PADLOC: a web server for the identification of antiviral defence systems in microbial genomes

LJ Payne, S Meaden, MR Mestre, C Palmer… - Nucleic acids …, 2022 - academic.oup.com
Most bacteria and archaea possess multiple antiviral defence systems that protect against
infection by phages, archaeal viruses and mobile genetic elements. Our understanding of …

The Ever-Expanding Pseudomonas Genus: Description of 43 New Species and Partition of the Pseudomonas putida Group

L Girard, C Lood, M Höfte, P Vandamme… - Microorganisms, 2021 - mdpi.com
The genus Pseudomonas hosts an extensive genetic diversity and is one of the largest
genera among Gram-negative bacteria. Type strains of Pseudomonas are well known to …

Galaxy and Apollo as a biologist-friendly interface for high-quality cooperative phage genome annotation

J Ramsey, H Rasche, C Maughmer… - PLOS Computational …, 2020 - journals.plos.org
In the modern genomic era, scientists without extensive bioinformatic training need to apply
high-power computational analyses to critical tasks like phage genome annotation. At the …

DNA methylation dynamics and dysregulation delineated by high-throughput profiling in the mouse

W Zhou, T Hinoue, B Barnes, O Mitchell, W Iqbal… - Cell genomics, 2022 - cell.com
We have developed a mouse DNA methylation array that contains 296,070 probes
representing the diversity of mouse DNA methylation biology. We present a mouse …

Estimating maximal microbial growth rates from cultures, metagenomes, and single cells via codon usage patterns

JL Weissman, S Hou… - Proceedings of the …, 2021 - National Acad Sciences
Maximal growth rate is a basic parameter of microbial lifestyle that varies over several orders
of magnitude, with doubling times ranging from a matter of minutes to multiple days. Growth …

Diverse variola virus (smallpox) strains were widespread in northern Europe in the Viking Age

B Mühlemann, L Vinner, A Margaryan, H Wilhelmson… - Science, 2020 - science.org
INTRODUCTION Variola virus (VARV), the causative agent of smallpox, is estimated to have
killed between 300 million and 500 million people in the 20 th century and was …

Review on the computational genome annotation of sequences obtained by next-generation sequencing

GF Ejigu, J Jung - Biology, 2020 - mdpi.com
Simple Summary Due to the development of high-throughput sequencing technologies,
computational genome annotation of sequences has become one of the principal research …

Microbial genome analysis: the COG approach

MY Galperin, DM Kristensen… - Briefings in …, 2019 - academic.oup.com
For the past 20 years, the Clusters of Orthologous Genes (COG) database had been a
popular tool for microbial genome annotation and comparative genomics. Initially created for …

The antiSMASH database, a comprehensive database of microbial secondary metabolite biosynthetic gene clusters

K Blin, MH Medema, R Kottmann, SY Lee… - Nucleic acids …, 2016 - academic.oup.com
Secondary metabolites produced by microorganisms are the main source of bioactive
compounds that are in use as antimicrobial and anticancer drugs, fungicides, herbicides and …

Functional genomics of the rapidly replicating bacterium Vibrio natriegens by CRISPRi

HH Lee, N Ostrov, BG Wong, MA Gold, AS Khalil… - Nature …, 2019 - nature.com
The fast-growing Gram-negative bacterium Vibrio natriegens is an attractive microbial
system for molecular biology and biotechnology due to its remarkably short generation time …