Yuri I. Wolf

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

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.

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.

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

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.

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

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

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.

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

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.

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.

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.

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

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.

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.

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.

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.

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

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

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

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.

This study shows that environmental variation and horizontal gene transfer can stabilize microbial diversity and ecological complexity in a mathematical model of competing populations.

This study uses mathematical modeling to show that optimal strategies for balancing somatic damage repair and asymmetric allocation depend on extrinsic mortality and damage accumulation rates, linking these to the evolutionary r/K selection theory.

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.

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.

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.

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

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.

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.