Erdal Toprak

The paper introduces a microfluidic system to study antibiotic responses in 3D cultures, revealing synergy, antagonism, and order-dependent drug efficacy.

This study maps how β-lactamase mutations confer resistance to different antibiotics, identifying generalist and specialist mutations with distinct mechanisms and positions.

The paper develops methods to infer mutant growth rates from pooled sequencing data by modeling growth and noise, improving accuracy over existing approaches.

The paper introduces a model to study how proteins transmit information over long distances without structural changes, finding that discrete motion enables this despite thermal noise.

This paper presents a rapid, low-cost protocol for isolating pathogenic bacteria from human blood, achieving over 70% efficiency within 30 minutes.

This study constructs a comprehensive mutant library of TEM-1 beta-lactamase and shows that higher-order epistasis drives unpredictable evolution of antibiotic resistance to novel substrates.

This study investigates drug-drug interactions in AML cell lines, finding widespread but non-conserved synergistic and antagonistic effects across different cell lines.

The paper shows that sequential antibiotic treatment leads to convergent multidrug resistance through extinction of resistance mutations, with single-cell RNA sequencing revealing metabolic and translational state changes.

This study investigates TolC protein dynamics in Gram-negative bacteria, identifying structural shifts that facilitate β-lactam efflux and resistance, with implications for antibiotic design.

The study shows that the TolC protein in E. coli is highly evolvable, making it a target for resistance against bacteriophages and bacterial toxins.