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 …

[HTML][HTML] Loss of epigenetic information as a cause of mammalian aging

JH Yang, M Hayano, PT Griffin, JA Amorim… - Cell, 2023 - cell.com
All living things experience an increase in entropy, manifested as a loss of genetic and
epigenetic information. In yeast, epigenetic information is lost over time due to the …

Transcriptome-wide profiling and quantification of N6-methyladenosine by enzyme-assisted adenosine deamination

YL **ao, S Liu, R Ge, Y Wu, C He, M Chen… - Nature …, 2023 - nature.com
Abstract N 6-methyladenosine (m6A), the most abundant internal messenger RNA
modification in higher eukaryotes, serves myriad roles in regulating cellular processes …

Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring

LE Colbert, MB El Alam, R Wang, T Karpinets, D Lo… - Cancer Cell, 2023 - cell.com
Tumor microbiota can produce active metabolites that affect cancer and immune cell
signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome …

[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 …

m6A RNA modifications are measured at single-base resolution across the mammalian transcriptome

L Hu, S Liu, Y Peng, R Ge, R Su, C Senevirathne… - Nature …, 2022 - nature.com
Functional studies of the RNA N 6-methyladenosine (m6A) modification have been limited
by an inability to map individual m6A-modified sites in whole transcriptomes. To enable such …

Haplotype-resolved diverse human genomes and integrated analysis of structural variation

P Ebert, PA Audano, Q Zhu, B Rodriguez-Martin… - Science, 2021 - science.org
INTRODUCTION The characterization of the full spectrum of genetic variation is critical to
understanding human health and disease. Recent technological advances have made it …

Cell-type-specific CAG repeat expansions and toxicity of mutant Huntingtin in human striatum and cerebellum

K Mätlik, M Baffuto, L Kus, AL Deshmukh, DA Davis… - Nature …, 2024 - nature.com
Brain region-specific degeneration and somatic expansions of the mutant Huntingtin (mHTT)
CAG tract are key features of Huntington's disease (HD). However, the relationships among …

[HTML][HTML] A pan-cancer analysis of the microbiome in metastatic cancer

TW Battaglia, IL Mimpen, JJH Traets, A van Hoeck… - Cell, 2024 - cell.com
Microbial communities are resident to multiple niches of the human body and are important
modulators of the host immune system and responses to anticancer therapies. Recent …