Sequencing and characterizing short tandem repeats in the human genome

HA Tanudisastro, IW Deveson, H Dashnow… - Nature Reviews …, 2024 - nature.com
Short tandem repeats (STRs) are highly polymorphic sequences throughout the human
genome that are composed of repeated copies of a 1–6-bp motif. Over 1 million variable …

Mutation and selection processes regulating short tandem repeats give rise to genetic and phenotypic diversity across species

M Verbiest, M Maksimov, Y Jin… - Journal of …, 2023 - academic.oup.com
Short tandem repeats (STRs) are units of 1–6 bp that repeat in a tandem fashion in DNA.
Along with single nucleotide polymorphisms and large structural variations, they are among …

Dissection of a rapidly evolving wheat resistance gene cluster by long-read genome sequencing accelerated the cloning of Pm69

Y Li, ZZ Wei, H Sela, L Govta, V Klymiuk… - Plant …, 2024 - cell.com
Gene cloning in repeat-rich polyploid genomes remains challenging. Here, we describe a
strategy for overcoming major bottlenecks in cloning of the powdery mildew resistance gene …

The enormous repetitive Antarctic krill genome reveals environmental adaptations and population insights

C Shao, S Sun, K Liu, J Wang, S Li, Q Liu, BE Deagle… - Cell, 2023 - cell.com
Antarctic krill (Euphausia superba) is Earth's most abundant wild animal, and its enormous
biomass is vital to the Southern Ocean ecosystem. Here, we report a 48.01-Gb chromosome …

Bacterial NLR-related proteins protect against phage

EM Kibby, AN Conte, AM Burroughs, TA Nagy… - Cell, 2023 - cell.com
Bacteria use a wide range of immune pathways to counter phage infection. A subset of these
genes shares homology with components of eukaryotic immune systems, suggesting that …

Spliceator: multi-species splice site prediction using convolutional neural networks

N Scalzitti, A Kress, R Orhand, T Weber, L Moulinier… - BMC …, 2021 - Springer
Background Ab initio prediction of splice sites is an essential step in eukaryotic genome
annotation. Recent predictors have exploited Deep Learning algorithms and reliable gene …

HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota

CY Kim, J Ma, I Lee - Nature communications, 2022 - nature.com
Advances in metagenomic assembly have led to the discovery of genomes belonging to
uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from …

SemiBin2: self-supervised contrastive learning leads to better MAGs for short-and long-read sequencing

S Pan, XM Zhao, LP Coelho - Bioinformatics, 2023 - academic.oup.com
Motivation Metagenomic binning methods to reconstruct metagenome-assembled genomes
(MAGs) from environmental samples have been widely used in large-scale metagenomic …

The versatile Pseudomonas aeruginosa biofilm matrix protein CdrA promotes aggregation through different extracellular exopolysaccharide interactions

C Reichhardt, HM Jacobs, M Matwichuk… - Journal of …, 2020 - Am Soc Microbiol
Pseudomonas aeruginosa is an important pathogen that causes chronic infections that
involve multicellular aggregates called biofilms. Within biofilms, bacteria are surrounded in a …

The haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar reveal novel pan-genome and allele-specific transcriptome features

W Qi, YW Lim, A Patrignani, P Schläpfer… - …, 2022 - academic.oup.com
Abstract Background Cassava (Manihot esculenta) is an important clonally propagated food
crop in tropical and subtropical regions worldwide. Genetic gain by molecular breeding has …