PLSDB: advancing a comprehensive database of bacterial plasmids

GP Schmartz, A Hartung, P Hirsch, F Kern… - Nucleic Acids …, 2022 - academic.oup.com
Plasmids are known to contain genes encoding for virulence factors and antibiotic
resistance mechanisms. Their relevance in metagenomic data processing is steadily …

Genetic compensation triggered by mutant mRNA degradation

MA El-Brolosy, Z Kontarakis, A Rossi, C Kuenne… - Nature, 2019 - nature.com
Genetic robustness, or the ability of an organism to maintain fitness in the presence of
harmful mutations, can be achieved via protein feedback loops. Previous work has …

Sequenceserver: a modern graphical user interface for custom BLAST databases

A Priyam, BJ Woodcroft, V Rai, I Moghul… - Molecular biology …, 2019 - academic.oup.com
Comparing newly obtained and previously known nucleotide and amino-acid sequences
underpins modern biological research. BLAST is a well-established tool for such …

Klumpy: A tool to evaluate the integrity of long‐read genome assemblies and illusive sequence motifs

G Madrigal, BF Minhas… - Molecular ecology …, 2025 - Wiley Online Library
The improvement and decreasing costs of third‐generation sequencing technologies has
widened the scope of biological questions researchers can address with de novo genome …

[HTML][HTML] The genetic basis of morphological diversity in domesticated goldfish

T Kon, Y Omori, K Fukuta, H Wada, M Watanabe… - Current Biology, 2020 - cell.com
Although domesticated goldfish strains exhibit highly diversified phenotypes in morphology,
the genetic basis underlying these phenotypes is poorly understood. Here, based on …

Targeting of mammalian glycans enhances phage predation in the gastrointestinal tract

SI Green, C Gu Liu, X Yu, S Gibson, W Salmen… - MBio, 2021 - Am Soc Microbiol
The human gastrointestinal mucosal surface consists of a eukaryotic epithelium, a
prokaryotic microbiota, and a carbohydrate-rich interface that separates them. In the …

Distinctive gene and protein characteristics of extremely piezophilic Colwellia

LM Peoples, TS Kyaw, JA Ugalde, KK Mullane… - BMC genomics, 2020 - Springer
Background The deep ocean is characterized by low temperatures, high hydrostatic
pressures, and low concentrations of organic matter. While these conditions likely select for …

A comparison of Oxford nanopore library strategies for bacterial genomics

T Sauvage, A Cormier, P Delphine - BMC genomics, 2023 - Springer
Abstract Background Oxford nanopore Technologies (ONT) provides three main library
preparation strategies to sequence bacterial genomes. These include tagmentation (TAG) …

Mitochondrial and chloroplast genomes provide insights into the evolutionary origins of quinoa (Chenopodium quinoa Willd.)

PJ Maughan, L Chaney, DJ Lightfoot, BJ Cox… - Scientific reports, 2019 - nature.com
Quinoa has recently gained international attention because of its nutritious seeds, prompting
the expansion of its cultivation into new areas in which it was not originally selected as a …

The Wolbachia mobilome in Culex pipiens includes a putative plasmid

J Reveillaud, SR Bordenstein, C Cruaud… - Nature …, 2019 - nature.com
Wolbachia is a genus of obligate intracellular bacteria found in nematodes and arthropods
worldwide, including insect vectors that transmit dengue, West Nile, and Zika viruses …