Athanasios Typas

Single-site DNA methylation activates retron defence by enabling effector tetramerisation

This study shows that single-site DNA methylation activates Retron-Sen2 by enabling RcaT tetramerisation, leading to retron disassembly and toxicity.

A microbiota-derived protease links phage susceptibility to host epithelial responses

This study identifies a bacterial protease that influences phage susceptibility and links it to host epithelial responses in ulcerative colitis.

In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex

The paper identifies and characterizes a non-canonical bacterial protein translocation-folding complex using cryo-electron tomography, proteomics, and structure prediction in Mycoplasma pneumoniae.

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses

This study reveals that phage T7 kinase broadly phosphorylates host and phage proteins, disabling bacterial defense systems through widespread phosphorylation.

Personalized microbiotas (counter-)select for antibiotic resistant pathogens

This study identifies how personalized gut microbiotas influence the competitiveness of antibiotic-resistant pathogens through carbohydrate competition and specific genetic mutations.

DNA-damaging combination treatments impose genotype-specific constraints on hypermutator evolvability

This study shows that combining DNA-damaging agents with antibiotics can reduce resistance evolution in specific hypermutator bacterial genotypes but not others.

A toolkit for transposon libraries and functional genomics in intestinal Bacteroidales

The paper develops tools for transposon mutagenesis in Bacteroidales to identify essential genes and functional elements across three gut bacteria.

Synergy between Enterobacteriaceae and dietary components shapes the competition between the dominant anaerobes of the human gut

The paper investigates how dietary components and Enterobacteriaceae influence competition between Prevotellaceae and Bacteroidaceae in the gut microbiota, finding that Enterobacteriaceae enhance Prevotellaceae dominance under specific conditions.

AlphaDesign: A de novo protein design framework based on AlphaFold

AlphaDesign uses AlphaFold to design novel protein structures, including monomers, dimers, and higher-order complexes, showing structural integrity and conformational switching capabilities.

Cis non-coding genetic variation drives gene expression changes in the E. coli and P. aeruginosa pangenomes

This study identifies cis non-coding genetic variants associated with gene expression changes in E. coli and P. aeruginosa pangenomes, revealing their role in antimicrobial resistance.

Elucidating the mechanisms of action and evolutionary relationships of phage anti-defence proteins

The paper develops EVADES, a database of phage anti-defence proteins, predicts mechanisms for 21 uncharacterized ADPs, and explores their evolutionary and functional relationships.

Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria

This study identifies nitroxoline's broad antibacterial activity against Gram-negative bacteria, its mode of action involving metal homeostasis and outer membrane disruption, and resistance mechanisms across multiple species.

Systematic mapping of antibiotic cross-resistance and collateral sensitivity with chemical genetics

The paper maps antibiotic cross-resistance and collateral sensitivity interactions using chemical genetic data and validates findings experimentally.

Essentiality of LD-Transpeptidation in Agrobacterium tumefaciens

This study identifies the essential role of LD-transpeptidation in Agrobacterium tumefaciens cell wall integrity and growth by analyzing LDTs and their genetic interactions.

Emergent survival and extinction of species within gut bacterial communities

The paper shows how species in gut bacterial communities can survive or go extinct based on resource availability and metabolic interactions, identifying emergent survival and community-driven extinctions.

Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome

The paper introduces a high-throughput glycoproteomics method to quantify brain glycoproteome changes induced by gut microbiome composition.

2FAST2Q: A general-purpose sequence search and counting program for FASTQ files

2FAST2Q is a tool for extracting and counting features in FASTQ files, demonstrating efficiency and usability compared to existing methods.

Impact of phosphorylation on thermal stability of proteins

The paper assesses the impact of phosphorylation on protein thermal stability using phospho-TPP in HeLa cells, finding that phosphorylation affects stability less than previously reported.

Bioactivity assessment of natural compounds using machine learning models based on drug target similarity

This paper develops a machine learning model to predict protein targets of natural compounds based on drug target similarity, identifying potential therapeutics with experimental validation.

Towards a systematic map of the functional role of protein phosphorylation

The paper systematically maps the functional role of phosphorylation by analyzing phospho-deficient mutants in yeast and linking yeast phenotypes to human functional relevance.

The impact of the genetic background on gene deletion phenotypes in Saccharomyces cerevisiae

The paper assesses how genetic background affects gene deletion phenotypes in yeast, finding significant variation across strains and conditions.

Comprehensive variant effect predictions of single nucleotide variants in model organisms

The paper benchmarks variant effect predictors and analyzes SNVs in H. sapiens, S. cerevisiae, and E. coli to predict molecular effects and generate protein complex burden scores.

Spatiotemporal proteomics uncovers cathepsin-dependent host cell death during bacterial infection

The paper quantifies host proteome dynamics during Salmonella infection, revealing cathepsin-dependent cell death mechanisms.

Phenotype prediction in an Escherichia coli strain panel

The paper predicts growth defects in Escherichia coli strains using genetic variant impact models and gene function data, achieving reliable predictions for up to 38% of tested conditions.

An Atlas of Human Kinase Regulation

This paper constructs a kinase regulation atlas using phosphopeptide quantifications to identify co-regulated kinases and their functional relationships, revealing key mediators in stem cell differentiation and Salmonella infection.