Nature Search

Single-cell analysis at the threshold

A discussion of some of the challenges and promise of single-cell technology.

Xi Chen
J Christopher Love
Sarah A Teichmann
Special Features08 Nov 2016
Nature Biotechnology

Volume: 34, P: 1111-1118
Reply to: UMI or not UMI, that is the question for scRNA-seq zero-inflation

Valentine Svensson
Research01 Feb 2021
Nature Biotechnology

Volume: 39, P: 160
Droplet scRNA-seq is not zero-inflated

Valentine Svensson
Correspondence14 Jan 2020
Nature Biotechnology

Volume: 38, P: 147-150
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

The authors describe an integrated atlas of the diverse cell types in the mouse primary motor cortex.

Zizhen Yao
Hanqing Liu
Eran A. Mukamel
ResearchOpen Access06 Oct 2021
Nature

Volume: 598, P: 103-110
Single-cell transcriptomics identifies CD44 as a marker and regulator of endothelial to haematopoietic transition

The endothelial to haematopoietic transition (EHT) is the process where haemogenic endothelium differentiates into haematopoietic stem and progenitor cells (HSPCs). Here the authors use single cell transcriptomics and antibody screening to identify CD44 as a marker of EHT that is required for EHT and HSPC development.

Morgan Oatley
Özge Vargel Bölükbası
Christophe Lancrin
ResearchOpen Access29 Jan 2020
Nature Communications

Volume: 11, P: 1-18
Power analysis of single-cell RNA-sequencing experiments

A comparison framework applied to 15 single-cell RNA-seq protocols reveals differences in accuracy and sensitivity and discusses the utility of RNA spike-in standards.

Valentine Svensson
Kedar Nath Natarajan
Sarah A Teichmann
Research06 Mar 2017
Nature Methods

Volume: 14, P: 381-387
Exponential scaling of single-cell RNA-seq in the past decade

Here Sarah Teichmann and colleagues provide a Perspective on the exponential scaling of single-cell RNA-sequencing experiments over the last decade, commenting on the methodological developments that have underpinned the advances in this technology.

Valentine Svensson
Roser Vento-Tormo
Sarah A Teichmann
Reviews01 Mar 2018
Nature Protocols

Volume: 13, P: 599-604
A multimodal cell census and atlas of the mammalian primary motor cortex

The BRAIN Initiative Cell Census Network has constructed a multimodal cell census and atlas of the mammalian primary motor cortex in a landmark effort towards understanding brain cell-type diversity, neural circuit organization and brain function.

Edward M. Callaway
Hong-Wei Dong
Susan Sunkin
ResearchOpen Access06 Oct 2021
Nature

Volume: 598, P: 86-102
A Python library for probabilistic analysis of single-cell omics data

Adam Gayoso
Romain Lopez
Nir Yosef
Correspondence07 Feb 2022
Nature Biotechnology

Volume: 40, P: 163-166
Transcriptome dynamics of CD4⁺ T cells during malaria maps gradual transit from effector to memory

CD4⁺ T cells are critical for effective responses to infection with the malaria parasite. Haque and colleagues use single-cell RNA sequencing and computational modeling to track T cell memory development during experimental Plasmodium infection of mice.

Megan S. F. Soon
Hyun Jae Lee
Ashraful Haque
Research12 Oct 2020
Nature Immunology

Volume: 21, P: 1597-1610
SpatialDE: identification of spatially variable genes

SpatialDE identifies genes with significant spatial expression patterns from multiplexed imaging or spatial RNA-sequencing data, and can cluster genes with similar spatial patterns as a form of expression-based tissue histology.

Valentine Svensson
Sarah A Teichmann
Oliver Stegle
Research19 Mar 2018
Nature Methods

Volume: 15, P: 343-346
Defining and benchmarking open problems in single-cell analysis

Malte D. Luecken
Scott Gigante
Smita Krishnaswamy
Correspondence01 Jul 2025
Nature Biotechnology

Volume: 43, P: 1035-1040
Single-cell RNA-sequencing resolves self-antigen expression during mTEC development

Ricardo J. Miragaia
Xiuwei Zhang
Tapio Lönnberg
ResearchOpen Access12 Jan 2018
Scientific Reports

Volume: 8, P: 1-13

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