Tim van Opijnen

This study identifies LptZ as a critical protein linking surface lipoprotein export to outer membrane vesicle biogenesis in Bacteroides, revealing a novel pathway and expanding the role of the Lpt machinery.

This study investigates how Yersinia pseudotuberculosis responds to macrophage-released metabolites during growth in synthetic microcolonies, identifying nitrosative stress and itaconate as key factors.

This study shows that RNA quality control through rny mutations enables antibiotic tolerance in Streptococcus pneumoniae by balancing transcriptional resilience and degradation.

This paper identifies a host-derived signal that induces rapid, tissue-specific capsule thickening in Streptococcus pneumoniae, independent of phase variation, and shows two genetic determinants involved in this process.

This study uses dual CRISPRi-Seq to identify genetic interactions in Streptococcus pneumoniae, revealing key genes in the cell cycle and new interactions in essential processes.

This paper shows diclofenac sensitizes colistin-resistant A. baumannii to colistin in vitro and in a mouse model, with reduced drug concentrations needed in vivo.

This paper improves the efficiency of noncanonical amino acid incorporation in mammalian cells by evolving tRNAEcLeu through directed evolution in mammalian cells.

CRISPRi-TnSeq maps genetic interactions between essential and nonessential genes in bacteria, identifying 1,334 interactions and revealing pathway dependencies and functional relationships.

This paper develops VADER, a virus-assisted directed evolution method for improving suppressor tRNAs in mammalian cells, resulting in more active and orthogonal tRNA mutants.

This paper introduces transcriptomic entropy as a generalizable predictor of bacterial fitness and antibiotic sensitivity across species and stress conditions using RNA-Seq and experimental evolution data.

BFClust improves pan-genome clustering by providing confidence scores and enabling cluster augmentation, outperforming existing methods in accuracy and scalability.

This paper identifies mutations that alter fluoroquinolone sensitivity in Acinetobacter baumannii and shows that preferential Topo IV poisoning leads to prophage induction and SOS response activation.

This paper predicts bacterial survival and adaptive evolution using multi-omics data, network analysis, and machine learning to identify coordinated responses and gene adaptation.