The LUCA and its complex virome

M Krupovic, VV Dolja, EV Koonin - Nature Reviews Microbiology, 2020 - nature.com
The last universal cellular ancestor (LUCA) is the most recent population of organisms from
which all cellular life on Earth descends. The reconstruction of the genome and phenotype …

Jumbo bacteriophages: an overview

Y Yuan, M Gao - Frontiers in microbiology, 2017 - frontiersin.org
Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages,
and are rarely isolated by conventional methods. These phages are designated “jumbo” …

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

HB Nielsen, M Almeida, AS Juncker… - Nature …, 2014 - nature.com
Most current approaches for analyzing metagenomic data rely on comparisons to reference
genomes, but the microbial diversity of many environments extends far beyond what is …

Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

AL Grazziotin, EV Koonin… - Nucleic acids research, 2016 - academic.oup.com
Viruses are the most abundant and diverse biological entities on earth, and while most of
this diversity remains completely unexplored, advances in genome sequencing have …

Bacteriophages and biofilms

DR Harper, HMRT Parracho, J Walker, R Sharp… - Antibiotics, 2014 - mdpi.com
Biofilms are an extremely common adaptation, allowing bacteria to colonize hostile
environments. They present unique problems for antibiotics and biocides, both due to the …

Evolution of the large nucleocytoplasmic DNA viruses of eukaryotes and convergent origins of viral gigantism

EV Koonin, N Yutin - Advances in Virus Research, 2019 - Elsevier
Abstract The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed
order “Megavirales”) comprise an expansive group of eukaryotic viruses that consists of the …

Expanding the marine virosphere using metagenomics

CM Mizuno, F Rodriguez-Valera, NE Kimes… - PLoS genetics, 2013 - journals.plos.org
Viruses infecting prokaryotic cells (phages) are the most abundant entities of the biosphere
and contain a largely uncharted wealth of genomic diversity. They play a critical role in the …

Computational methods for Gene Orthology inference

DM Kristensen, YI Wolf, AR Mushegian… - Briefings in …, 2011 - academic.oup.com
Accurate inference of orthologous genes is a pre-requisite for most comparative genomics
studies, and is also important for functional annotation of new genomes. Identification of …

The double-stranded DNA virosphere as a modular hierarchical network of gene sharing

J Iranzo, M Krupovic, EV Koonin - MBio, 2016 - Am Soc Microbiol
Virus genomes are prone to extensive gene loss, gain, and exchange and share no
universal genes. Therefore, in a broad-scale study of virus evolution, gene and genome …

Phage therapy in the twenty-first century: facing the decline of the antibiotic era; is it finally time for the age of the phage?

S Hesse, S Adhya - Annual review of microbiology, 2019 - annualreviews.org
Burgeoning problems of antimicrobial resistance dictate that new solutions be developed to
combat old foes. Use of lytic bacteriophages (phages) for the treatment of drug-resistant …