Thomas Hackl

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

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.

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

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.

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.

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

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.

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.

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

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

The paper isolates and characterizes four new Prochlorococcus strains, revealing physiological and genomic features that expand the understanding of its macroevolutionary history.

This study sequenced the genome of Anthostomella pinea and analyzed its secondary metabolites, revealing 91 biosynthetic gene clusters and the antibiotic xanthoepocin.

The paper investigates how polymicrobial communities affect conjugation rates of uropathogenic E. coli in artificial urine medium, finding that Gram-positive enterococci enhance conjugation rates.

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

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

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