E. V. Koonin

The paper identifies 3,738 new phage genomes from human gut metagenomes, classifying them into three new candidate families and revealing novel phage-host interaction mechanisms.

This study identifies cell-type-specific regulatory changes in human, chimpanzee, and rhesus macaque cortical neurons, revealing human-specific regulatory elements linked to language and psychiatric disorders.

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.

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

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.

This study shows that Asgard archaea possess ESCRT complexes with eukaryotic-like structural and functional features, suggesting they are evolutionary precursors to eukaryotic ESCRTs.

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.

The paper characterizes two viral channelrhodopsins, showing they are Ca2+-dependent Na+/K+ channels with unique optogenetic properties and structural differences from known channelrhodopsins.

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

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

The paper analyzes double substitutions within codons to determine how selection pressures differ across substitution classes and how they affect fitness valley crossing.

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.

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

This study reconstructs the evolution of the global RNA virome using RdRp phylogenetics, revealing new insights into viral origins and gene exchange.

The paper examines the probability of multi-mutational leaps in evolution and finds they are rare under typical conditions but could be significant in specific scenarios like population bottlenecks.

The paper identifies genome plasticity and selection landscape as key factors driving gene content evolution in prokaryotes through mathematical modeling and analysis of microbial genomes.

The paper analyzes mutation and selection in tumors to show a critical point where mutation load correlates with survival, revealing two opposing regimes and deviations from neutrality in extreme cases.

The paper constructs a cancer-mutation network to analyze driver mutation specificity and estimates the number of drivers required for different cancers.

This paper explores analogies between physical principles and biological evolution, suggesting that concepts like frustration and percolation may explain the emergence of biological complexity.

The paper demonstrates that genetic parasites are inevitable due to thermodynamic instability of parasite-free states in replicator systems.

The paper estimates the relative contributions of selection and loss bias to gene dynamics in prokaryotes using mathematical modeling and comparative genomics.

The paper identifies CRISPR-Cas systems within Tn7-like transposons, showing they are truncated and function in pre-crRNA processing but not target cleavage, and proposes a mechanism for their role in transposon spread.

The paper identifies novel viruses infecting uncultured marine Group II Euryarchaeota using genome-centric metagenomics, revealing their abundance and potential ecological significance.

The paper identifies two CRISPR-Cas VI-B systems with Cas13b and characterizes their RNA interference activity and regulation by Csx27 and Csx28.