A5009767888- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Research Data Management Practices
- Genomics and Phylogenetic Studies
- Advanced Proteomics Techniques and Applications
- Bacterial Genetics and Biotechnology
- CRISPR and Genetic Engineering
- Enterobacteriaceae and Cronobacter Research
- Legume Nitrogen Fixing Symbiosis
- Bacteriophages and microbial interactions
- Glycosylation and Glycoproteins Research
- Probiotics and Fermented Foods
- Plant Pathogenic Bacteria Studies
- Insect symbiosis and bacterial influences
- RNA and protein synthesis mechanisms
- Plant-Microbe Interactions and Immunity
- Machine Learning in Bioinformatics
- Software Engineering Research
University of Canterbury
2015-2024
Technical University of Denmark
2016-2022
Novo Nordisk Foundation
2020
The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the model organism
Computational biology provides software tools for testing and making inferences about biological data. In the face of increasing volumes data, heuristic methods that trade speed accuracy may be employed. We have studied these trade-offs using results a large number independent benchmarks, evaluated whether external factors, including speed, author reputation, journal impact, recency developer efforts, are indicative accurate software.We find citations age unreliable predictors accuracy. This...
Pseudomonas syringae pv. actinidiae (Psa), the causal agent of kiwifruit canker, is one most devastating plant diseases recent times. We have generated two mini-Tn5-based random insertion libraries Psa ICMP 18884. The first, a 'phenotype interest' (POI) library, consists 10,368 independent mutants gridded into 96-well plates. By replica plating onto selective media, POI library was successfully screened for auxotrophic and motility mutants. Lipopolysaccharide (LPS) biosynthesis with...
Abstract Background Computational biology provides widely used and powerful software tools for testing making inferences about biological data. In the face of rapidly increasing volumes data, heuristic methods that trade speed accuracy may be employed. We are have studied these trade-offs using results a large number independent benchmarks, evaluated whether external factors indicative accurate software. Method extracted ranks from benchmarks different bioinformatic tools, speed, author...
Abstract UDP-dependent glycosyltransferases (UGTs) are enzymes that glycosylate a wide variety of natural products, thereby modifying their physico-chemical properties, i.e. solubility, stability, reactivity, and function. To successfully leverage the UGTs in biocatalytic processes, we need to be able screen characterise them vitro , which requires efficient heterologous expression amenable hosts, preferably Escherichia coli . However, many insoluble when expressed standard attempted...
Abstract The Enterobacteriaceae are a scientifically and medically important clade of bacteria, containing the gut commensal model organism Escherichia coli , as well several major human pathogens including multiple serovars Salmonella enterica Klebsiella pneumoniae . Essential gene sets have been determined for members Enterobacteriaceae, with E. Keio single-gene deletion library often regarded gold standard essentiality studies. However, it remains unclear how varies between related...