Yuri I. Wolf

A large, distinct family of RNase H fold nucleases associated with numerous defense systems in prokaryotes

The paper identifies and characterizes a new family of prokaryotic defense proteins, WARDs, which are associated with various defense systems and provide phage resistance.

Computational modeling of an RNA-peptide world

This study uses computational simulations to show that short random peptides enhance RNA evolution and structural diversity, suggesting an RNA-peptide world in early life.

Loss of replication and transcription systems accompanying transition to nucleus-dependent replication in Ariadnavirales, a proposed new order in nucleocytoviricot class Megaviricetes

The paper identifies a new viral order, Ariadnavirales, based on genomic analysis of SmDNAV, which lacks key replication and transcription genes, indicating host-dependent replication.

Evolutionary implications of phenotype switching for growth and survival of tumors in stochastic environments.

This study shows that tumor cells adapt to changing environments through phenotypic switching, with optimal survival achieved by blocking mesenchymal to epithelial transition.

Diversity and evolution of the ribovirian class Stelpaviricetes

This study identifies 103 putative families within the Stelpaviricetes class of ribovirians, revealing their evolutionary relationships and suggesting a protist origin for the class and fungal origin for Potyviridae.

Diverse bacterial pattern recognition receptors sense the core phage proteome

The paper identifies 90 structurally distinct STAND NTPase families in bacteria and archaea that recognize phage proteins, revealing their role in antiviral defense.

Hawaiian Geothermal Fumaroles Contain Diverse and Novel Viruses

This study identifies novel viruses from Hawaiian fumaroles using metagenomics, revealing new viral clades and ecological patterns.

YprA family helicases provide the missing link between diverse prokaryotic immune systems

The paper identifies YprA family helicases as a missing link connecting DISARM and Druantia immune systems in prokaryotes, revealing new defense classes and their antiviral mechanisms.

Eco-evolutionary dynamics of defense systems in mobile genetic elements: Cui bono?

The paper develops a mathematical model to explore why mobile genetic elements (MGEs) frequently carry defense systems, finding that the strength of inter-MGE interference determines whether these systems are beneficial or costly.

The heterogeneous selection landscape of genome evolution in prokaryotes

The paper examines the relationship between genome size and selection pressure in prokaryotes, revealing heterogeneous selection patterns across bacteria and archaea.

Dominant contribution of Asgard archaea to eukaryogenesis

Constrained-tree hypothesis testing on 4,290 core eukaryotic protein clusters attributes 50% of likelihood weight to Asgard archaea; Alphaproteobacterial ancestry is largely confined to oxidative phosphorylation and iron-sulfur cluster biogenesis.

The key role of cheaters in the persistence of cooperation

This paper shows that cheaters can promote cooperation by enabling group survival in a multi-level selection model, challenging the classical view that cheaters destabilize cooperation.

Ecological Determinants of Altruism in Prokaryote Antivirus Defense

The paper models prokaryotic antivirus defense strategies and finds that immunity is preferred at high viral pressure and PCD at low host population size, with potential antagonism from overinvestment in immunity.

Taxonomy-free fecal microbiome profiles enable robust prediction of immunotherapy response and toxicity in melanoma

This study identifies microbiome-derived protein biomarkers for predicting immunotherapy response and toxicity in melanoma without relying on taxonomic classification.

Evolution of antivirus defense in prokaryotes depending on the environmental virus prevalence and virome dynamics

This study develops a mathematical model to show that prokaryotes evolve antivirus defense strategies based on environmental virus prevalence, with adaptive immunity optimal in stable environments and HGT dominant in fluctuating ones.

Mosquito vector ecologies are destabilizing as a result of climate change

The paper uses machine learning to estimate Aedes mosquito habitability globally, showing increasing risk in temperate regions and decreasing risk near the equator due to climate change.

In silico evolution of globular protein folds from random sequences

This study uses a computational simulator to show how globular protein folds can evolve from random sequences, finding that stable folds emerge with 3-8 amino acid replacements per site.

Evolution of gene order in prokaryotes is driven primarily by gene gain and loss

This study quantifies the contribution of gene gain and loss versus genome rearrangements to gene order evolution in bacteria and archaea, finding gene gain and loss dominate.

"Paraxenoviridae", a putative family of ubiquitous marine bacteriophages with double-stranded RNA genomes

The paper identifies a new family of marine bacteriophages with double-stranded RNA genomes, named Paraxenoviridae, based on genomic and structural analyses.

The protein structurome of Orthornavirae and its dark matter

The paper uses protein structure prediction to analyze dark matter proteins in Orthornavirae, identifying new domains and highlighting the prevalence of disordered regions.

Jumping DNA polymerases in bacteriophages

The paper identifies instances of DNA polymerase (DNAP) swapping among bacteriophages, showing gene replacements between families and subfamilies without altering surrounding gene organization.

Long range segmentation of prokaryotic genomes by gene age and functionality

The paper identifies long-range gene clustering in prokaryotic genomes based on gene age and functionality, suggesting it results from genome rearrangement rather than conservation.

Defense systems and horizontal gene transfer in bacteria

The paper examines whether bacterial defense systems reduce horizontal gene transfer by analyzing HGT rates and the presence of 73 defense systems in 12 bacterial species.

Diversity, Origin and Evolution of the ESCRT Systems

This paper reconstructs the evolution of ESCRT systems in archaea, identifying homologs in Asgardarchaeota and other groups, suggesting an early origin of ESCRT components and their connection to the ubiquitin system.

Widespread CRISPR repeat-like RNA regulatory elements in CRISPR-Cas systems

The paper identifies CRISPR repeat-like RNA elements in CRISPR-Cas systems that function as regulatory guides, showing their prevalence in type I and V-A systems.

A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

Non-essential ribosomal proteins in bacteria and archaea identified using COGs

The paper identifies non-essential ribosomal proteins in bacteria and archaea by analyzing gene absences in the COG database and linking them to ribosome structure and genome evolution.

Allosteric activation of SARS-CoV-2 RdRp by remdesivir triphosphate and other phosphorylated nucleotides

The paper investigates how phosphorylated nucleotides like remdesivir triphosphate and ppGpp activate SARS-CoV-2 RdRp through allosteric mechanisms involving the NiRAN domain and Nsp7/8 subunits.

Expanding diversity of Asgard archaea and the elusive ancestry of eukaryotes

The paper expands the phylogenetic and metabolic diversity of Asgard archaea and suggests eukaryotes may have originated from an unknown ancestral lineage outside extant archaea.

Modified base-binding EVE and DCD Domains Implicated in the Origins of Programmed Cell Death and the piRNA Pathway

The paper identifies EVE and DCD domains that recognize modified bases in DNA and RNA, linking them to programmed cell death, cell cycle control, and the piRNA pathway across prokaryotes and eukaryotes.