B. O. Palsson

Biological and Genetic Determinants of Glycolysis: Phosphofructokinase Isoforms Boost Energy Status of Stored Red Blood Cells and Transfusion Outcomes

The paper identifies genetic polymorphisms and metabolite levels in stored red blood cells that correlate with hemolysis and transfusion outcomes.

Trade-off Between Resistance and Persistence in High Cell Density Escherichia Coli Cultures

The paper investigates high cell density physiology in Escherichia coli, revealing a trade-off between resistance and persistence through transcriptional analysis and machine learning.

A treasure trove of 1,034 actinomycete genomes

The paper provides over 1,000 high-quality Actinomycetia genomes, revealing genomic structures and biosynthetic gene cluster organization with ecological and biotechnological implications.

Data-Driven Strain Design Towards Mitigating Biomanufacturing Stresses

This paper identifies mutations improving stress tolerance in E. coli for melatonin production using a data-driven approach integrating adaptive evolution data and multi-omics analysis.

Proteome allocation is linked to transcriptional regulation through a modularized transcriptome

The paper investigates modularization of bacterial transcriptomes and proteomes to uncover relationships between their compositions and regulatory mechanisms.

Elucidation of independently modulated genes in Streptococcus pyogenes reveals carbon sources that control its expression of hemolytic toxins

The paper identifies carbon sources that regulate hemolytic toxin expression in Streptococcus pyogenes using transcriptome-wide independent component analysis.

Coordination of CcpA and CodY regulators in Staphylococcus aureus USA300 strains

This paper uses ICA to modularize the TRN of S. aureus USA300 and combines it with a metabolic model to show coordination between CcpA and CodY in regulating carbon and amino acid metabolism.

Origin of electroneutrality in living system

The paper proposes a mechanism where positive membrane potentials in protocells enhance organic intermediate concentrations, driving early metabolic cycles and explaining the evolution of lipid membranes and ion channels.

Data-Driven Strain Design Using Aggregated Adaptive Laboratory Evolution Mutational Data

This paper presents a data-driven workflow to design microbial strains using aggregated ALE mutational data, revealing gene-centric mutations that significantly alter cellular states.

Elucidating the CodY regulon in Staphylococcus aureus USA300 substrains

This study identifies the CodY regulon in two closely related S. aureus USA300 strains, revealing conserved and strain-specific regulatory patterns and metabolic roles of CodY.

Identifying the effect of vancomycin on HA-MRSA strains using bacteriological and physiological media

The paper examines vancomycin's effect on HA-MRSA USA100 strains using bacteriological and physiological media through growth curves, RNA sequencing, and exo-metabolomics.

Synthesis of the novel transporter YdhC, is regulated by the YdhB transcription factor controlling adenosine and adenine uptake.

The paper shows that YdhB (AdnB) activates ydhC gene expression in E. coli, encoding an adenosine/adenine transporter, and demonstrates its role in nitrogen metabolism and growth under specific conditions.

PtrR (YneJ) is a novel E. coli transcription factor regulating the putrescine stress response and glutamate utilization

This paper identifies PtrR as a dual activator/repressor in E. coli that regulates putrescine stress response and glutamate utilization through transcriptional control of multiple genes.

Pangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens

This study uses pangenome analytics to analyze two-component systems in ESKAPEE pathogens, revealing their phylogenetic distribution and sequence variation, and highlights their potential as targets for antibiotic resistance.

Adaptive laboratory evolution of Escherichia coli under acid stress

This study evolves E. coli under acid stress and identifies genetic and expression changes that enhance acid tolerance.

Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production

This study uses adaptive laboratory evolution to identify chemical tolerance mechanisms in E. coli and shows how pre-tolerized strains can enhance biochemical production.

Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

This study identifies a two-dimensional rate-yield tradeoff in evolved E. coli strains using multi-scale modeling.

Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

This study identifies and characterizes 16 uncharacterized transcription factors in E. coli K-12 MG1655 using computational prediction and experimental validation.

Modeling genome-wide evolution of catalytic turnover rates: Strong epistasis shaped modern enzyme kinetics

The paper models the evolution of enzyme turnover rates using genome-scale metabolic and population genetics models, finding strong epistasis shapes kcat evolution and limits adaptation.

Escher-FBA: A web application for interactive flux balance analysis

Escher-FBA provides an interactive web tool for performing flux balance analysis without coding, enabling users to explore metabolic networks and generate hypotheses.

The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures

The paper classifies S. aureus strains based on AgrAC TCS genomic arrangements, linking agr types to virulence factor presence and protein structural properties.