Automated methods for cell type annotation on scRNA-seq data

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments

(2020) H. Atakan Ekiz et al.   BMC BIOINFORMATICS

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

(2020) Ziwei Wang et al.   Briefings in Functional Genomics

Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis

(2020) Chiaowen Joyce Hsiao et al.   GENOME RESEARCH

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects

(2020) Elisabetta Mereu et al.   NATURE BIOTECHNOLOGY

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

(2020) Yinghao Cao et al.   Frontiers in Genetics

Comparative transcriptomics of primary cells in vertebrates

(2020) Tanvir Alam et al.   GENOME RESEARCH

scClassify: sample size estimation and multiscale classification of cells using single and multiple reference

(2020) Yingxin Lin et al.   Molecular Systems Biology

Tissue Stem Cells: Architects of Their Niches

(2020) Elaine Fuchs et al.   Cell Stem Cell

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

Challenges in unsupervised clustering of single-cell RNA-seq data

(2019) Vladimir Yu Kiselev et al.   NATURE REVIEWS GENETICS

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

(2019) Peng Xie et al.   NUCLEIC ACIDS RESEARCH

Integrative single-cell analysis

(2019) Tim Stuart et al.   NATURE REVIEWS GENETICS

LAmbDA: Label Ambiguous Domain Adaptation Dataset Integration Reduces Batch Effects and Improves Subtype Detection

(2019) Travis S Johnson et al.   BIOINFORMATICS

scMatch: a single-cell gene expression profile annotation tool using reference datasets

(2019) Rui Hou et al.   BIOINFORMATICS

Deep Learning in the Biomedical Applications: Recent and Future Status

(2019) Ryad Zemouri et al.   Applied Sciences-Basel

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

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

Evaluation of single-cell classifiers for single-cell RNA sequencing data sets

(2019) Xinlei Zhao et al.   BRIEFINGS IN BIOINFORMATICS

High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell

(2019) Song Chen et al.   NATURE BIOTECHNOLOGY

An ultra high-throughput method for single-cell joint analysis of open chromatin and transcriptome

(2019) Chenxu Zhu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Random forest based similarity learning for single cell RNA sequencing data

(2018) Maziyar Baran Pouyan et al.   BIOINFORMATICS

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

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Deep learning in biomedicine

(2018) Michael Wainberg et al.   NATURE BIOTECHNOLOGY

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

M3Drop: dropout-based feature selection for scRNASeq

(2018) Tallulah S Andrews et al.   BIOINFORMATICS

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

(2018) et al.   NATURE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

Dimensionality reduction for visualizing single-cell data using UMAP

(2018) Etienne Becht et al.   NATURE BIOTECHNOLOGY

CancerSEA: a cancer single-cell state atlas

(2018) Huating Yuan et al.   NUCLEIC ACIDS RESEARCH

Correction: 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

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

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

(2016) Hendrik G. Stunnenberg et al.   CELL

Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq

(2016) Barbara Treutlein et al.   NATURE

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

The Technology and Biology of Single-Cell RNA Sequencing

(2015) Aleksandra A. Kolodziejczyk et al.   MOLECULAR CELL

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

CellNet: Network Biology Applied to Stem Cell Engineering

(2014) Patrick Cahan et al.   CELL

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

The promise of single-cell sequencing

(2013) James Eberwine et al.   NATURE METHODS

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH