I. N. Zheludev

Viroid-like colonists of human microbiomes

The paper identifies a new class of viroid-like elements, Obelisks, prevalent in human microbiomes and capable of persistent colonization.

Tertiary folds of the SL5 RNA from the 5' proximal region of SARS-CoV-2 and related coronaviruses

This paper determines the 3D structures of SL5 RNA domains from six coronaviruses, revealing conserved tertiary features with implications for protein-binding and antiviral targets.

Restriction Endonuclease-based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing

This paper introduces a method to enrich DNA from specific organisms in metagenomic samples using restriction endonucleases and methylated motifs, achieving 11- to 142-fold enrichment for Escherichia coli and Salmonella enterica.

Extant hybrids of RNA viruses and viroid-like elements

The paper identifies ambiviruses as viroid-like elements with rolling circle replication and their own viral RdRP, suggesting a hybrid evolutionary origin between RNA viruses and sub-viral elements.

Exploring the evolutionary history of kinetic stability in the alpha-lytic protease family

This study investigates how sequence variation in the alpha-lytic protease family relates to kinetic stability and energy landscapes, finding that pro-region size and specific amino acids influence folding speed and stability.

Cryo-electron Microscopy and Exploratory Antisense Targeting of the 28-kDa Frameshift Stimulation Element from the SARS-CoV-2 RNA Genome

The paper uses cryo-EM and ASO experiments to study the SARS-CoV-2 FSE structure and its potential as an antiviral target, finding a complex tertiary structure but challenges in effective inactivation.

De novo 3D models of SARS-CoV-2 RNA elements and small- molecule-binding RNAs to aid drug discovery

The paper provides 3D models of SARS-CoV-2 RNA elements and small-molecule-binding RNAs to support drug discovery efforts using computational modeling and experimental validation.

Ribosolve: Rapid determination of three-dimensional RNA-only structures

Ribosolve rapidly determines 3D RNA-only structures using cryo-EM, chemical mapping, and Rosetta modeling, validated by multiple benchmarks and showing high accuracy.