Opportunities and challenges in long-read sequencing data analysis

SL Amarasinghe, S Su, X Dong, L Zappia, ME Ritchie… - Genome biology, 2020 - Springer
Long-read technologies are overcoming early limitations in accuracy and throughput,
broadening their application domains in genomics. Dedicated analysis tools that take into …

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 …

Blocking PD-L1–PD-1 improves senescence surveillance and ageing phenotypes

TW Wang, Y Johmura, N Suzuki, S Omori, T Migita… - Nature, 2022 - nature.com
The accumulation of senescent cells is a major cause of age-related inflammation and
predisposes to a variety of age-related diseases. However, little is known about the …

Distinct contributions of partial and full EMT to breast cancer malignancy

F Lüönd, N Sugiyama, R Bill, L Bornes, C Hager… - Developmental cell, 2021 - cell.com
Epithelial-mesenchymal transition (EMT) is a transient, reversible process of cell de-
differentiation where cancer cells transit between various stages of an EMT continuum …

IL-1β+ macrophages fuel pathogenic inflammation in pancreatic cancer

N Caronni, F La Terza, FM Vittoria, G Barbiera… - Nature, 2023 - nature.com
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with high resistance to
therapies. Inflammatory and immunomodulatory signals co-exist in the pancreatic tumour …

[HTML][HTML] Mucosal fungi promote gut barrier function and social behavior via Type 17 immunity

I Leonardi, IH Gao, WY Lin, M Allen, XV Li, WD Fiers… - Cell, 2022 - cell.com
Fungal communities (the mycobiota) are an integral part of the gut microbiota, and the
disruption of their integrity contributes to local and gut-distal pathologies. Yet, the …

Chromatin profiles classify castration-resistant prostate cancers suggesting therapeutic targets

F Tang, D Xu, S Wang, CK Wong… - Science, 2022 - science.org
In castration-resistant prostate cancer (CRPC), the loss of androgen receptor (AR)
dependence leads to clinically aggressive tumors with few therapeutic options. We used …

[HTML][HTML] MYB orchestrates T cell exhaustion and response to checkpoint inhibition

C Tsui, L Kretschmer, S Rapelius, SS Gabriel… - Nature, 2022 - nature.com
CD8+ T cells that respond to chronic viral infections or cancer are characterized by the
expression of inhibitory receptors such as programmed cell death protein 1 (PD-1) and by …

Inulin fibre promotes microbiota-derived bile acids and type 2 inflammation

M Arifuzzaman, TH Won, TT Li, H Yano, S Digumarthi… - Nature, 2022 - nature.com
Dietary fibres can exert beneficial anti-inflammatory effects through microbially fermented
short-chain fatty acid metabolites,, although the immunoregulatory roles of most fibre diets …

Cellular and transcriptional dynamics of human neutrophils at steady state and upon stress

E Montaldo, E Lusito, V Bianchessi, N Caronni… - Nature …, 2022 - nature.com
Traditionally viewed as poorly plastic, neutrophils are now recognized as functionally
diverse; however, the extent and determinants of neutrophil heterogeneity in humans remain …