Orchestrating single-cell analysis with Bioconductor

RA Amezquita, ATL Lun, E Becht, VJ Carey… - Nature …, 2020 - nature.com
Recent technological advancements have enabled the profiling of a large number of
genome-wide features in individual cells. However, single-cell data present unique …

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

TS Andrews, VY Kiselev, D McCarthy, M Hemberg - Nature protocols, 2021 - nature.com
Single-cell RNA sequencing (scRNA-seq) is a popular and powerful technology that allows
you to profile the whole transcriptome of a large number of individual cells. However, the …

High-dimensional single-cell analysis of human natural killer cell heterogeneity

L Rebuffet, JE Melsen, B Escalière… - Nature …, 2024 - nature.com
Natural killer (NK) cells are innate lymphoid cells (ILCs) contributing to immune responses to
microbes and tumors. Historically, their classification hinged on a limited array of surface …

Cancer-associated fibroblast classification in single-cell and spatial proteomics data

L Cords, S Tietscher, T Anzeneder… - Nature …, 2023 - nature.com
Cancer-associated fibroblasts (CAFs) are a diverse cell population within the tumour
microenvironment, where they have critical effects on tumour evolution and patient …

Identification of a broadly fibrogenic macrophage subset induced by type 3 inflammation

T Fabre, AMS Barron, SM Christensen, S Asano… - Science …, 2023 - science.org
Macrophages are central orchestrators of the tissue response to injury, with distinct
macrophage activation states playing key roles in fibrosis progression and resolution …

A concerted neuron–astrocyte program declines in ageing and schizophrenia

E Ling, J Nemesh, M Goldman, N Kamitaki, N Reed… - Nature, 2024 - nature.com
Human brains vary across people and over time; such variation is not yet understood in
cellular terms. Here we describe a relationship between people's cortical neurons and …

Human distal airways contain a multipotent secretory cell that can regenerate alveoli

MC Basil, FL Cardenas-Diaz, JJ Kathiriya, MP Morley… - Nature, 2022 - nature.com
The human lung differs substantially from its mouse counterpart, resulting in a distinct distal
airway architecture affected by disease pathology in chronic obstructive pulmonary disease …

Identification of a protective microglial state mediated by miR-155 and interferon-γ signaling in a mouse model of Alzheimer's disease

Z Yin, S Herron, S Silveira, K Kleemann… - Nature …, 2023 - nature.com
Microglia play a critical role in brain homeostasis and disease progression. In
neurodegenerative conditions, microglia acquire the neurodegenerative phenotype (MGnD) …

[HTML][HTML] Spatially resolved multi-omics deciphers bidirectional tumor-host interdependence in glioblastoma

VM Ravi, P Will, J Kueckelhaus, N Sun, K Joseph… - Cancer cell, 2022 - cell.com
Glioblastomas are malignant tumors of the central nervous system hallmarked by subclonal
diversity and dynamic adaptation amid developmental hierarchies. The source of dynamic …

Auto-aggressive CXCR6+ CD8 T cells cause liver immune pathology in NASH

M Dudek, D Pfister, S Donakonda, P Filpe, A Schneider… - Nature, 2021 - nature.com
Nonalcoholic steatohepatitis (NASH) is a manifestation of systemic metabolic disease
related to obesity, and causes liver disease and cancer,. The accumulation of metabolites …