Y. I. Wolf

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.

Microbial diversity and ecological complexity emerging from environmental variation and horizontal gene transfer in a simple mathematical model.

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

Unicellular life balances asymmetric allocation and repair of somatic damage representing the origin of r/K selection

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.

CoCoNuTs: A diverse subclass of Type IV restriction systems predicted to target RNA

The paper identifies and characterizes CoCoNuTs, a new subclass of Type IV restriction systems that target RNA, with additional potential DNA targeting capabilities and regulatory mechanisms.

Compensatory Relationship between Low Complexity Regions and Gene Paralogy in the Evolution of Prokaryotes

The paper shows an inverse correlation between low complexity regions and gene paralogy in prokaryotic evolution, suggesting compensatory relationships between short-term and long-term evolutionary mechanisms.

Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes

This paper models the coevolution of reproducers and replicators to identify conditions for the origin of genomes and symmetrical cell division.

Host Age Structure Defines Interactions with Pathogens: Grandparent Effect under Collaboration and Virulent Mutualism under Competition

The paper uses mathematical modeling to show how host age structure affects pathogen interactions, finding that virulent pathogens can benefit competitive populations while harming collaborative ones.

A vast world of viroid-like circular RNAs revealed by mining metatranscriptomes

The paper identifies 11,420 viroid-like circular RNAs across 5,131 metatranscriptomes and 1,344 plant transcriptomes, revealing a five-fold increase in known viroid-like agents and novel ribozyme combinations.

Varidnaviruses in the human gut: a major expansion of the order Vinavirales

This study identifies and characterizes varidnaviruses in the human gut virome, revealing their prevalence as prophages and suggesting limited active infections.

S51 family peptidases provide resistance to peptidyl-nucleotide antibiotic McC

The paper identifies S51 family peptidases, named MccG, that cleave toxic isoaspartyl-nucleotides from peptide-nucleotide antibiotics, providing resistance in bacteria.

Conservation and evolution of the sporulation gene set in diverse members of the Firmicutes

The paper analyzes sporulation gene conservation across 180 Firmicutes genomes to identify lineage-specific losses and confirm the vertical inheritance of sporulation genes.

Human pathogenic RNA viruses establish non-competing lineages by occupying independent niches

This study analyzes 27 human pathogenic RNA viruses to show they form multiple co-circulating lineages with low turnover rates, occupying non-competing epidemiological niches.

Towards a Theory of Evolution as Multilevel Learning

This paper develops a theory of biological evolution as multilevel learning, using neural networks and learning principles to explain replication, selection, and complexity emergence.

Epistasis at the SARS-CoV-2 RBD Interface and the Propitiously Boring Implications for Vaccine Escape

This study analyzes epistatic interactions among RBD mutations in SARS-CoV-2 variants to assess their impact on vaccine escape potential.

A Ratio-Dependent Model of Replicator-Genetic Parasite Coevolution Demonstrates Instability of the Parasite-Free State

The paper uses a ratio-dependent Lotka-Volterra model to show that the parasite-free state in replicator-parasite coevolution is unstable, supporting the hypothesis that genetic parasites are inherent to life.

Horizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes

The paper examines the evolutionary factors shaping the U-shaped gene commonality distribution in prokaryotic pangenomes and identifies the horizontal gene transfer barrier as a key factor.

Prediction of the virus incubation period for COVID-19 and future outbreaks

The paper predicts the upper limit of the incubation period for viruses like SARS-CoV-2 using genomic features to aid in outbreak control.

Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2

This study analyzes 300,000 SARS-CoV-2 genomes to show ongoing adaptive evolution, with positive selection in spike and nucleocapsid proteins and regional diversification over time.

Seeker: Alignment-free identification of bacteriophage genomes by deep learning

Seeker identifies unknown bacteriophages in metagenomic data using deep learning without relying on sequence similarity to known phages.

Phylogenetic evidence of headful packaging strategy in gene transfer agents

The paper reconstructs the evolutionary history of GTA terminase to show RcGTA evolved from a headful packaging virus.

Punctuated equilibrium as the default mode of evolution of large populations on fitness landscapes dominated by saddle points in the weak-mutation limit

The paper shows that in large populations with weak mutation rates, evolution primarily occurs in stasis near saddle points on fitness landscapes, with rapid transitions between these points when beneficial mutations are fixed.

Unique genomic features of crAss-like phages, the dominant component of the human gut virome

The paper identifies nearly 600 crAss-like phage genomes from human gut microbiomes, revealing unique genomic features and anti-defense mechanisms.

Selection for reducing energy cost of protein production drives the GC content and amino acid composition bias in gene transfer agents

This paper shows that GTA genes evolve under positive selection for reduced energy cost of protein production, suggesting GTAs are bacterial adaptations for horizontal gene transfer under nutrient stress.

Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses

This study identifies genomic features distinguishing highly pathogenic SARS-CoV-2, SARS-CoV, and MERS-CoV from less pathogenic coronaviruses using comparative genomics and machine learning.

Histidine-Triad Hydrolases Provide Resistance to Peptide-Nucleotide Antibiotics

The paper identifies histidine triad hydrolases as enzymes conferring resistance to peptide-nucleotide antibiotics like microcin C by hydrolyzing their toxic phosphoramide bond.

Vast diversity of anti-CRISPR proteins predicted with a machine-learning approach

The paper predicts 2,500 novel anti-CRISPR protein families using a machine learning approach and validates one candidate's anti-CRISPR activity.

Homologous recombination substantially delays sequence but not gene content divergence of prokaryotic populations

The paper shows homologous recombination delays sequence divergence but not gene content divergence in prokaryotic populations, explaining rapid gene turnover before significant sequence divergence.

Proteomic and Genomic Signatures of Repeat-instability in Cancer and Adjacent Normal Tissues

The paper quantifies repeat-instability in cancer and normal tissues using proteomic and genomic data, identifying tumor-specific signatures linked to progression and tumorigenic state.

Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism

The paper reports the discovery of new NCLDV genomes from deep-sea sediments, expanding the ocean megavirome and supporting independent origins of viral gigantism.