Daan H. de Groot

The paper systematically compares novel fluorescent proteins in budding yeast to evaluate their characteristics for research applications.

Bonsai provides a tree-based visualization method for single-cell omics data that accurately represents distances and structures without distortion, offering novel biological insights.

The paper shows that growth rate affects the sensitivity of gene regulatory switches in E. coli, with experiments confirming theoretical predictions about inducer concentration thresholds.

This paper introduces ecmtool, a tool that enumerates elementary conversion modes to fully characterize metabolic capabilities from genome-scale networks.

The paper develops a theory to describe all possible molecular states of cellular self-fabrication, identifying Elementary Growth Modes as the fundamental building blocks of cellular phenotype.

The paper shows that overflow metabolism arises from two growth-limiting constraints across different metabolic models.

The paper shows that maximizing microbial growth rate limits the number of active metabolic pathways to the number of enzyme expression constraints, explaining simple metabolic behaviors through evolutionary optimization.

The paper characterizes 27 fluorescent proteins in vivo in yeast, finding differences from in vitro data and showing how codon optimization affects their properties.