Identifying cell types to interpret scRNA-seq data: how, why and more possibilities

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

SuperCT: a supervised-learning framework for enhanced characterization of single-cell transcriptomic profiles

(2019) Peng Xie et al.   NUCLEIC ACIDS RESEARCH

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

(2019) Jurrian K de Kanter et al.   NUCLEIC ACIDS RESEARCH

Chemoresistance Evolution in Triple-Negative Breast Cancer Delineated by Single-Cell Sequencing

(2018) Charissa Kim et al.   CELL

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

(2018) Xinyi Guo et al.   NATURE MEDICINE

Single-cell profiling of breast cancer T cells reveals a tissue-resident memory subset associated with improved prognosis

(2018) Peter Savas et al.   NATURE MEDICINE

Phenotype molding of stromal cells in the lung tumor microenvironment

(2018) Diether Lambrechts et al.   NATURE MEDICINE

scmap: projection of single-cell RNA-seq data across data sets

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq

(2018) Mariella G. Filbin et al.   SCIENCE

Single-cell Wnt signaling niches maintain stemness of alveolar type 2 cells

(2018) Ahmad N. Nabhan et al.   SCIENCE

Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation

(2018) William Stephenson et al.   Nature Communications

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

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

(2018) Livnat Jerby-Arnon et al.   CELL

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

(2018) et al.   NATURE

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

(2017) Todd M Gierahn et al.   NATURE METHODS

Research Highlights

(2017) Fadi Issa   TRANSPLANTATION

Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer

(2017) Woosung Chung et al.   Nature Communications

Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma

(2017) Spyros Darmanis et al.   Cell Reports

A Targetable EGFR-Dependent Tumor-Initiating Program in Breast Cancer

(2017) Paul Savage et al.   Cell Reports

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

The International Human Epigenome Consortium: A Blueprint for Scientific Collaboration and Discovery

(2016) Hendrik G. Stunnenberg et al.   CELL

The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability

(2016) Alexander D. Diehl et al.   Journal of Biomedical Semantics

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

The Types of Retinal Ganglion Cells: Current Status and Implications for Neuronal Classification

(2015) Joshua R. Sanes et al.   Annual Review of Neuroscience

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

(2015) Evan Z. Macosko et al.   CELL

Joseph von Gerlach (1820–1896)

(2015) Frank W. Stahnisch   JOURNAL OF NEUROLOGY

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

(2014) Simone Picelli et al.   Nature Protocols

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

(2014) D. A. Jaitin et al.   SCIENCE

Beyond the transcriptome: completion of act one of the Immunological Genome Project

(2013) Charles C Kim et al.   CURRENT OPINION IN IMMUNOLOGY

Identification of transcriptional regulators in the mouse immune system

(2013) Vladimir Jojic et al.   NATURE IMMUNOLOGY

Genetic and Environmental Determinants of Human NK Cell Diversity Revealed by Mass Cytometry

(2013) A. Horowitz et al.   Science Translational Medicine

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY