E. coli

This paper develops a statistical framework to identify candidate genetic interactions from adaptive laboratory evolution data using co-occurrence and mutual exclusivity patterns.

This paper demonstrates associative learning and memory erasure in a synthetic multicellular system using five E. coli strains communicating via a shared quorum-sensing signal.

The paper identifies Sgl{varphi}Cb5 as targeting MraY and shows convergent evolution between ssRNA and ssDNA phage Sgls.

The paper experimentally validates bacterial sense-to-sense genetic code variants using cell-free translation and proteomics, showing Trp incorporation at CGG codons in E. coli and Anaerococcus prevotii.

The paper introduces combined-FISH to quantify antibiotic resistance gene copy numbers in single bacterial cells and links them to host identity in complex environments.

The paper develops a computational model to show that Hsp70 chaperones only delay, not prevent, protein aggregation, depending on client-specific kinetic and thermodynamic properties.

This study investigates how ribosome-mediated protein folding imposes sequence constraints by analyzing mutations in E. coli DHFR using deep mutational scanning and fluorogenic sensors.

This study shows that reduced swimming motility accompanies B-lactam antibiotic resistance in E. coli through efflux mechanisms, with motility recovery after antibiotic removal.

This study demonstrates the transferability of homoserine lactone sensors between Bacillales bacteria, enabling programmable interphyla communication between Gram-negative and Gram-positive species.

The paper infers cell division parameters in E. coli under nonsteady growth conditions using single-cell size trajectories and time-resolved models.

This paper introduces a workflow that decouples quantification and identification in label-free top-down proteomics, improving proteome coverage and quantification precision.

This paper compares isothermal amplification methods (LAMP and RPA) with qPCR for detecting natterjack toad eDNA, finding RPA matches qPCR sensitivity while LAMP is less sensitive.

The paper introduces MIST, a framework that integrates single-molecule trajectory data with cellular context to improve molecular phenotyping in E. coli.

This study evaluates the precision of 13C metabolic flux analysis using different glucose tracers to estimate non-oxidative glycolysis fluxes in E. coli.

Hybrax simplifies hybrid bioprocess modeling by providing a framework that automates model setup and data handling, enabling reproducible and reusable models.

This study examines genomic features and resistance mechanisms in vancomycin-resistant Enterococcus faecalis ST525 isolates, revealing variable linezolid resistance despite a single mutational mechanism.

The paper identifies two groups of previously uncharacterized cargo genes in F plasmids of pathogenic E. coli, potentially contributing to virulence and antimicrobial targets.

This study demonstrates that an inducible CRISPR/Cas12a2 system can reduce bacterial growth and plasmid DNA in vitro and in vivo by targeting resistance transcripts.

The paper shows that MurJ, a Lipid II flippase, dynamically coordinates bacterial growth and division by transiently capturing at division sites during septal synthesis.

The paper shows stochastic RNA repair in E. coli leads to phenotypic heterogeneity and state switching in antibiotic responses.

The paper identifies PICJIs as large mobile genetic elements in E. coli and Salmonella that spread antimicrobial resistance and defense systems via a specific bacteriophage.

The paper develops a scalable assay and a protein language model to predict monomeric yield of proteins in E. coli, showing it can be learned and designed.

This study shows Escherichia coli has an intrinsic timekeeping system that anticipates daily temperature cycles through rhythmic curli plaque formation.

This study presents cryo-EM structures of RtcB2 bound to damaged E. coli 30S subunits, revealing how the enzyme recognizes and repairs ribosomal RNA.

The paper develops a thermodynamic model linking transcriptome organization to growth state by analyzing RNA folding free energies across cell cycle and stress adaptation.

The paper develops a biosensor platform using monomeric streptavidin to evaluate binding domains for small molecules and proteins, demonstrating ligand-dependent activation with biotinylated targets.

The paper identifies a new DarTG subfamily in E. coli that uses a helicase protein to promote ADP-ribosylation of DNA purines, expanding the known functions of helicases in bacterial immunity.

This study investigates the role of chromosomally-encoded Hok/Sok toxin/antitoxin systems in inhibiting phage infection in E. coli, finding that Hok proteins significantly reduce infection by BASEL phages.

This study analyzes the tryptophan system in E. coli to show how multiple feedback loops enable rapid response and noise mitigation.