Thomas Hackl

Metabolite co-variation networks reveal keystone functions and an emergent pathogen state in the human urobiome.

This paper uses metabolomics co-variation networks to analyze urobiome-pathogen interactions, identifying keystone species and emergent pathogen states in a synthetic urobiome model.

Curated high-quality genomes of 39 diverse halophilic archaea

The paper presents high-quality chromosome-level genomes of 39 haloarchaeal strains, expanding genomic resources and enabling comparative studies of archaeal biology and virus-host interactions.

An expanded urine culturing workflow to cultivate and characterize diverse urobiome isolates

This paper introduces an expanded urine culturing workflow to recover diverse urobiome isolates from postmenopausal women, enabling better characterization of previously underrepresented taxa.

A Tripartite Co-culture System Reveals Defensive Mutualism Between a Nanobdellati Symbiont and Its Host

The paper establishes a tripartite co-culture system to study defensive mutualism between a Nanobdellati symbiont and its host, revealing glycan-mediated protection against viral infection.

Genomic insights into antiviral defense systems in haloarchaea and their impact on virus susceptibility

This study identifies antiviral defense systems in haloarchaea and finds that hosts with more defense systems are less susceptible to viral infection, while receptor availability primarily determines host range.

Strain-level diversity of giant viruses infecting chlorarachniophyte algae in the subtropical North Pacific

The paper describes four isolates of a giant virus infecting chlorarachniophyte algae, highlighting strain-level genetic and epigenetic variation.

De novo whole genome assembly of the globally invasive green shore crab Carcinus maenas (Linnaeus, 1758) via long-read Oxford Nanopore MinION sequencing

The paper presents a de novo whole genome assembly of the green shore crab using long-read sequencing and provides a DNA extraction protocol for brachyuran crabs.

Unravelling the functional diversity of type III polyketide synthases in fungi

This study characterizes fungal type III polyketide synthases (T3PKSs) by analyzing their genomic context and substrate specificity, and develops a machine learning model to predict their substrate preferences.

When things add up: environmental structure and microbial interactions drive antibiotic resistance plasmid evolution

This study shows how environmental structure and microbial interactions influence antibiotic resistance plasmid evolution in E. coli, with community contexts leading to higher tolerance and structured environments allowing prolonged resistance evolution.

detectEVE: fast, sensitive and precise detection of endogenous viral elements in genomic data

detectEVE identifies non-retroviral endogenous viral elements in genomic data with high sensitivity and specificity, offering a faster and more accurate alternative to existing tools.

Host-Exclusive Primer Design Enables Effective Metabarcoding via Nanopore Long-Read Sequencing

The paper develops a host-exclusive primer design workflow for long-read metabarcoding, enabling efficient amplification of fungal rDNA from mixed DNA samples.

Diverse rhizosphere-associated Pseudomonas genomes isolated along the marine-terrestrial transition zone of a Wadden island salt march

The paper isolates and characterizes 67 diverse Pseudomonas genomes from a salt march salt marsh to study their role in soil development and succession.

proovframe: frameshift-correction for long-read (meta)genomics

proovframe corrects frameshift errors in long-read (meta)genomics data using protein-to-nucleotide alignments, improving data quality without requiring high sequencing depth.

MOSGA 2: Comparative genomics and validation tools

MOSGA 2 provides advanced genomic analysis tools for annotation, validation, and comparative genomics across multiple datasets.

Four high-quality draft genome assemblies of the marine heterotrophic nanoflagellate Cafeteria roenbergensis

The paper presents four high-quality draft genome assemblies of Cafeteria roenbergensis, enabling evolutionary analysis of heterotrophic protists.