Current best practices in single‐cell RNA‐seq analysis: a tutorial

MD Luecken, FJ Theis - Molecular systems biology, 2019 - embopress.org
Single‐cell RNA‐seq has enabled gene expression to be studied at an unprecedented
resolution. The promise of this technology is attracting a growing user base for single‐cell …

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 …

Long COVID manifests with T cell dysregulation, inflammation and an uncoordinated adaptive immune response to SARS-CoV-2

K Yin, MJ Peluso, X Luo, R Thomas, MG Shin… - Nature …, 2024 - nature.com
Long COVID (LC) occurs after at least 10% of severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) infections, yet its etiology remains poorly understood. We used …

The enteric nervous system relays psychological stress to intestinal inflammation

KM Schneider, N Blank, Y Alvarez, K Thum… - Cell, 2023 - cell.com
Mental health profoundly impacts inflammatory responses in the body. This is particularly
apparent in inflammatory bowel disease (IBD), in which psychological stress is associated …

The scverse project provides a computational ecosystem for single-cell omics data analysis

I Virshup, D Bredikhin, L Heumos, G Palla… - Nature …, 2023 - nature.com
Single-cell omics technologies have enabled the creation of comprehensive cell atlases
across tissues and species and delivered key insights into the biological mechanisms …

[HTML][HTML] MicrobiotaProcess: A comprehensive R package for deep mining microbiome

S Xu, L Zhan, W Tang, Q Wang, Z Dai, L Zhou, T Feng… - The Innovation, 2023 - cell.com
The data output from microbiome research is growing at an accelerating rate, yet mining the
data quickly and efficiently remains difficult. There is still a lack of an effective data structure …

Oxidative phosphorylation selectively orchestrates tissue macrophage homeostasis

SK Wculek, I Heras-Murillo, A Mastrangelo, D Mañanes… - Immunity, 2023 - cell.com
In vitro studies have associated oxidative phosphorylation (OXPHOS) with anti-inflammatory
macrophages, whereas pro-inflammatory macrophages rely on glycolysis. However, the …

Effect of long-term caloric restriction on DNA methylation measures of biological aging in healthy adults from the CALERIE trial

R Waziry, CP Ryan, DL Corcoran, KM Huffman… - Nature Aging, 2023 - nature.com
The geroscience hypothesis proposes that therapy to slow or reverse molecular changes
that occur with aging can delay or prevent multiple chronic diseases and extend healthy …

Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation

S Kaluscha, S Domcke, C Wirbelauer, MB Stadler… - Nature …, 2022 - nature.com
Cytosine methylation efficiently silences CpG-rich regulatory regions of genes and repeats
in mammalian genomes. To what extent this entails direct inhibition of transcription factor …

β-Hydroxybutyrate suppresses colorectal cancer

O Dmitrieva-Posocco, AC Wong, P Lundgren… - Nature, 2022 - nature.com
Colorectal cancer (CRC) is among the most frequent forms of cancer, and new strategies for
its prevention and therapy are urgently needed. Here we identify a metabolite signalling …