Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

S Ardui, A Ameur, JR Vermeesch… - Nucleic acids …, 2018‏ - academic.oup.com
Short read massive parallel sequencing has emerged as a standard diagnostic tool in the
medical setting. However, short read technologies have inherent limitations such as GC …

Metagenomic sequencing for microbial DNA in human samples: emerging technological advances

Y Shi, G Wang, HCH Lau, J Yu - International journal of molecular …, 2022‏ - mdpi.com
Whole genome metagenomic sequencing is a powerful platform enabling the simultaneous
identification of all genes from entirely different kingdoms of organisms in a complex sample …

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing

A Tourancheau, EA Mead, XS Zhang, G Fang - Nature methods, 2021‏ - nature.com
Bacterial DNA methylation occurs at diverse sequence contexts and plays important
functional roles in cellular defense and gene regulation. Existing methods for detecting DNA …

Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution

Y Kong, L Cao, G Deikus, Y Fan, EA Mead, W Lai… - Science, 2022‏ - science.org
The discovery of N6-methyldeoxyadenine (6mA) across eukaryotes led to a search for
additional epigenetic mechanisms. However, some studies have highlighted confounding …

Sequencing-based analysis of microbiomes

Y Pinto, AS Bhatt - Nature Reviews Genetics, 2024‏ - nature.com
Microbiomes occupy a range of niches and, in addition to having diverse compositions, they
have varied functional roles that have an impact on agriculture, environmental sciences, and …

DISARM is a widespread bacterial defence system with broad anti-phage activities

G Ofir, S Melamed, H Sberro, Z Mukamel… - Nature …, 2018‏ - nature.com
The evolutionary pressure imposed by phage predation on bacteria and archaea has
resulted in the development of effective anti-phage defence mechanisms, including …

The bacterial epigenome

MA Sánchez-Romero, J Casadesús - Nature Reviews Microbiology, 2020‏ - nature.com
In all domains of life, genomes contain epigenetic information superimposed over the
nucleotide sequence. Epigenetic signals control DNA–protein interactions and can cause …

Navigating the pitfalls of map** DNA and RNA modifications

Y Kong, EA Mead, G Fang - Nature Reviews Genetics, 2023‏ - nature.com
Chemical modifications to nucleic acids occur across the kingdoms of life and carry
important regulatory information. Reliable high-resolution map** of these modifications is …

Widespread adenine N6-methylation of active genes in fungi

SJ Mondo, RO Dannebaum, RC Kuo, KB Louie… - Nature …, 2017‏ - nature.com
Abstract N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present
at low levels in plant and animal genomes,,,, but its prevalence and association with …

Colorectal cancer-associated microbiota contributes to oncogenic epigenetic signatures

I Sobhani, E Bergsten, S Couffin, A Amiot… - Proceedings of the …, 2019‏ - pnas.org
Sporadic colorectal cancer (CRC) is a result of complex interactions between the host and
its environment. Environmental stressors act by causing host cell DNA alterations implicated …