A5013387749- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- Bioinformatics and Genomic Networks
- CRISPR and Genetic Engineering
- Single-cell and spatial transcriptomics
- Viral Infectious Diseases and Gene Expression in Insects
- Metabolomics and Mass Spectrometry Studies
- Toxin Mechanisms and Immunotoxins
- Botulinum Toxin and Related Neurological Disorders
- Clostridium difficile and Clostridium perfringens research
- bioluminescence and chemiluminescence research
- Protein Structure and Dynamics
- Virus-based gene therapy research
Novo Nordisk Foundation
2022-2025
Technical University of Denmark
2022-2025
The University of Queensland
2020
Abstract Genome-scale metabolic models (GEMs) are indispensable for studying and engineering cellular metabolism. Here, we present i CHO3K, a community-consensus, manually-curated reconstruction of the Chinese Hamster network. In addition to accounting 11004 reactions associated with 3597 genes, CHO3K includes 3489 protein structures structural descriptors >70% its 7377 metabolites, enabling deeper exploration link between molecular structure We used contextualize transcriptomics...
This paper presents Maud, a command-line application that implements Bayesian statistical inference for kinetic models of biochemical metabolic reaction networks. Maud takes into account quantitative information from omics experiments and background knowledge as well structural about mechanisms, regulatory interactions, enzyme knockouts. Our reviews the existing options in this area, case study illustrating how can be used to analyze network, explains biological, statistical, computational...
The Warburg effect is ubiquitous in proliferative mammalian cells, including cancer but poses challenges for biopharmaceutical production, as lactate accumulation inhibits cell growth and protein production. Previous efforts to eliminate production via knockout have failed bioprocessing since dehydrogenase has proven essential. However, here we eliminated the Chinese hamster ovary (CHO) HEK293 cells by simultaneously knocking out regulators involved a negative feedback loop that typically...
Kinetic models of metabolism are crucial to understand the inner workings cell metabolism. By taking into account enzyme regulation, detailed kinetic can provide accurate predictions metabolic fluxes. Comprehensive consideration regulation requires highly parameterized non-linear models, which challenging build and fit using available modelling tools. Here, we present a computational package implementing GRASP framework for building cellular defining mechanisms reference state described by...
Abstract Summary Shu is a visualization tool that integrates diverse data types into metabolic map, with focus on supporting multiple conditions and visualizing distributions. The goal to provide unified platform for handling the growing volume of multi-omics data, leveraging maps developed by modeling community. In addition, shu offers streamlined python API, based Grammar Graphics, easy integration pipelines. Availability implementation Freely available at https://github.com/biosustain/shu...
Summary: Shu is a visualization tool that integrates diverse data types into metabolic map, with focus on supporting multiple conditions and visualizing distributions. The goal to provide unified platform for handling the growing volume of multi-omics data, leveraging maps developed by modeling community. Additionally, shu offers streamlined python API, based Grammar Graphics, easy integration pipelines. Availability implementation: Freely available at https://github.com/biosustain/shu under...