[PDF][PDF] edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets

Y Chen, L Chen, ATL Lun, PL Baldoni… - Nucleic Acids …, 2025 - academic.oup.com
Abstract edgeR is an R/Bioconductor software package for differential analyses of
sequencing data in the form of read counts for genes or genomic features. Over the past 15 …

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 …

Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology

H Mathys, Z Peng, CA Boix, MB Victor, N Leary, S Babu… - Cell, 2023 - cell.com
Alzheimer's disease (AD) is the most common cause of dementia worldwide, but the
molecular and cellular mechanisms underlying cognitive impairment remain poorly …

FOXO1 enhances CAR T cell stemness, metabolic fitness and efficacy

JD Chan, CM Scheffler, I Munoz, K Sek, JN Lee… - Nature, 2024 - nature.com
Chimeric antigen receptor (CAR) T cell therapy has transformed the treatment of
haematological malignancies such as acute lymphoblastic leukaemia, B cell lymphoma and …

Live-seq enables temporal transcriptomic recording of single cells

W Chen, O Guillaume-Gentil, PY Rainer, CG Gäbelein… - Nature, 2022 - nature.com
Single-cell transcriptomics (scRNA-seq) has greatly advanced our ability to characterize
cellular heterogeneity. However, scRNA-seq requires lysing cells, which impedes further …

Multi-omic machine learning predictor of breast cancer therapy response

SJ Sammut, M Crispin-Ortuzar, SF Chin, E Provenzano… - Nature, 2022 - nature.com
Breast cancers are complex ecosystems of malignant cells and the tumour
microenvironment. The composition of these tumour ecosystems and interactions within …

Neurotoxic reactive astrocytes induce cell death via saturated lipids

KA Guttenplan, MK Weigel, P Prakash… - Nature, 2021 - nature.com
Astrocytes regulate the response of the central nervous system to disease and injury and
have been hypothesized to actively kill neurons in neurodegenerative disease,,,,–. Here we …

[HTML][HTML] Intratumoral CD8+ T cells with a tissue-resident memory phenotype mediate local immunity and immune checkpoint responses in breast cancer

B Virassamy, F Caramia, P Savas, S Sant, J Wang… - Cancer Cell, 2023 - cell.com
CD8+ tumor-infiltrating lymphocytes with a tissue-resident memory T (T RM) cell phenotype
are associated with favorable prognosis in patients with triple-negative breast cancer …

Pathogenic variants damage cell composition and single cell transcription in cardiomyopathies

D Reichart, EL Lindberg, H Maatz, AMA Miranda… - Science, 2022 - science.org
Pathogenic variants in genes that cause dilated cardiomyopathy (DCM) and arrhythmogenic
cardiomyopathy (ACM) convey high risks for the development of heart failure through …

Single-cell multi-omics analysis of the immune response in COVID-19

E Stephenson, G Reynolds, RA Botting… - Nature medicine, 2021 - nature.com
Abstract Analysis of human blood immune cells provides insights into the coordinated
response to viral infections such as severe acute respiratory syndrome coronavirus 2, which …