Supervised classification enables rapid annotation of cell atlases

HA Pliner, J Shendure, C Trapnell - Nature methods, 2019 - nature.com
Single-cell molecular profiling technologies are gaining rapid traction, but the manual
process by which resulting cell types are typically annotated is labor intensive and rate …

Assessing GPT-4 for cell type annotation in single-cell RNA-seq analysis

W Hou, Z Ji - Nature Methods, 2024 - nature.com
Here we demonstrate that the large language model GPT-4 can accurately annotate cell
types using marker gene information in single-cell RNA sequencing analysis. When …

Annotation of spatially resolved single-cell data with STELLAR

M Brbić, K Cao, JW Hickey, Y Tan, MP Snyder… - Nature …, 2022 - nature.com
Accurate cell-type annotation from spatially resolved single cells is crucial to understand
functional spatial biology that is the basis of tissue organization. However, current …

CellTagging: combinatorial indexing to simultaneously map lineage and identity at single-cell resolution

W Kong, BA Biddy, K Kamimoto, JM Amrute… - Nature protocols, 2020 - nature.com
Single-cell technologies are offering unparalleled insight into complex biology, revealing the
behavior of rare cell populations that are masked in bulk population analyses. One current …

Revealing the vectors of cellular identity with single-cell genomics

A Wagner, A Regev, N Yosef - Nature biotechnology, 2016 - nature.com
Single-cell genomics has now made it possible to create a comprehensive atlas of human
cells. At the same time, it has reopened definitions of a cell's identity and of the ways in …

MARS: discovering novel cell types across heterogeneous single-cell experiments

M Brbić, M Zitnik, S Wang, AO Pisco, RB Altman… - Nature …, 2020 - nature.com
Although tremendous effort has been put into cell-type annotation, identification of
previously uncharacterized cell types in heterogeneous single-cell RNA-seq data remains a …

[HTML][HTML] A decade of molecular cell atlases

SR Quake - Trends in genetics, 2022 - cell.com
In recent years there has been tremendous progress towards deep molecular
characterization of cell types using single-cell transcriptome sequencing, creating so-called …

Leveraging the Cell Ontology to classify unseen cell types

S Wang, AO Pisco, A McGeever, M Brbic… - Nature …, 2021 - nature.com
Single cell technologies are rapidly generating large amounts of data that enables us to
understand biological systems at single-cell resolution. However, joint analysis of datasets …

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

DA Cusanovich, R Daza, A Adey, HA Pliner… - Science, 2015 - science.org
Technical advances have enabled the collection of genome and transcriptome data sets
with single-cell resolution. However, single-cell characterization of the epigenome has …

Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID

A Cortal, L Martignetti, E Six, A Rausell - Nature biotechnology, 2021 - nature.com
Because of the stochasticity associated with high-throughput single-cell sequencing, current
methods for exploring cell-type diversity rely on clustering-based computational approaches …