R. Andrés Floto

Spatially patterned, spectral single-molecule microscopy

This paper introduces a new spectral single-molecule microscopy technique using spatially patterned detectors, achieving spectral and positional resolution without complex optical components.

Spatial lung niches shape Pseudomonas aeruginosa persistence

This study uses spatial transcriptomics to map Pseudomonas aeruginosa niches in lung tissue from CF and COPD patients, revealing distinct bacterial states and host interactions linked to infection persistence.

Pseudomonas aeruginosa balances cytotoxicity and motility to counter phagocytosis by macrophages

This study shows that Pseudomonas aeruginosa uses motility to enhance phagocytosis by macrophages, while reduced motility in chronic infections helps evade engulfment, and T3SS activity enables acute immune evasion.

Antibiotic lethality dictates mycobacterial infection outcomes

This study introduces ASCT to assess bacterial killing in real-time and links drug tolerance to clinical outcomes in mycobacterial infections.

Defence systems drive accessory genome interactions in Pseudomonas aeruginosa.

The paper analyzes defence system interactions in Pseudomonas aeruginosa genomes to understand their role in shaping accessory genome dynamics and ecological patterns.

Mutational spectra reveal influenza virus transmission routes and adaptation

This study uses mutational spectra to infer influenza virus transmission routes and adaptive mutations enabling sustained respiratory transmission.

Verapamil limits inflammation by restoring VGCC-driven epithelial Ca2+ in models of cystic fibrosis

This study shows verapamil reduces inflammation in cystic fibrosis by normalizing epithelial calcium signaling and oxidative stress in zebrafish and human cells.

A contextualised protein language model reveals the functional syntax of bacterial evolution

Trained on over 1.3 million bacterial genomes represented as ordered protein sequences, the transformer foundation model Bacformer predicts protein interactions, operons, essentiality, and phenotypes while generating trait-conditioned synthetic proteomes.

Curcumin-mediated NRF2 induction limits inflammatory damage in preclinical models of cystic fibrosis

This study shows curcumin improves inflammation and tissue damage in cystic fibrosis by restoring NRF2 activity in zebrafish and patient-derived airway organoids.

AllTheBacteria: a community resource empowers biology and discovers novel peptide antibiotics

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

Calculating and applying pathogen mutational spectra using MutTui

The paper introduces MutTui, a tool to calculate and compare mutational spectra of DNA and RNA pathogens using multiple sequence data types.

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.