Construction of a human cell landscape at single-cell level

A single-cell molecular map of mouse gastrulation and early organogenesis

(2019) Blanca Pijuan-Sala et al.   NATURE

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

A human liver cell atlas reveals heterogeneity and epithelial progenitors

(2019) Nadim Aizarani et al.   NATURE

Conserved cell types with divergent features in human versus mouse cortex

(2019) Rebecca D. Hodge et al.   NATURE

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

(2018) Arnau Sebé-Pedrós et al.   CELL

Mapping the Mouse Cell Atlas by Microwell-Seq

(2018) Xiaoping Han et al.   CELL

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing

(2018) Shuai Gao et al.   NATURE CELL BIOLOGY

Cell type transcriptome atlas for the planarianSchmidtea mediterranea

(2018) Christopher T. Fincher et al.   SCIENCE

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics

(2018) Mireya Plass et al.   SCIENCE

Evolution of pallium, hippocampus, and cortical cell types revealed by single-cell transcriptomics in reptiles

(2018) Maria Antonietta Tosches et al.   SCIENCE

Single-cell reconstruction of developmental trajectories during zebrafish embryogenesis

(2018) Jeffrey A. Farrell et al.   SCIENCE

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor

(2018) Megan Crow et al.   Nature Communications

Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis

(2018) Mei Wang et al.   Cell Stem Cell

A single-cell atlas of the airway epithelium reveals the CFTR-rich pulmonary ionocyte

(2018) Lindsey W. Plasschaert et al.   NATURE

RNA velocity of single cells

(2018) Gioele La Manno et al.   NATURE

Intra-tumour diversification in colorectal cancer at the single-cell level

(2018) Sophie F. Roerink et al.   NATURE

Single-cell transcriptomes from human kidneys reveal the cellular identity of renal tumors

(2018) Matthew D. Young et al.   SCIENCE

The adult human testis transcriptional cell atlas

(2018) Jingtao Guo et al.   CELL RESEARCH

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

(2018) et al.   NATURE

Single-cell reconstruction of the early maternal–fetal interface in humans

(2018) Roser Vento-Tormo et al.   NATURE

Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas

(2018) Shengbao Suo et al.   Cell Reports

Multilineage communication regulates human liver bud development from pluripotency

(2017) J. Gray Camp et al.   NATURE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain

(2017) Blue B Lake et al.   NATURE BIOTECHNOLOGY

Human haematopoietic stem cell lineage commitment is a continuous process

(2017) Lars Velten et al.   NATURE CELL BIOLOGY

SCENIC: single-cell regulatory network inference and clustering

(2017) Sara Aibar et al.   NATURE METHODS

Integrative single-cell and cell-free plasma RNA transcriptomics elucidates placental cellular dynamics

(2017) Jason C. H. Tsang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors

(2017) Alexandra-Chloé Villani et al.   SCIENCE

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells

(2016) Gioele La Manno et al.   CELL

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

(2016) Åsa Segerstolpe et al.   Cell Metabolism

De Novo Prediction of Stem Cell Identity using Single-Cell Transcriptome Data

(2016) Dominic Grün et al.   Cell Stem Cell

Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

(2016) Florian Schmidt et al.   NUCLEIC ACIDS 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

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

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

Defining the three cell lineages of the human blastocyst by single-cell RNA-seq

(2015) P. Blakeley et al.   DEVELOPMENT

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

(2015) Florian Buettner et al.   NATURE BIOTECHNOLOGY

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development

(2015) J. Gray Camp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Reconstructing lineage hierarchies of the distal lung epithelium using single-cell RNA-seq

(2014) Barbara Treutlein et al.   NATURE

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

(2013) Alex K. Shalek et al.   NATURE

Using networks to measure similarity between genes: association index selection

(2013) Juan I Fuxman Bass et al.   NATURE METHODS

Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells

(2013) Liying Yan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

Unlocking the secrets of the genome

(2009) Susan E. Celniker et al.   NATURE

mRNA-Seq whole-transcriptome analysis of a single cell

(2009) Fuchou Tang et al.   NATURE METHODS