Frederik Schulz

A giant virus with a 4-megabase genome and a vastly expanded repeatome.

The paper describes Sissivirus, a giant virus with a 4-megabase genome and a large repeatome, identifying repeat accumulation as a key driver of its genome expansion.

A geothermal amoeba sets a new upper temperature limit for eukaryotes

This study identifies a geothermal amoeba that divides at 63°C, setting a new upper temperature limit for eukaryotes and challenging existing paradigms about eukaryotic thermal tolerance.

Machine learning prediction of eukaryotic hosts for giant viruses

This study develops GVHoP, a machine learning tool that predicts eukaryotic hosts for giant viruses using genomic data, achieving high accuracy and revealing novel host associations across environments.

A genomic catalog of Earth's bacterial and archaeal symbionts

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.

Evidence for the acquisition of a proteorhodopsin-like rhodopsin by a chrysophyte-infecting giant virus

This paper describes the isolation and characterization of the first cultivated chrysophyte-infecting virus, ChrysoHV, which encodes a proteorhodopsin not previously found in viral genomes.

Vicennial metagenomic time series unveils evolutionary dynamics of giant viruses in a freshwater ecosystem

This study uses a 20-year metagenomic time series to analyze the evolutionary dynamics of giant viruses in Lake Mendota, revealing gene duplication, horizontal transfer, and adaptive responses to environmental changes.

Global Metagenomics Reveals Plastid Diversity and Unexplored Algal Lineages

This study uses global metagenomics to discover new plastid sequences and challenge existing models of plastid evolution in photosynthetic eukaryotes.

Protists as mediators of complex microbial and viral associations

This study investigates protist-associated microbiomes and viromes using single-cell isolation and metagenomics, revealing unique microbial and viral interactions and their ecological roles.

Genome-resolved expansion of Nucleocytoviricota and Mirusviricota reveals new diversity, functional potential, and biotechnological applications

The paper expands the database of giant virus genomes, identifies new viral taxa and functions, and highlights potential biotechnological applications.

Functional characterization of red-shifted rhodopsin channels from giant viruses explored by a machine-learning model for long-wavelength optogenetics

The paper uses a machine-learning model to predict red-shifted channelrhodopsin variants, identifying ChR024 with a maximum absorption wavelength of ~578 nm for optogenetics.

Rapid terabase-scale simulation of realistic metagenomes for experimental design and pathogen detection with RandomReadsMG

RandomReadsMG simulates realistic metagenomes for benchmarking and AI/ML training, offering faster performance and accurate depth distribution modeling.

Global Environmental Genomics Reveals Vast Uncultivated Protist Diversity and Taxonomic Blind Spots

The paper analyzes global protist diversity using metagenomes and single-cell genomes, revealing extensive uncultivated and unclassified protist lineages and taxonomic blind spots.

Conservative taxonomy and quality assessment of giant virus genomes with GVClass

GVClass identifies and classifies giant virus genomes with high precision and provides quality assessments for genome completeness and contamination.

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. nov.

This paper proposes a new genus and species, Patescibacterium danicum, to provide nomenclatural stability for the phylum Ca. Patescibacteria.

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

The paper analyzes time-series metagenomic data from Lake Mendota to study changes in protistan ecology, revealing shifts in community structure linked to invasive species and environmental factors.

You can move, but you can't hide: identification of mobile genetic elements with geNomad

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

A new method for rapid genome classification, clustering, visualization, and novel taxa discovery from metagenome

Genome Constellation improves taxa assignment and discovers novel taxa in metagenomic datasets by clustering genomes based on k-mer similarities.