A5061509713- Gene Regulatory Network Analysis
- Bacterial Genetics and Biotechnology
- RNA and protein synthesis mechanisms
- Viral Infectious Diseases and Gene Expression in Insects
- CRISPR and Genetic Engineering
- Microbial Metabolic Engineering and Bioproduction
- Genomics and Phylogenetic Studies
- Protein Structure and Dynamics
- Nuclear Receptors and Signaling
- Neuroscience and Neural Engineering
- Machine Learning in Bioinformatics
- Genetics, Bioinformatics, and Biomedical Research
- AI in cancer detection
- Radiomics and Machine Learning in Medical Imaging
- CAR-T cell therapy research
- Cell Image Analysis Techniques
- Immune Cell Function and Interaction
University of Edinburgh
2019-2025
Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts equilibrium resource allocation in host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models quantify defects caused by synthetic circuits. Simulations reveal a complex relation between circuit output capacity for expression. For weak induction heterologous genes, protein can be increased at expense defects. Yet stronger induction,...
Synthetic biology often involves engineering microbial strains to express high-value proteins. Thanks progress in rapid DNA synthesis and sequencing, deep learning has emerged as a promising approach build sequence-to-expression models for strain optimization. But such need large costly training data that create steep entry barriers many laboratories. Here we study the relation between accuracy efficiency an atlas of machine trained on datasets varied size sequence diversity. We show can...
Transcriptional control of transgene expression can be linked to dynamic changes in cellular states if this is accompanied by differential transcription factors (TFs). Synthetic promoters (SPs) designed respond the desired TFs provide regulation with compactness, specificity, and orthogonality. T cells display differentially expressed according functional state. In solid tumors, highly immunosuppressive TME chronic exposure antigens lead a progression from dysfunctional state known as...
Abstract Synthetic gene circuits perturb the physiology of their cellular host. The extra load on endogenous processes shifts equilibrium resource allocation in host, leading to slow growth and reduced biosynthesis. Here we built integrated host-circuit models quantify defects caused by synthetic circuits. Simulations reveal a complex relation between circuit output capacity for expression. For weak induction heterologous genes, protein can be increased at expense defects. Yet stronger...
Abstract Many applications of synthetic biology involve engineering microbial strains to express high-value proteins. Thanks advances in rapid DNA synthesis and sequencing, deep learning has emerged as a promising approach build sequence-to-expression models for strain design optimization. Such models, however, require large amounts training data that are costly acquire, which creates substantial entry barriers many laboratories. Here, we study the relation between model accuracy efficiency...
Heterologous gene expression draws resources from host cells. These include vital components to sustain growth and replication, the resulting cellular burden is a widely recognised bottleneck in design of robust circuits. In this tutorial we discuss use computational models that integrate circuits physiology Through various cases, illustrate power host-circuit predict impact parameters on both circuit functionality. Our approach relies new generation for microbial can flexibly accommodate...