A. I. Flamholz

Annotation-free prediction of microbial dioxygen utilization

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

The proteome is a terminal electron acceptor

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

A map of the rubisco biochemical landscape

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.

Closed ecosystems extract energy through self-organized nutrient cycles

The paper introduces a conceptual model explaining how closed microbial ecosystems self-organize to stabilize nutrient cycles and extract energy efficiently.

Optical O2 sensors also respond to redox active molecules commonly secreted by bacteria

The paper shows that bacterial secretions, particularly redox-active molecules, can interfere with optical O2 sensors, complicating O2 measurements in bacterial cultures and biofilms.

Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2 through geologic time should be re-evaluated

The paper measures carbon isotope fractionation of an ancestral rubisco in cyanobacteria, showing that evolutionary changes in photosynthesis physiology, not just atmospheric CO2, affect the carbon isotope record.

Trajectories for the evolution of bacterial CO2-concentrating mechanisms

This paper studies the evolution of bacterial CO2-concentrating mechanisms by engineering E. coli to express ancestral forms of these systems and testing their growth under varying CO2 concentrations.

Anthroponumbers.org: A Quantitative Database Of Human Impacts on Planet Earth

The paper introduces a database of human impacts on Earth, providing curated quantitative data and analysis of their interconnected effects.

Photorespiration pathways in a chemolithoautotroph

This study identifies a novel photorespiration pathway in chemolithoautotrophic bacteria, revealing the glycerate pathway as the main route and the malate cycle as an oxidative alternative.