Natalia Ivanova

Planetary-scale metagenomic search reveals new patterns of CRISPR targeting

The paper analyzes CRISPR spacers from metagenomic data to reveal patterns of CRISPR targeting across Earth's biomes, identifying selection pressures and non-host phage interactions.

Coevolutionary mining of prokaryotic non-coding elements with a genome language model

Minerva extracts RNA base-pairing, protein-contact and repeat maps from a genome language model without alignments, flagging unannotated structured loci and a phage ncRNA array reverse-transcribed into short cDNAs.

Tetranucleotide frequencies differentiate genomic boundaries and metabolic strategies across environmental microbiomes

The paper develops a tool to analyze tetranucleotide frequencies in metagenomes, revealing environmental-specific microbial community patterns and metabolic trends across 12,000 samples.

Microbial Metagenomes Across a Complete Phytoplankton Bloom Cycle:High-Resolution Sampling Every 4 Hours Over 22 Days

The paper describes a high-resolution microbial metagenome dataset collected over 22 days during a phytoplankton bloom cycle, including gene abundances and time-matched environmental data.

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.

Deeplasmid: Deep learning accurately separates plasmids from bacterial chromosomes

Deeplasmid uses deep learning to accurately distinguish plasmids from bacterial chromosomes in assembled genomes, achieving high precision and validating novel plasmid detection.

The DOE JGI Metagenome Workflow

The paper describes a metagenome processing workflow that includes assembly, annotation, and binning, and provides tools for researchers to apply it to their data.

Solagigasbacteria: Lone genomic giants among the uncultured bacterial phyla

The paper identifies Solagigasbacteria as a newly named candidate phylum with large genomes and versatile metabolism, found in diverse terrestrial ecosystems.

Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria

The paper analyzes genome sequences of facultative endohyphal bacteria from diverse fungi, finding no genome reduction and no universal pathways for host interaction.