scDeepSort: a pre-trained cell-type annotation method for single-cell transcriptomics using deep learning with a weighted graph neural network

Automated methods for cell type annotation on scRNA-seq data

(2021) Giovanni Pasquini et al.   Computational and Structural Biotechnology Journal

scGNN is a novel graph neural network framework for single-cell RNA-Seq analyses

(2021) Juexin Wang et al.   Nature Communications

Molecular architecture of the developing mouse brain

(2021) Gioele La Manno et al.   NATURE

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

New avenues for systematically inferring cell-cell communication: through single-cell transcriptomics data

(2020) Xin Shao et al.   Protein & Cell

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

(2020) Yinghao Cao et al.   Frontiers in Genetics

Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

(2020) Jie Liao et al.   TRENDS IN BIOTECHNOLOGY

A Comprehensive Survey on Graph Neural Networks

(2020) Zonghan Wu et al.   IEEE Transactions on Neural Networks and Learning Systems

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

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

Supervised classification enables rapid annotation of cell atlases

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

Probabilistic cell-type assignment of single-cell RNA-seq for tumor microenvironment profiling

(2019) Allen W. Zhang et al.   NATURE METHODS

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Artificial Intelligence, Machine Learning, Deep Learning, and Cognitive Computing: What Do These Terms Mean and How Will They Impact Health Care?

(2018) Stefano A. Bini   JOURNAL OF ARTHROPLASTY

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

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

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

(2018) Arpiar Saunders et al.   CELL

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

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

(2018) et al.   NATURE

A primer on deep learning in genomics

(2018) James Zou et al.   NATURE GENETICS

A web server for comparative analysis of single-cell RNA-seq data

(2018) Amir Alavi et al.   Nature Communications

A unified deep-learning network to accurately segment insulin granules of different animal models imaged under different electron microscopy methodologies

(2018) Xiaoya Zhang et al.   Protein & Cell

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

(2017) Chiara Medaglia et al.   SCIENCE

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

Mastering the game of Go with deep neural networks and tree search

(2016) David Silver et al.   NATURE

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

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

Game-playing software holds lessons for neuroscience

(2015) Elizabeth Gibney   NATURE

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

(2014) D. A. Jaitin et al.   SCIENCE