Annotation of cell types (ACT): a convenient web server for cell type annotation

Single-cell profiling reveals differences between human classical adenocarcinoma and mucinous adenocarcinoma

(2023) Fang-Jie Hu et al.   Communications Biology

Single-cell sequencing reveals the evolution of immune molecules across multiple vertebrate species

(2023) Anjun Jiao et al.   Journal of Advanced Research

A single-cell atlas of human and mouse white adipose tissue

(2022) Margo P. Emont et al.   NATURE

Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data

(2022) Aleksandr Ianevski et al.   Nature Communications

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

(2022) Ignasius Joanito et al.   NATURE GENETICS

Genenames.org: the HGNC resources in 2023

(2022) Ruth L Seal et al.   NUCLEIC ACIDS RESEARCH

Toward comprehensive functional analysis of gene lists weighted by gene essentiality scores

(2021) Rui Fan et al.   BIOINFORMATICS

Mitogen‐activated protein kinase activity drives cell trajectories in colorectal cancer

(2021) Florian Uhlitz et al.   EMBO Molecular Medicine

Tutorial: guidelines for annotating single-cell transcriptomic maps using automated and manual methods

(2021) Zoe A. Clarke et al.   Nature Protocols

Fibroblast fusion to the muscle fiber regulates myotendinous junction formation

(2021) Wesal Yaseen et al.   Nature Communications

A single–cell type transcriptomics map of human tissues

(2021) Max Karlsson et al.   Science Advances

A conserved dendritic-cell regulatory program limits antitumour immunity

(2020) Barbara Maier et al.   NATURE

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

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

(2020) Yinghao Cao et al.   Frontiers in Genetics

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

(2020) Yingxin Lin et al.   Molecular Systems Biology

A single-cell atlas of the human substantia nigra reveals cell-specific pathways associated with neurological disorders

(2020) Devika Agarwal et al.   Nature Communications

Mouse Genome Database (MGD): Knowledgebase for mouse–human comparative biology

(2020) Judith A Blake et al.   NUCLEIC ACIDS RESEARCH

Evaluation of Cell Type Annotation R Packages on Single-cell RNA-seq Data

(2020) Qianhui Huang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

(2019) Ilias Angelidis et al.   Nature Communications

Altered human oligodendrocyte heterogeneity in multiple sclerosis

(2019) Sarah Jäkel et al.   NATURE

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Neuronal vulnerability and multilineage diversity in multiple sclerosis

(2019) Lucas Schirmer et al.   NATURE

Clonal replacement of tumor-specific T cells following PD-1 blockade

(2019) Kathryn E. Yost et al.   NATURE MEDICINE

SCINA: Semi-Supervised Analysis of Single Cells in Silico

(2019) Zhang et al.   Genes

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

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

Transcript-indexed ATAC-seq for precision immune profiling

(2018) Ansuman T. Satpathy et al.   NATURE MEDICINE

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

(2018) Vladimir Yu Kiselev et al.   NATURE METHODS

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

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

(2018) et al.   NATURE

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

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

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

(2015) Evan Z. Macosko et al.   CELL

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

(2014) Melissa A Haendel et al.   Journal of Biomedical Semantics

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS