SPEED: Single-cell Pan-species atlas in the light of Ecology and Evolution for Development and Diseases

Somatic mutation rates scale with lifespan across mammals

(2022) Alex Cagan et al.   NATURE

Single-cell genomic profiling of human dopamine neurons identifies a population that selectively degenerates in Parkinson’s disease

(2022) Tushar Kamath et al.   NATURE NEUROSCIENCE

Joint profiling of gene expression and chromatin accessibility during amphioxus development at single-cell resolution

(2022) Pengcheng Ma et al.   Cell Reports

Single-cell RNA sequencing reveals SARS-CoV-2 infection dynamics in lungs of African green monkeys

(2021) Emily Speranza et al.   Science Translational Medicine

Single cell brain atlas of Parkinson’s disease mouse model

(2021) Jixing Zhong et al.   Journal of Genetics and Genomics

Inference and analysis of cell-cell communication using CellChat

(2021) Suoqin Jin et al.   Nature Communications

ShinyCell: simple and sharable visualization of single-cell gene expression data

(2021) John F Ouyang et al.   BIOINFORMATICS

A High-Resolution Cell Atlas of the Domestic Pig Lung and an Online Platform for Exploring Lung Single-Cell Data

(2021) Lijing Zhang et al.   Journal of Genetics and Genomics

Single-cell atlas of domestic pig cerebral cortex and hypothalamus

(2021) Jiacheng Zhu et al.   Science Bulletin

UCSC Cell Browser: visualize your single-cell data

(2021) Matthew L Speir et al.   BIOINFORMATICS

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Single-cell transcriptome analysis reveals the dynamics of human immune cells during early fetal skin development

(2021) Yingping Xu et al.   Cell Reports

Identification of distinct tumor cell populations and key genetic mechanisms through single cell sequencing in hepatoblastoma

(2021) Alexander Bondoc et al.   Communications Biology

VThunter: a database for single-cell screening of virus target cells in the animal kingdom

(2021) Dongsheng Chen et al.   NUCLEIC ACIDS RESEARCH

Single cell atlas for 11 non-model mammals, reptiles and birds

(2021) Dongsheng Chen et al.   Nature Communications

Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains

(2020) Ekaterina Khrameeva et al.   GENOME RESEARCH

Construction of a human cell landscape at single-cell level

(2020) Xiaoping Han et al.   NATURE

SC2disease: a manually curated database of single-cell transcriptome for human diseases

(2020) Tianyi Zhao et al.   NUCLEIC ACIDS RESEARCH

CSEA-DB: an omnibus for human complex trait and cell type associations

(2020) Yulin Dai et al.   NUCLEIC ACIDS RESEARCH

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

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Dissecting lung development and fibrosis at single-cell resolution

(2019) Donna L. Farber et al.   Genome Medicine

A cellular census of human lungs identifies novel cell states in health and in asthma

(2019) Felipe A. Vieira Braga et al.   NATURE MEDICINE

Cross-Species Single-Cell Analysis Reveals Divergence of the Primate Microglia Program

(2019) Laufey Geirsdottir et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Single-Cell Transcriptomic Analysis of Human Lung Provides Insights into the Pathobiology of Pulmonary Fibrosis

(2018) Paul A Reyfman et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting

(2018) Merav Cohen et al.   CELL

ArrayExpress update – from bulk to single-cell expression data

(2018) Awais Athar et al.   NUCLEIC ACIDS RESEARCH

CancerSEA: a cancer single-cell state atlas

(2018) Huating Yuan et al.   NUCLEIC ACIDS RESEARCH

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

TFBSbank: a platform to dissect the big data of protein–DNA interaction in human and model species

(2016) Dongsheng Chen et al.   NUCLEIC ACIDS RESEARCH

The Association between Gene-Environment Interactions and Diseases Involving the Human GST Superfamily with SNP Variants

(2016) Antoinesha Hollman et al.   International Journal of Environmental Research and Public Health

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS