The technological landscape and applications of single-cell multi-omics

A Baysoy, Z Bai, R Satija, R Fan - Nature Reviews Molecular Cell …, 2023 - nature.com
Single-cell multi-omics technologies and methods characterize cell states and activities by
simultaneously integrating various single-modality omics methods that profile the …

Gene regulatory network inference in the era of single-cell multi-omics

P Badia-i-Mompel, L Wessels, S Müller-Dott… - Nature Reviews …, 2023 - nature.com
The interplay between chromatin, transcription factors and genes generates complex
regulatory circuits that can be represented as gene regulatory networks (GRNs). The study …

Single-cell proteomics enabled by next-generation sequencing or mass spectrometry

HM Bennett, W Stephenson, CM Rose, S Darmanis - Nature Methods, 2023 - nature.com
In the last decade, single-cell RNA sequencing routinely performed on large numbers of
single cells has greatly advanced our understanding of the underlying heterogeneity of …

Glycoproteomics

I Bagdonaite, SA Malaker, DA Polasky… - Nature Reviews …, 2022 - nature.com
Protein glycosylation involves the co-translational or post-translational addition of glycans to
proteins and is a crucial protein modification in health and disease. The aim of …

Unbiased spatial proteomics with single-cell resolution in tissues

A Mund, AD Brunner, M Mann - Molecular Cell, 2022 - cell.com
Mass spectrometry (MS)-based proteomics has become a powerful technology to quantify
the entire complement of proteins in cells or tissues. Here, we review challenges and recent …

Single-cell proteomic and transcriptomic analysis of macrophage heterogeneity using SCoPE2

H Specht, E Emmott, AA Petelski, RG Huffman… - Genome biology, 2021 - Springer
Background Macrophages are innate immune cells with diverse functional and molecular
phenotypes. This diversity is largely unexplored at the level of single-cell proteomes …

mRNAs, proteins and the emerging principles of gene expression control

C Buccitelli, M Selbach - Nature Reviews Genetics, 2020 - nature.com
Gene expression involves transcription, translation and the turnover of mRNAs and proteins.
The degree to which protein abundances scale with mRNA levels and the implications in …

Large-scale deep multi-layer analysis of Alzheimer's disease brain reveals strong proteomic disease-related changes not observed at the RNA level

ECB Johnson, EK Carter, EB Dammer, DM Duong… - Nature …, 2022 - nature.com
The biological processes that are disrupted in the Alzheimer's disease (AD) brain remain
incompletely understood. In this study, we analyzed the proteomes of more than 1,000 brain …

Ultra‐high sensitivity mass spectrometry quantifies single‐cell proteome changes upon perturbation

AD Brunner, M Thielert, C Vasilopoulou… - Molecular systems …, 2022 - embopress.org
Single‐cell technologies are revolutionizing biology but are today mainly limited to imaging
and deep sequencing. However, proteins are the main drivers of cellular function and in …

Initial recommendations for performing, benchmarking and reporting single-cell proteomics experiments

L Gatto, R Aebersold, J Cox, V Demichev, J Derks… - Nature …, 2023 - nature.com
Analyzing proteins from single cells by tandem mass spectrometry (MS) has recently
become technically feasible. While such analysis has the potential to accurately quantify …