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

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

Childhood cerebellar tumours mirror conserved fetal transcriptional programs

(2019) Maria C. Vladoiu et al.   NATURE

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

The landscape of genomic alterations across childhood cancers

(2018) Susanne N. Gröbner et al.   NATURE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

Exponential scaling of single-cell RNA-seq in the past decade

(2018) Valentine Svensson et al.   Nature Protocols

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

(2018) Xiaotu Ma et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

CellBIC: bimodality-based top-down clustering of single-cell RNA sequencing data reveals hierarchical structure of the cell type

(2018) Junil Kim et al.   NUCLEIC ACIDS RESEARCH

CaSTLe – Classification of single cells by transfer learning: Harnessing the power of publicly available single cell RNA sequencing experiments to annotate new experiments

(2018) Yuval Lieberman et al.   PLoS One

CancerSEA: a cancer single-cell state atlas

(2018) Huating Yuan et al.   NUCLEIC ACIDS RESEARCH

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

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

(2017) Huipeng Li et al.   NATURE GENETICS

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Single-cell mRNA quantification and differential analysis with Census

(2017) Xiaojie Qiu et al.   NATURE METHODS

Reversed graph embedding resolves complex single-cell trajectories

(2017) Xiaojie Qiu et al.   NATURE METHODS

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

(2017) Woosung Chung et al.   Nature Communications

Estimation of immune cell content in tumour tissue using single-cell RNA-seq data

(2017) Max Schelker et al.   Nature Communications

Massively parallel digital transcriptional profiling of single cells

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Measuring Signaling and RNA-Seq in the Same Cell Links Gene Expression to Dynamic Patterns of NF-κB Activation

(2017) Keara Lane et al.   Cell Systems

What Is Your Conceptual Definition of “Cell Type” in the Context of a Mature Organism?

(2017)   Cell Systems

Expression of Markers of Hepatocellular Differentiation in Pancreatic Acinar Cell Neoplasms

(2016) Gokce Askan et al.   AMERICAN JOURNAL OF CLINICAL PATHOLOGY

Single-cell triple omics sequencing reveals genetic, epigenetic and transcriptomic heterogeneity in hepatocellular carcinomas

(2016) Yu Hou et al.   CELL RESEARCH

Single-cell barcoding and sequencing using droplet microfluidics

(2016) Rapolas Zilionis et al.   Nature Protocols

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

(2016) I. Tirosh et al.   SCIENCE

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

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

Design and Analysis of Single-Cell Sequencing Experiments

(2015) Dominic Grün et al.   CELL

Single-cell messenger RNA sequencing reveals rare intestinal cell types

(2015) Dominic Grün et al.   NATURE

Single-cell chromatin accessibility reveals principles of regulatory variation

(2015) Jason D. Buenrostro et al.   NATURE

Decoding the regulatory network of early blood development from single-cell gene expression measurements

(2015) Victoria Moignard et al.   NATURE BIOTECHNOLOGY

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state

(2015) Assaf Rotem et al.   NATURE BIOTECHNOLOGY

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Single-Cell Analysis in Cancer Genomics

(2015) Assieh Saadatpour et al.   TRENDS IN GENETICS

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

(2014) Simone Picelli et al.   Nature Protocols

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma

(2014) A. P. Patel et al.   SCIENCE

Expression of human cationic trypsinogen (PRSS1) in murine acinar cells promotes pancreatitis and apoptotic cell death

(2014) T Athwal et al.   Cell Death & Disease

Lineage Tracing Evidence for Transdifferentiation of Acinar to Duct Cells and Plasticity of Human Pancreas

(2011) Isabelle Houbracken et al.   GASTROENTEROLOGY

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

StellaTUM: current consensus and discussion on pancreatic stellate cell research

(2011) Mert Erkan et al.   GUT

Pancreatic ductal cells in development, regeneration, and neoplasia

(2011) Maximilian Reichert et al.   JOURNAL OF CLINICAL INVESTIGATION