Manuel Banzhaf

CAZyme Annotation of Five Parasitic Trichomonads Reveals a Conserved Repertoire of Host Glycan Targeting Proteins

The paper annotates CAZymes in five parasitic trichomonads, identifying 1,406 genes and revealing conserved mucin O-glycan-targeting and antibacterial CAZyme toolkits.

Restoring Antibiotic Sensitivity via Metabolic Pathway Manipulation in Pseudomonas aeruginosa

The paper shows that combining biotin biosynthesis inhibition with metformin reduces Pseudomonas aeruginosa virulence and restores antibiotic sensitivity by targeting metabolic pathways.

Systematic chemical genomic screening of Vibrio cholerae maps gene-phenotype relationships

This study uses chemical genomics to identify gene-phenotype relationships in Vibrio cholerae by screening 104 stress conditions across 3,026 single-gene mutants, revealing 1,518 significant growth phenotypes including 88 unannotated genes.

Periplasmic SacB as a robust counter-selection tool for genome engineering in the polyploid bacterium Zymomonas mobilis

This paper confirms Zymomonas mobilis is polyploid and introduces a SacB-based counter-selection system for genome engineering.

Enriching the Human Stool Microeukaryotes for Shotgun Sequencing

This study develops a method to enrich microeukaryotes in human stool samples for shotgun sequencing, improving their representation and taxonomic diversity in metagenomic libraries.

A Type VII-secreted toxin enables inter-mycobacterial competition

The paper identifies a type VII-secreted toxin in mycobacteria that enables inter-bacterial competition by targeting arabinogalactan.

High-dimensional Characterization of Genome-Environment Fitness Landscapes in Klebsiella pneumoniae

This paper characterizes genome-environment interactions in Klebsiella pneumoniae using chemical genomics and machine learning to predict fitness across diverse conditions.

ChemGenXplore: An Interactive Tool for Exploring and Analysing Chemical Genomic Data

ChemGenXplore provides an interactive web tool for visualizing and analyzing chemical genomic data, enabling users to explore pre-implemented and uploaded datasets with various analytical features.

An evolutionarily conserved laterally acquired toolkit enables microbiota targeting by Trichomonas

This study identifies a conserved molecular toolkit in Trichomonas species acquired through lateral gene transfer, enabling interaction with microbiota and potentially influencing host inflammation.

Wild-type and single-O-antigen repeat outer-membrane vesicles induce equivalent protection against homologous and heterologous Salmonella challenge

This study shows that OMVs with different O-antigen lengths induce similar protection against Salmonella infections, and boosting enhances cross-protection.

Plasmid Permissiveness of Wastewater Microbiomes can be Predicted from 16S rDNA sequences by Machine Learning

The paper uses machine learning to predict plasmid permissiveness in wastewater microbiomes from 16S rDNA sequences, showing moderate-to-strong correlations with experimental data.

ChemGAPP; A Package for Chemical Genomics Analysis and Phenotypic Profiling.

ChemGAPP is a package for chemical genomics analysis and phenotypic profiling that integrates quality control and provides sub-packages for different screening types.

TraDIS-validate: a method for curating ordered gene-replacement libraries

TraDIS-validate is a method to validate ordered gene-replacement libraries, achieving 99.7% accuracy in identifying correct kanamycin cassette positions in the Keio library.

Bacterial sirtuin CobB and PRPP synthase crosstalk in the regulation of protein acetylation in Escherichia coli

This study shows that CobB and PRPP synthase form a complex that regulates protein acetylation and deacetylation in E. coli, impacting metabolism and cellular pathways.

Uncovering the dynamic mechanisms of the Pseudomonas aeruginosa quorum sensing and virulence networks using Boolean modelling

This study uses Boolean modelling to analyze the dynamic mechanisms of Pseudomonas aeruginosa quorum sensing and virulence networks, revealing the roles of stochasticity and node connectivity in network dynamics and robustness.