Verena Siewers

Supervised generative design of regulatory DNA forgene expression control

This paper introduces ExpressionGAN, a deep learning model that generates functional regulatory DNA with specified expression levels, outperforming random mutagenesis approaches.

Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0

The paper upgrades the GECKO method to create enzyme-constrained models for yeast and human, revealing common metabolic adaptations under stress.

Fine-tuning of coumaric acid synthesis to increase naringenin production in yeast

This study improves (2S)-naringenin production in yeast by fine-tuning p-coumaric acid synthesis, reducing its extracellular accumulation and increasing yield to 933 mg/L.

A Single Chromosome Strain of S. cerevisiae Exhibits Diminished Ethanol Metabolism and Tolerance.

This study shows that a single chromosome yeast strain has reduced ethanol metabolism and growth compared to wildtype.

Does co-expression of Yarrowia lipolytica genes encoding Yas1p, Yas2p and Yas3p make a potential alkane-responsive biosensor in Saccharomyces cerevisiae?

The paper evaluates the potential of Yarrowia lipolytica's alkane-sensing TFs as a biosensor in Saccharomyces cerevisiae but finds they do not function as expected in the new host.

Gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure

The paper uses deep learning to show that gene expression levels are encoded in both coding and non-coding regions of the gene regulatory structure across multiple organisms.

Stress-Induced Expression is Enriched for Evolutionarily Young Genes in Diverse Budding Yeasts

The paper identifies stress-induced genes in budding yeasts and finds they are enriched for young, non-essential genes that evolve rapidly.

Saccharomyces cerevisiae displays a stable transcription start site landscape in multiple conditions

The paper shows that the transcription start site landscape in Saccharomyces cerevisiae remains stable across different environmental conditions and identifies a negative correlation between TSS shape index and expression levels.

Investigation of putative regulatory acetylation sites in Fas2p of Saccharomyces cerevisiae

This study investigates the regulatory impact of acetylation sites on Fas2p in yeast by mutating lysine residues to glutamine or arginine and analyzing effects on fatty acid biosynthesis.

Quantitative in vivo evaluation of the reverse β-oxidation pathway for fatty acid production in Saccharomyces cerevisiae

The paper evaluates the reverse β-oxidation pathway in Saccharomyces cerevisiae for fatty acid production and finds no significant improvement in efficiency.