Avi I. Flamholz

This paper develops a framework of living circuits using ecosystems as a model, showing that adaptive rules enable phase transitions and near-maximal dissipation in nonequilibrium systems.

The paper maps the sequence-to-function relationship of rubisco by assaying single amino acid mutants in E. coli, identifying conserved positions and mutations that improve CO2 affinity.

The paper develops a mathematical model showing microbial proteins adapt to maintain redox balance, improving growth by aligning biomass redox state with nutrients.

This paper predicts microbial dioxygen utilization from genome sequences without gene annotation, achieving >70% accuracy and demonstrating environmental correlations.

The paper uses metabolic modeling and sequence analysis to show that coenzyme redundancy reduces protein costs and promotes coenzyme specificity in E. coli.

The paper demonstrates that a bacterial CO2 concentrating mechanism enables E. coli to fix CO2 from ambient air using 20 CCM genes.

The paper re-examines tradeoffs between Rubisco kinetic parameters using data from ~300 organisms, finding that most correlations are attenuated and only one tradeoff model remains.

The paper identifies a novel class of inorganic carbon transporters in chemoautotrophic bacteria through a genome-wide screen and characterizes their function as energy-coupled bicarbonate pumps.