Matthias Heinemann

Cell cycle-dependent protein dynamics in budding yeast resolved by deconvolution of bulk proteomics

The paper develops a computational method to deconvolve cell cycle-dependent protein dynamics from bulk proteomics data in budding yeast and identifies 563 proteins with such dynamics.

Thermo-Flux: generation and analysis of comprehensive thermodynamic-stoichiometric metabolic network models

Thermo-Flux converts stoichiometric metabolic models into thermodynamic-stoichiometric models to improve flux predictions through automated mass and charge balancing and integration of Gibbs energy data.

Accessible Gibbs energy at metabolic activation limits long-term cell growth

The paper shows that accessible Gibbs energy at metabolic activation limits long-term cell growth by constraining metabolic reorganization and ATP production.

Condition-dependent, amorphous protein agglomerates control cytoplasmic rheology

The paper shows that protein agglomerates in E. coli regulate cytoplasmic rheology, with diffusion inversely correlating with amino acid metabolism protein abundance.

Cell cycle dynamics of redox state and lipid metabolism in S. cerevisiae, S. pombe and murine leukaemia cells

The paper uses time-lapse microscopy to show that redox state and lipid metabolism oscillate during the cell cycle in three eukaryotic organisms.

Lipid droplet dynamics during the budding yeast cell cycle influence the timing of cell cycle START

The paper investigates lipid droplet dynamics during the budding yeast cell cycle and finds that their oscillation influences the timing of cell cycle START.

Detecting Nuclear Pore Complex assembly in living cells

This paper introduces a nanobody-based method to detect newly forming nuclear pore complexes in yeast, revealing novel insights into their assembly and localization.

OsTIR1F74G Expression Controls Basal and Auxin-Induced Degradation Rates of the AID System in Yeast

This study quantifies how OsTIR1F74G expression affects basal and auxin-induced degradation rates of AID-tagged proteins in yeast, showing dependencies on expression levels and auxin type.

Alternatives to photorespiration: A systems-level analysis reveals mechanisms of enhanced plant productivity

Modelling 12 alternative photorespiratory pathways predicts the largest carbon-export gains for carbon-fixing designs (TaCo); complete decarboxylation bypasses help mainly by releasing CO2 in chloroplasts, raising carboxylation and recapturing lost CO2.

Comparison of two sampling, quenching and extraction methods for quantitative yeasts metabolomics

This study compares two metabolite extraction methods for yeast, finding that cold-solvent extraction underestimates phosphorylated sugars and nucleotides, while methanol-quenching with boiling-ethanol-extraction provides more accurate quantification.

A photo-switchable yeast isocitrate dehydrogenase to control metabolic flux through the citric acid cycle

This paper develops a photo-switchable isocitrate dehydrogenase in yeast to dynamically control citric acid cycle flux using optogenetics.

A synthetic RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux

The paper develops an RNA-based biosensor for fructose-1,6-bisphosphate that reports glycolytic flux in yeast cells using FACS-seq screening.

A robust method for generating, quantifying and testing large amounts of Escherichia coli persisters

The paper describes methods to generate and quantify antibiotic-tolerant E. coli persisters using nutrient shifts and flow cytometry.

Unbiased metabolic flux inference through combined thermodynamic and 13C flux analysis

This paper introduces an unbiased method for metabolic flux inference by integrating thermodynamic constraints and 13C labeling data, revealing novel flux patterns in budding yeast.

Measuring glycolytic flux in single yeast cells with an orthogonal synthetic biosensor

The paper develops a synthetic biosensor to measure glycolytic flux in single yeast cells using fluorescence microscopy to identify metabolic subpopulations.