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Most Recent Articles: Genome Biology
Updated: 21 hours 19 min ago

OnTAD: hierarchical domain structure reveals the divergence of activity among TADs and boundaries

Wed, 18/12/2019 - 5:30am
The spatial organization of chromatin in the nucleus has been implicated in regulating gene expression. Maps of high-frequency interactions between different segments of chromatin have revealed topologically a...
Categories: Bioinformatics Trends

Systematic underestimation of the epigenetic clock and age acceleration in older subjects

Tue, 17/12/2019 - 5:30am
The Horvath epigenetic clock is widely used. It predicts age quite well from 353 CpG sites in the DNA methylation profile in unknown samples and has been used to calculate “age acceleration” in various tissues...
Categories: Bioinformatics Trends

HOPS: automated detection and authentication of pathogen DNA in archaeological remains

Mon, 16/12/2019 - 5:30am
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from arc...
Categories: Bioinformatics Trends

PASTMUS: mapping functional elements at single amino acid resolution in human cells

Mon, 16/12/2019 - 5:30am
Identification of functional elements for a protein of interest is important for achieving a mechanistic understanding. However, it remains cumbersome to assess each and every amino acid of a given protein in ...
Categories: Bioinformatics Trends

SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Mon, 16/12/2019 - 5:30am
Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not un...
Categories: Bioinformatics Trends

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

Mon, 16/12/2019 - 5:30am
Sequencing technology and assembly algorithms have matured to the point that high-quality de novo assembly is possible for large, repetitive genomes. Current assemblies traverse transposable elements (TEs) and...
Categories: Bioinformatics Trends

deSALT: fast and accurate long transcriptomic read alignment with de Bruijn graph-based index

Mon, 16/12/2019 - 5:30am
The alignment of long-read RNA sequencing reads is non-trivial due to high sequencing errors and complicated gene structures. We propose deSALT, a tailored two-pass alignment approach, which constructs graph-b...
Categories: Bioinformatics Trends

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April 2020