Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software

Bacteriophages Roam the Wheat Phyllosphere

(2022) Laura Milena Forero-Junco et al.   Viruses-Basel

Epigenetic Memories: The Hidden Drivers of Bacterial Persistence?

(2021) Leise Riber et al.   TRENDS IN MICROBIOLOGY

A widespread pathway for substitution of adenine by diaminopurine in phage genomes

(2021) Yan Zhou et al.   SCIENCE

Real-time mapping of nanopore raw signals

(2021) Haowen Zhang et al.   BIOINFORMATICS

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

(2021) Romualdas Vaisvila et al.   GENOME RESEARCH

Metaviromes Reveal the Dynamics of Pseudomonas Host-Specific Phages Cultured and Uncultured by Plaque Assay

(2021) Katrine Wacenius Skov Alanin et al.   Viruses-Basel

Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2

(2021) Aaron M. Fleming et al.   ACS Central Science

DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data

(2021) Jose Bonet et al.   BIOINFORMATICS

A genome-phenome association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA

(2021) Weiwei Yang et al.   eLife

GC bias affects genomic and metagenomic reconstructions, underrepresenting GC-poor organisms

(2020) Patrick Denis Browne et al.   GigaScience

Gaussian Mixture Model-Based Unsupervised Nucleotide Modification Number Detection Using Nanopore Sequencing Readouts

(2020) Hongxu Ding et al.   BIOINFORMATICS

Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs

(2020) Witold Kot et al.   NUCLEIC ACIDS RESEARCH

Detection, Structure and Function of Modified DNA Bases

(2019) Alexandre Hofer et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

Latest techniques to study DNA methylation

(2019) Quentin Gouil et al.   Essays in Biochemistry

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Identification and biosynthesis of thymidine hypermodifications in the genomic DNA of widespread bacterial viruses

(2018) Yan-Jiun Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Odd “RB” Phage—Identification of Arabinosylation as a New Epigenetic Modification of DNA in T4-Like Phage RB69

(2018) Julie Thomas et al.   Viruses-Basel

Nanopore sequencing meets epigenetics

(2017) Michael C Schatz   NATURE METHODS

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Bacteriophage DNA glucosylation impairs target DNA binding by type I and II but not by type V CRISPR–Cas effector complexes

(2017) Marnix Vlot et al.   NUCLEIC ACIDS RESEARCH

Biosynthesis and Function of Modified Bases in Bacteria and Their Viruses

(2016) Peter Weigele et al.   CHEMICAL REVIEWS

Epigenetics: from the past to the present

(2016) Nubia Andrea Villota-Salazar et al.   Frontiers in Life Science

Base-resolution detection ofN4-methylcytosine in genomic DNA using 4mC-Tet-assisted-bisulfite- sequencing

(2015) Miao Yu et al.   NUCLEIC ACIDS RESEARCH

Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing

(2015) Paul-Andre Genest et al.   NUCLEIC ACIDS RESEARCH

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Type II restriction endonucleases—a historical perspective and more

(2014) Alfred Pingoud et al.   NUCLEIC ACIDS RESEARCH

CRISPR/Cas9-Mediated Phage Resistance Is Not Impeded by the DNA Modifications of Phage T4

(2014) Stephanie J. Yaung et al.   PLoS One

Mass spectrometry analysis of nucleosides and nucleotides

(2013) Ed Dudley et al.   MASS SPECTROMETRY REVIEWS

Revenge of the phages: defeating bacterial defences

(2013) Julie E. Samson et al.   NATURE REVIEWS MICROBIOLOGY

Type I restriction enzymes and their relatives

(2013) W. A. M. Loenen et al.   NUCLEIC ACIDS RESEARCH

Type III restriction-modification enzymes: a historical perspective

(2013) Desirazu N. Rao et al.   NUCLEIC ACIDS RESEARCH

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

(2012) E. E. Schadt et al.   GENOME RESEARCH

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

(2011) Tyson A. Clark et al.   NUCLEIC ACIDS RESEARCH

Enzymatic approaches and bisulfite sequencing cannot distinguish between 5-methylcytosine and 5-hydroxymethylcytosine in DNA

(2010) Colm Nestor et al.   BIOTECHNIQUES

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS