Reconstruction of cell spatial organization from single-cell RNA sequencing data based on ligand-receptor mediated self-assembly

Systemic sclerosis-associated interstitial lung disease

(2020) Apostolos Perelas et al.   Lancet Respiratory Medicine

A homozygous SFTPA1 mutation drives necroptosis of type II alveolar epithelial cells in patients with idiopathic pulmonary fibrosis

(2019) Akio Takezaki et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Gene expression cartography

(2019) Mor Nitzan et al.   NATURE

Deregulated Mucosal Immune Surveillance through Gut-Associated Regulatory T Cells and PD-1+T Cells in Human Colorectal Cancer

(2018) Hanae Fujimoto et al.   JOURNAL OF IMMUNOLOGY

Global characterization of T cells in non-small-cell lung cancer by single-cell sequencing

(2018) Xinyi Guo et al.   NATURE MEDICINE

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

(2018) Xiao Wang et al.   SCIENCE

The Pharmacology of T Cell Therapies

(2018) Michael C. Milone et al.   Molecular Therapy-Methods & Clinical Development

Precise spatio-temporal interruption of regulatory T cell-mediated CD8+ T cell suppression leads to tumor immunity

(2018) Xiaoyu Zhou et al.   CANCER RESEARCH

A Structured Tumor-Immune Microenvironment in Triple Negative Breast Cancer Revealed by Multiplexed Ion Beam Imaging

(2018) Leeat Keren et al.   CELL

Paired-cell sequencing enables spatial gene expression mapping of liver endothelial cells

(2018) Keren Bahar Halpern et al.   NATURE BIOTECHNOLOGY

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade

(2018) Livnat Jerby-Arnon et al.   CELL

Defining T Cell States Associated with Response to Checkpoint Immunotherapy in Melanoma

(2018) Moshe Sade-Feldman et al.   CELL

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Multi-axial self-organization properties of mouse embryonic stem cells into gastruloids

(2018) Leonardo Beccari et al.   NATURE

Lineage tracking reveals dynamic relationships of T cells in colorectal cancer

(2018) Lei Zhang et al.   NATURE

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

(2017) Keren Bahar Halpern et al.   NATURE

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

(2017) Chiara Medaglia et al.   SCIENCE

PD-1 Blockade with Pembrolizumab in Advanced Merkel-Cell Carcinoma

(2016) Paul T. Nghiem et al.   NEW ENGLAND JOURNAL OF MEDICINE

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

(2016) I. Tirosh et al.   SCIENCE

Quantitative approaches for investigating the spatial context of gene expression

(2016) Je H. Lee   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

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

Adoptive cell transfer as personalized immunotherapy for human cancer

(2015) S. A. Rosenberg et al.   SCIENCE

A draft network of ligand–receptor-mediated multicellular signalling in human

(2015) Jordan A. Ramilowski et al.   Nature Communications

Non-redundant requirement for CXCR3 signalling during tumoricidal T-cell trafficking across tumour vascular checkpoints

(2015) M. E. Mikucki et al.   Nature Communications

Targeting TLR2 Attenuates Pulmonary Inflammation and Fibrosis by Reversion of Suppressive Immune Microenvironment

(2014) H.-Z. Yang et al.   JOURNAL OF IMMUNOLOGY

CD63 Tetraspanin Is a Negative Driver of Epithelial-to-Mesenchymal Transition in Human Melanoma Cells

(2014) Antonella Lupia et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Clustering by fast search and find of density peaks

(2014) A. Rodriguez et al.   SCIENCE

Tertiary lymphoid structures in cancer and beyond

(2014) Marie-Caroline Dieu-Nosjean et al.   TRENDS IN IMMUNOLOGY

Pathogenesis of Idiopathic Pulmonary Fibrosis

(2013) Paul J. Wolters et al.   Annual Review of Pathology-Mechanisms of Disease

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

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS