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 …

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 …

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 …

Transfer learning enables predictions in network biology

CV Theodoris, L Xiao, A Chopra, MD Chaffin… - Nature, 2023 - nature.com
Mapping gene networks requires large amounts of transcriptomic data to learn the
connections between genes, which impedes discoveries in settings with limited data …

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 …

APOE4 impairs myelination via cholesterol dysregulation in oligodendrocytes

JW Blanchard, LA Akay, J Davila-Velderrain… - Nature, 2022 - nature.com
APOE4 is the strongest genetic risk factor for Alzheimer's disease,–. However, the effects of
APOE4 on the human brain are not fully understood, limiting opportunities to develop …

[HTML][HTML] Mild respiratory COVID can cause multi-lineage neural cell and myelin dysregulation

A Fernández-Castañeda, P Lu, AC Geraghty, E Song… - Cell, 2022 - cell.com
COVID survivors frequently experience lingering neurological symptoms that resemble
cancer-therapy-related cognitive impairment, a syndrome for which white matter microglial …

Identification of a tumour immune barrier in the HCC microenvironment that determines the efficacy of immunotherapy

Y Liu, Z Xun, K Ma, S Liang, X Li, S Zhou, L Sun… - Journal of …, 2023 - Elsevier
Background & Aims The tumour microenvironment (TME) is a crucial mediator of cancer
progression and therapeutic outcome. The TME subtype correlates with patient response to …

Pan-cancer T cell atlas links a cellular stress response state to immunotherapy resistance

Y Chu, E Dai, Y Li, G Han, G Pei, DR Ingram… - Nature medicine, 2023 - nature.com
Tumor-infiltrating T cells offer a promising avenue for cancer treatment, yet their states
remain to be fully characterized. Here we present a single-cell atlas of T cells from 308,048 …

[HTML][HTML] Dynamic CD8+ T cell responses to cancer immunotherapy in human regional lymph nodes are disrupted in metastatic lymph nodes

MK Rahim, TLH Okholm, KB Jones, EE McCarthy… - Cell, 2023 - cell.com
CD8+ T cell responses are critical for anti-tumor immunity. While extensively profiled in the
tumor microenvironment, recent studies in mice identified responses in lymph nodes (LNs) …