Best practices for single-cell analysis across modalities

L Heumos, AC Schaar, C Lance, A Litinetskaya… - Nature Reviews …, 2023 - nature.com
Recent advances in single-cell technologies have enabled high-throughput molecular
profiling of cells across modalities and locations. Single-cell transcriptomics data can now …

Methods and applications for single-cell and spatial multi-omics

K Vandereyken, A Sifrim, B Thienpont… - Nature Reviews Genetics, 2023 - nature.com
The joint analysis of the genome, epigenome, transcriptome, proteome and/or metabolome
from single cells is transforming our understanding of cell biology in health and disease. In …

TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining

C Chen, Y Wu, J Li, X Wang, Z Zeng, J Xu, Y Liu… - Molecular plant, 2023 - cell.com
Since the official release of the stand-alone bioinformatics toolkit TBtools in 2020, its
superior functionality in data analysis has been demonstrated by its widespread adoption by …

An integrated cell atlas of the lung in health and disease

L Sikkema, C Ramírez-Suástegui, DC Strobl… - Nature medicine, 2023 - nature.com
Single-cell technologies have transformed our understanding of human tissues. Yet, studies
typically capture only a limited number of donors and disagree on cell type definitions …

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 …

cGAS–STING drives ageing-related inflammation and neurodegeneration

MF Gulen, N Samson, A Keller, M Schwabenland… - Nature, 2023 - nature.com
Low-grade inflammation is a hallmark of old age and a central driver of ageing-associated
impairment and disease. Multiple factors can contribute to ageing-associated inflammation; …

scGPT: toward building a foundation model for single-cell multi-omics using generative AI

H Cui, C Wang, H Maan, K Pang, F Luo, N Duan… - Nature …, 2024 - nature.com
Generative pretrained models have achieved remarkable success in various domains such
as language and computer vision. Specifically, the combination of large-scale diverse …

CellMarker 2.0: an updated database of manually curated cell markers in human/mouse and web tools based on scRNA-seq data

C Hu, T Li, Y Xu, X Zhang, F Li, J Bai… - Nucleic acids …, 2023 - academic.oup.com
Abstract CellMarker 2.0 (http://bio-bigdata. hrbmu. edu. cn/CellMarker or http://117.50.
127.228/CellMarker/) is an updated database that provides a manually curated collection of …

[HTML][HTML] Dietary tryptophan metabolite released by intratumoral Lactobacillus reuteri facilitates immune checkpoint inhibitor treatment

MJ Bender, AC McPherson, CM Phelps, SP Pandey… - Cell, 2023 - cell.com
The use of probiotics by cancer patients is increasing, including among those undergoing
immune checkpoint inhibitor (ICI) treatment. Here, we elucidate a critical microbial-host …

Mechanisms of antigen escape from BCMA-or GPRC5D-targeted immunotherapies in multiple myeloma

H Lee, S Ahn, R Maity, N Leblay, B Ziccheddu… - Nature medicine, 2023 - nature.com
B cell maturation antigen (BCMA) target loss is considered to be a rare event that mediates
multiple myeloma (MM) resistance to anti-BCMA chimeric antigen receptor T cell (CAR T) or …