Nikos C. Kyrpides

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.

ArthroVerse compiles and annotates protein families from arthropod-associated microbiomes to explore functional diversity and host-microbe interactions.

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.

The paper identifies novel enzybiotic candidates targeting human bacterial pathogens by analyzing viral-host associations in a large viral genome database.

This study uses machine learning to predict symbiotic lifestyles in microbial genomes, identifying 15-23% of uncultivated microbes as potential symbionts and creating a new catalog of symbiont genomes.

WasteFams catalogs 3,887 non-redundant protein families from wastewater metagenomes and metatranscriptomes, providing structural, taxonomic, and functional annotations for microbial function discovery.

The paper identifies 182 bacterial strains, including 14 novel Gram-positive species, in NASA Mars 2020 cleanrooms, highlighting their biotechnological potential despite being undetected by metagenomic sequencing.

VPF-Class 2.0 improves viral classification by using a supervised model on marker-composition features, achieving high accuracy and interpretability.

The paper introduces a scalable pipeline for grouping protein sequences into families, showing it matches curated databases and scales linearly with input size.

The paper identifies millions of new protein families from global metagenomic data, expanding the known repertoire of protein families and revealing potential novel functions.

The paper presents a global virome atlas, UHGV, and identifies genomic factors influencing phage-host interactions.

metagRoot provides a database of 71,091 enriched protein families from plant root microbiomes, annotated with structural and functional information to aid in microbiome research.

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

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.

geNomad identifies and annotates mobile genetic elements in sequencing data, discovering millions of new viruses and plasmids in public metagenomes.

The paper investigates how plant-associated microbiomes in nutrient-poor Brazilian campos rupestres substrates contribute to nutrient cycling, revealing novel microbial populations and mechanisms for phosphorus and nitrogen turnover.

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

CheckV estimates completeness of metagenome-assembled viral contigs against GenBank plus 76,262 metagenome-derived complete genomes and trims host flanks; 86.9% of IMG/VR contigs were low-quality.

The paper benchmarks computational metagenomics software using complex datasets, showing strengths and limitations in assembly, binning, and taxonomic profiling.

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