the Splenic T Cell Zones Independently of CCR7, but the Subsequent Expansion and Trafficking Patterns of Effector T Cells after Infection Are Dysregulated in the Absence of CCR7 Migratory Cues

(2015) N. Sharma et al.   JOURNAL OF IMMUNOLOGY

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

(2015) Antonio Scialdone et al.   METHODS

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Spatiotemporal Basis of Innate and Adaptive Immunity in Secondary Lymphoid Tissue

(2014) Hai Qi et al.   Annual Review of Cell and Developmental Biology

Tissue-Resident Macrophage Enhancer Landscapes Are Shaped by the Local Microenvironment

(2014) Yonit Lavin et al.   CELL

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue

(2014) Ditte Lovatt et al.   NATURE METHODS

Dynamic signaling by T follicular helper cells during germinal center B cell selection

(2014) Z. Shulman 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

T Follicular Helper Cell Dynamics in Germinal Centers

(2013) Z. Shulman et al.   SCIENCE

Bisphosphonates Target B Cells to Enhance Humoral Immune Responses

(2013) Elena Tonti et al.   Cell Reports

Fate mapping analysis of lymphoid cells expressing the NKp46 cell surface receptor

(2011) E. Narni-Mancinelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germinal Center Dynamics Revealed by Multiphoton Microscopy with a Photoactivatable Fluorescent Reporter

(2010) Gabriel D. Victora et al.   CELL

Subcapsular sinus macrophages prevent CNS invasion on peripheral infection with a neurotropic virus

(2010) Matteo Iannacone et al.   NATURE

Single-Molecule Approaches to Stochastic Gene Expression

(2009) Arjun Raj et al.   Annual Review of Biophysics