Impact of reduced-representation sequencing protocols on detecting population structure in a threatened marsupial
Sign Up to like & getrecommendations! Published in 2019 at "Molecular Biology Reports"
DOI: 10.1007/s11033-019-04966-6
Abstract: Reduced-representation sequencing methods have wide utility in conservation genetics of non-model species. Several methods are now available that reduce genome complexity to examine a wide range of markers in a large number of individuals. We… read more here.
Keywords: reduced representation; population; representation sequencing; population structure ... See more keywords
A comprehensive evaluation of alignment software for reduced representation bisulfite sequencing data
Sign Up to like & getrecommendations! Published in 2018 at "Bioinformatics"
DOI: 10.1093/bioinformatics/bty174
Abstract: Motivation The rapid development of next-generation sequencing technology provides an opportunity to study genome-wide DNA methylation at single-base resolution. However, depletion of unmethylated cytosines brings challenges for aligning bisulfite-converted sequencing reads to a large reference.… read more here.
Keywords: methylation; cpg sites; reduced representation; rrbssim ... See more keywords
DepthFinder: a tool to determine the optimal read depth for reduced-representation sequencing
Sign Up to like & getrecommendations! Published in 2020 at "Bioinformatics"
DOI: 10.1093/bioinformatics/btz473
Abstract: MOTIVATION Identification of DNA sequence variations such as single nucleotide polymorphisms (SNPs) is a fundamental step towards genetic studies. Reduced-representation sequencing methods have been developed as alternatives to whole genome sequencing to reduce costs and… read more here.
Keywords: read depth; depthfinder; representation sequencing; tool ... See more keywords
Novel enzyme-based reduced representation method for DNA methylation profiling with low inputs
Sign Up to like & getrecommendations! Published in 2024 at "Nucleic Acids Research"
DOI: 10.1101/2024.05.24.595803
Abstract: DNA methylation at cytosine-phospho-guanine (CpG) residues is a vital biological process that regulates cell identity and function. Although widely used, bisulfite-based cytosine conversion procedures for DNA methylation sequencing require high temperature and extreme pH, which… read more here.
Keywords: methylation; reduced representation; method; dna methylation ... See more keywords
epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.
Sign Up to like & getrecommendations! Published in 2022 at "Molecular ecology resources"
DOI: 10.1111/1755-0998.13597
Abstract: Several reduced representation bisulfite sequencing methods have been developed in recent years to determine cytosine methylation de novo in non-model species. Here, we present epiGBS2, a laboratory protocol based on epiGBS (Gurp et al., 2016)… read more here.
Keywords: pipeline; reduced representation; representation bisulfite; bisulfite sequencing ... See more keywords
ReducedâRepresentation Sequencing Detects TransâArctic Connectivity and Local Adaptation in Polar Cod (Boreogadus saida)
Sign Up to like & getrecommendations! Published in 2025 at "Molecular Ecology"
DOI: 10.1111/mec.17706
Abstract: Information on connectivity and genetic structure of marine organisms remains sparse in frontier ecosystems such as the Arctic Ocean. Filling these knowledge gaps becomes increasingly urgent, as the Arctic is undergoing rapid physical, ecological and… read more here.
Keywords: reduced representation; cod boreogadus; polar cod; connectivity ... See more keywords
Abstract 7022: Whole genome and reduced representation enzymatic methyl-seq enable cost effective methylomes
Sign Up to like & getrecommendations! Published in 2024 at "Cancer Research"
DOI: 10.1158/1538-7445.am2024-7022
Abstract: DNA methylation is an epigenetic regulator of gene expression with important functions in development and diseases such as cancer. Traditionally, sodium bisulfite conversion was used to distinguish 5-methylcytosines (5mC) and 5-hydroxymethylcytosines (5hmC) from cytosines. However,… read more here.
Keywords: methylation; reduced representation; seq; cost ... See more keywords
Discovery of thermophilic Bacillales using reduced-representation genotyping for identification
Sign Up to like & getrecommendations! Published in 2020 at "BMC Microbiology"
DOI: 10.1186/s12866-020-01800-z
Abstract: This study demonstrates the use of reduced-representation genotyping to provide preliminary identifications for thermophilic bacterial isolates. The approach combines restriction enzyme digestion and PCR with next-generation sequencing to provide thousands of short-read sequences from across… read more here.
Keywords: reduced representation; microbiology; identification; genome ... See more keywords