E. coli

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.

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

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.

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

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.

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

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

This study identifies rdar biofilm formation in clinical uropathogenic E. coli and shows subinhibitory ciprofloxacin suppresses it in resistant isolates.

The paper introduces DIFFRACT, a framework that uses local fractal dimension changes in protein interaction networks to detect functional reorganization, showing its utility in identifying novel biological roles in RAVER1-deficient cells.

The paper develops computational algorithms to accurately estimate bacterial population growth rates using single-cell models and applies them to study antibiotic response heterogeneity and chemotaxis effects.

The paper presents a droplet-based workflow for antimicrobial screening in complex matrices, showing it can detect MICs at lower concentrations and reveal extract-specific aggregation effects.

This study shows H-NS in E. coli undergoes a conformational switch at 37°C, enabling nucleoid reorganization that enhances growth, resolving the silencing paradox.

The paper shows that single-cell growth rates increase with flagellar gene activity, contradicting bulk measurements, and attributes this to inherited growth factors.

The paper characterizes EstS, a macrolide esterase from E. coli, showing it preferentially inactivates spiramycin and tylosin, explaining resistance phenotypes.

The paper models oxidative stress response in E. coli using a genome-scale metabolic model to show that bimodal killing under H2O2 stress emerges from network topology and stochastic sampling.

This study shows that magnetic fields affect flavin autofluorescence in E. coli, with the effect depending on metabolic state and suppressed by carbon sources.

The paper identifies synergistic drug pairs in branched metabolic networks by analyzing topological complementarity in the E. coli folate pathway.

This paper introduces FBA-Hyb, a hybrid model integrating metabolic networks into bioprocess modeling, achieving higher predictive accuracy and stoichiometric consistency.

This study shows that 13C-MFA in E. coli is sensitive to biomass composition, emphasizing the need for accurate biomass formulations in flux analysis.

The paper investigates how cell state transitions in Prochlorococcus marinus MED4 affect transcriptome-proteome alignment through regulatory mechanisms involving RpaB and HimA.

This study examines how diaphorin affects E. coli transcription, revealing widespread changes in translation, metabolism, transport, and stress responses.

The paper studies RNA phage infection dynamics in E. coli, showing bacterial population rebound despite viral replication and cell death.

The paper shows that VIPR systems in E. coli mediate competition between phages and their satellite counterparts, with satellites using decoy RNAs to counteract repression.

This study quantifies how specific membrane surface area (sMSA) constrains Escherichia coli growth rates and energy metabolism across aerobic and anaerobic conditions.

This study develops a mathematical model to predict synthetic gene circuit function during bacterial stationary phase by measuring transcription and translation dynamics over time.

This paper uses ICA to analyze TraDIS-Xpress data from E. coli, identifying functional modules of antimicrobial resistance genes across multiple stress conditions.