Transformer for one stop interpretable cell type annotation

Deep learning shapes single-cell data analysis

(2022) Qin Ma et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Interpretable deep learning: interpretation, interpretability, trustworthiness, and beyond

(2022) Xuhong Li et al.   KNOWLEDGE AND INFORMATION SYSTEMS

Decoding the transcriptome of calcified atherosclerotic plaque at single-cell resolution

(2022) Tom Alsaigh et al.   Communications Biology

A pan-cancer single-cell transcriptional atlas of tumor infiltrating myeloid cells

(2021) Sijin Cheng et al.   CELL

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

Benchmarking atlas-level data integration in single-cell genomics

(2021) Malte D. Luecken et al.   NATURE METHODS

Pan-cancer single-cell landscape of tumor-infiltrating T cells

(2021) Liangtao Zheng et al.   SCIENCE

SciBet as a portable and fast single cell type identifier

(2020) Chenwei Li et al.   Nature Communications

SCSA: A Cell Type Annotation Tool for Single-Cell RNA-seq Data

(2020) Yinghao Cao et al.   Frontiers in Genetics

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

(2020) Ji-Hye Choi et al.   BMC BIOINFORMATICS

A single-cell transcriptomic atlas characterizes ageing tissues in the mouse

(2020)   NATURE

Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST

(2020) Zhi-Jie Cao et al.   Nature Communications

Synovial cell cross-talk with cartilage plays a major role in the pathogenesis of osteoarthritis

(2020) Ching-Heng Chou et al.   Scientific Reports

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Pancreatic acinar differentiation is guided by differential laminin deposition

(2019) Charlotte Heymans et al.   Scientific Reports

Two distinct interstitial macrophage populations coexist across tissues in specific subtissular niches

(2019) Svetoslav Chakarov et al.   SCIENCE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Comprehensive single cell mRNA profiling reveals a detailed roadmap for pancreatic endocrinogenesis

(2019) Aimée Bastidas-Ponce et al.   DEVELOPMENT

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

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

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

SingleCellNet: A Computational Tool to Classify Single Cell RNA-Seq Data Across Platforms and Across Species

(2019) Yuqi Tan et al.   Cell Systems

Single-Cell Analysis of Human Mononuclear Phagocytes Reveals Subset-Defining Markers and Identifies Circulating Inflammatory Dendritic Cells

(2019) Charles-Antoine Dutertre et al.   IMMUNITY

Supervised classification enables rapid annotation of cell atlases

(2019) Hannah A. Pliner et al.   NATURE METHODS

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

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

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

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Molecular Diversity and Specializations among the Cells of the Adult Mouse Brain

(2018) Arpiar Saunders et al.   CELL

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

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

(2018) et al.   NATURE

Multiplexed droplet single-cell RNA-sequencing using natural genetic variation

(2017) Hyun Min Kang et al.   NATURE BIOTECHNOLOGY

RNA Sequencing of Single Human Islet Cells Reveals Type 2 Diabetes Genes

(2016) Yurong Xin et al.   Cell Metabolism

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes

(2016) Åsa Segerstolpe et al.   Cell Metabolism

Single-cell transcriptomes identify human islet cell signatures and reveal cell-type–specific expression changes in type 2 diabetes

(2016) Nathan Lawlor et al.   GENOME RESEARCH

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

Identification of cell types from single-cell transcriptomes using a novel clustering method

(2015) Chen Xu et al.   BIOINFORMATICS

Diffusion maps for high-dimensional single-cell analysis of differentiation data

(2015) Laleh Haghverdi et al.   BIOINFORMATICS

Regulation of mouse chondrocyte differentiation by CCAAT/enhancer-binding proteins

(2015) Tomotake OKUMA et al.   BIOMEDICAL RESEARCH-TOKYO

FGFR1 signaling in hypertrophic chondrocytes is attenuated by the Ras-GAP neurofibromin during endochondral bone formation

(2015) Matthew R. Karolak et al.   HUMAN MOLECULAR GENETICS

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

IFN-γ induces lipogenesis in mouse mesangial cells via the JAK2/STAT1 pathway

(2013) Jun Hao et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

Entering the era of single-cell transcriptomics in biology and medicine

(2013) Rickard Sandberg   NATURE METHODS