Mapping the mouse cell atlas by microwell-seq

X Han, R Wang, Y Zhou, L Fei, H Sun, S Lai… - Cell, 2018 - cell.com
Single-cell RNA sequencing (scRNA-seq) technologies are poised to reshape the current
cell-type classification system. However, a transcriptome-based single-cell atlas has not …

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

E Mereu, A Lafzi, C Moutinho, C Ziegenhain… - Nature …, 2020 - nature.com
Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the
transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands …

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

S Islam, U Kjällquist, A Moliner, P Zajac, JB Fan… - Genome …, 2011 - genome.cshlp.org
Our understanding of the development and maintenance of tissues has been greatly aided
by large-scale gene expression analysis. However, tissues are invariably complex, and …

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

Y Lin, Y Cao, HJ Kim, A Salim, TP Speed… - Molecular systems …, 2020 - embopress.org
Automated cell type identification is a key computational challenge in single‐cell RNA‐
sequencing (sc RNA‐seq) data. To capitalise on the large collection of well‐annotated sc …

From tissues to cell types and back: single-cell gene expression analysis of tissue architecture

X Chen, SA Teichmann, KB Meyer - Annual Review of …, 2018 - annualreviews.org
With the recent transformative developments in single-cell genomics and, in particular,
single-cell gene expression analysis, it is now possible to study tissues at the single-cell …

SINCERA: a pipeline for single-cell RNA-Seq profiling analysis

M Guo, H Wang, SS Potter, JA Whitsett… - PLoS computational …, 2015 - journals.plos.org
A major challenge in developmental biology is to understand the genetic and cellular
processes/programs driving organ formation and differentiation of the diverse cell types that …

Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram

T Biancalani, G Scalia, L Buffoni, R Avasthi, Z Lu… - Nature …, 2021 - nature.com
Charting an organs' biological atlas requires us to spatially resolve the entire single-cell
transcriptome, and to relate such cellular features to the anatomical scale. Single-cell and …

Integrating single-cell transcriptomic data across different conditions, technologies, and species

A Butler, P Hoffman, P Smibert, E Papalexi… - Nature …, 2018 - nature.com
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied
to experiments representing a single condition, technology, or species to discover and …

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

M Plass, J Solana, FA Wolf, S Ayoub, A Misios… - Science, 2018 - science.org
INTRODUCTION Understanding the differentiation of stem cells into the vast amount of cell
types that form the human body is a central problem of basic and medical science. The …

Construction of a human cell landscape at single-cell level

X Han, Z Zhou, L Fei, H Sun, R Wang, Y Chen, H Chen… - Nature, 2020 - nature.com
Single-cell analysis is a valuable tool for dissecting cellular heterogeneity in complex
systems. However, a comprehensive single-cell atlas has not been achieved for humans …