A5070522172- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Microbial Metabolic Engineering and Bioproduction
- Gene Regulatory Network Analysis
- Fungal and yeast genetics research
- Viral Infectious Diseases and Gene Expression in Insects
- Genomics and Chromatin Dynamics
- Insect symbiosis and bacterial influences
- Bacterial Genetics and Biotechnology
- Advanced biosensing and bioanalysis techniques
Chalmers University of Technology
2017-2023
Novo Nordisk Foundation
2023
Technical University of Denmark
2023
Abstract Design of de novo synthetic regulatory DNA is a promising avenue to control gene expression in biotechnology and medicine. Using mutagenesis typically requires screening sizable random libraries, which limits the designs span merely short section promoter restricts their expression. Here, we prototype deep learning strategy based on generative adversarial networks (GAN) by directly from genomic transcriptomic data. Our ExpressionGAN can traverse entire sequence-expression landscape...
Engineering Saccharomyces cerevisiae for industrial-scale production of valuable chemicals involves extensive modulation its metabolism. Here, we identified novel gene expression fine-tuning set-ups to enhance endogenous metabolic fluxes toward increasing levels acetyl-CoA and malonyl-CoA. dCas9-based transcriptional regulation was combined together with a malonyl-CoA responsive intracellular biosensor select beneficial set-ups. The candidate genes screening were predicted using genome-scale...
Standardisation of genetic parts has become a topic increasing interest over the last decades. The promise simplifying molecular cloning procedures, while at same time making them more predictable and reproducible led to design several biological standards, one which is modular (MoClo). Yeast MoClo toolkit provides large library characterised combined with comprehensive flexible assembly strategy. Here we aimed (1) simplify adoption standard by providing simple tool for including new in...
Directed evolution is a preferred strategy to improve the function of proteins such as enzymes that act bottlenecks in metabolic pathways. Common directed approaches rely on error-prone PCR-based libraries where number possible variants usually limited by cellular transformation efficiencies. Targeted vivo mutagenesis can advance and help overcome limitations library generation. In current study, we aimed develop high-efficiency time-controllable targeted toolkit yeast Saccharomyces...
Abstract In order to control gene expression, regulatory DNA variants are commonly designed using random synthetic approaches with mutagenesis and screening. This however limits the size of span merely a part single region, whereas whole structure including coding adjacent non-coding regions is involved in controlling expression. Here, we prototype deep neural network strategy that models structures generates de novo functional prespecified expression levels. By learning directly from...
ABSTRACT Alkane-based biofuels are desirable to produce at a commercial scale as these have properties similar our current petroleum-derived transportation fuels. Rationally engineering microorganisms compound, such alkanes, is, however, challenging. Metabolic engineers therefore increasingly implementing evolutionary approaches combined with high-throughput screening tools, including metabolite biosensors, identify productive targets. Engineering Saccharomyces cerevisiae alkanes can be...
Alkane-based biofuels are desirable to produce at a commercial scale as these have properties similar current petroleum-derived transportation fuels. Rationally engineering microorganisms compound, such alkanes, is, however, challenging. Metabolic engineers therefore increasingly implementing evolutionary approaches combined with high-throughput screening tools, including metabolite biosensors, identify productive cells. Engineering Saccharomyces cerevisiae alkanes could be facilitated by...